repo_name stringlengths 7 104 | file_path stringlengths 13 198 | context stringlengths 67 7.15k | import_statement stringlengths 16 4.43k | code stringlengths 40 6.98k | prompt stringlengths 227 8.27k | next_line stringlengths 8 795 |
|---|---|---|---|---|---|---|
reelyactive/ble-android-sdk | library/src/main/java/com/reelyactive/blesdk/support/ble/BluetoothLeScannerCompat.java | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Clock.java
// public interface Clock {
//
// /**
// * @return current time in milliseconds
// */
// public long currentTimeMillis();
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// public long elapsedRealtimeNanos();
//
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
| import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import android.app.AlarmManager;
import android.app.PendingIntent;
import android.os.Build;
import com.reelyactive.blesdk.support.ble.util.Clock;
import com.reelyactive.blesdk.support.ble.util.Logger; | }
/**
* Get the current active ble scan time that has been set
*
* @VisibleForTesting
*/
int getScanActiveMillis() {
return (overrideScanActiveMillis != -1) ? overrideScanActiveMillis : scanActiveMillis;
}
/**
* Get the current idle ble scan time that has been set
*
* @VisibleForTesting
*/
int getScanIdleMillis() {
return (overrideScanActiveMillis != -1) ? overrideScanIdleMillis : scanIdleMillis;
}
/**
* Update the repeating alarm wake-up based on the period defined for the scanner If there are
* no clients, or a batch scan running, it will cancel the alarm.
*/
protected void updateRepeatingAlarm() {
// Apply Scan Mode (Cycle Parameters)
setScanMode(getMaxPriorityScanMode());
if (!hasClients()) {
// No listeners. Remove the repeating alarm, if there is one.
getAlarmManager().cancel(getAlarmIntent()); | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Clock.java
// public interface Clock {
//
// /**
// * @return current time in milliseconds
// */
// public long currentTimeMillis();
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// public long elapsedRealtimeNanos();
//
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/BluetoothLeScannerCompat.java
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import android.app.AlarmManager;
import android.app.PendingIntent;
import android.os.Build;
import com.reelyactive.blesdk.support.ble.util.Clock;
import com.reelyactive.blesdk.support.ble.util.Logger;
}
/**
* Get the current active ble scan time that has been set
*
* @VisibleForTesting
*/
int getScanActiveMillis() {
return (overrideScanActiveMillis != -1) ? overrideScanActiveMillis : scanActiveMillis;
}
/**
* Get the current idle ble scan time that has been set
*
* @VisibleForTesting
*/
int getScanIdleMillis() {
return (overrideScanActiveMillis != -1) ? overrideScanIdleMillis : scanIdleMillis;
}
/**
* Update the repeating alarm wake-up based on the period defined for the scanner If there are
* no clients, or a batch scan running, it will cancel the alarm.
*/
protected void updateRepeatingAlarm() {
// Apply Scan Mode (Cycle Parameters)
setScanMode(getMaxPriorityScanMode());
if (!hasClients()) {
// No listeners. Remove the repeating alarm, if there is one.
getAlarmManager().cancel(getAlarmIntent()); | Logger.logInfo("Scan : No clients left, canceling alarm."); |
reelyactive/ble-android-sdk | library/src/main/java/com/reelyactive/blesdk/support/ble/NoBluetoothLeScannerCompat.java | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/SystemClock.java
// public class SystemClock implements Clock {
//
// /**
// * @return current time in milliseconds
// */
// @Override
// public long currentTimeMillis() {
// return System.currentTimeMillis();
// }
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// @Override
// @TargetApi(VERSION_CODES.JELLY_BEAN_MR1)
// public long elapsedRealtimeNanos() {
// return android.os.SystemClock.elapsedRealtimeNanos();
// }
// }
| import android.app.AlarmManager;
import android.app.PendingIntent;
import android.content.Context;
import android.content.Intent;
import com.reelyactive.blesdk.support.ble.util.Logger;
import com.reelyactive.blesdk.support.ble.util.SystemClock;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.concurrent.ConcurrentHashMap; | package com.reelyactive.blesdk.support.ble;
/**
* Created by saiimons on 16-03-17.
*/
public class NoBluetoothLeScannerCompat extends BluetoothLeScannerCompat {
private final Map<ScanCallback, ScanSettings> callbacksMap = new ConcurrentHashMap<>();
public NoBluetoothLeScannerCompat(Context context, AlarmManager alarmManager) {
super( | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/SystemClock.java
// public class SystemClock implements Clock {
//
// /**
// * @return current time in milliseconds
// */
// @Override
// public long currentTimeMillis() {
// return System.currentTimeMillis();
// }
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// @Override
// @TargetApi(VERSION_CODES.JELLY_BEAN_MR1)
// public long elapsedRealtimeNanos() {
// return android.os.SystemClock.elapsedRealtimeNanos();
// }
// }
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/NoBluetoothLeScannerCompat.java
import android.app.AlarmManager;
import android.app.PendingIntent;
import android.content.Context;
import android.content.Intent;
import com.reelyactive.blesdk.support.ble.util.Logger;
import com.reelyactive.blesdk.support.ble.util.SystemClock;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.concurrent.ConcurrentHashMap;
package com.reelyactive.blesdk.support.ble;
/**
* Created by saiimons on 16-03-17.
*/
public class NoBluetoothLeScannerCompat extends BluetoothLeScannerCompat {
private final Map<ScanCallback, ScanSettings> callbacksMap = new ConcurrentHashMap<>();
public NoBluetoothLeScannerCompat(Context context, AlarmManager alarmManager) {
super( | new SystemClock(), |
reelyactive/ble-android-sdk | library/src/main/java/com/reelyactive/blesdk/support/ble/NoBluetoothLeScannerCompat.java | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/SystemClock.java
// public class SystemClock implements Clock {
//
// /**
// * @return current time in milliseconds
// */
// @Override
// public long currentTimeMillis() {
// return System.currentTimeMillis();
// }
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// @Override
// @TargetApi(VERSION_CODES.JELLY_BEAN_MR1)
// public long elapsedRealtimeNanos() {
// return android.os.SystemClock.elapsedRealtimeNanos();
// }
// }
| import android.app.AlarmManager;
import android.app.PendingIntent;
import android.content.Context;
import android.content.Intent;
import com.reelyactive.blesdk.support.ble.util.Logger;
import com.reelyactive.blesdk.support.ble.util.SystemClock;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.concurrent.ConcurrentHashMap; | package com.reelyactive.blesdk.support.ble;
/**
* Created by saiimons on 16-03-17.
*/
public class NoBluetoothLeScannerCompat extends BluetoothLeScannerCompat {
private final Map<ScanCallback, ScanSettings> callbacksMap = new ConcurrentHashMap<>();
public NoBluetoothLeScannerCompat(Context context, AlarmManager alarmManager) {
super(
new SystemClock(),
alarmManager,
PendingIntent.getBroadcast(
context,
0,
new Intent(context, ScanWakefulBroadcastReceiver.class).putExtra(ScanWakefulService.EXTRA_USE_LOLLIPOP_API, false), 0)
);
}
@Override
public boolean startScan(List<ScanFilter> filters, ScanSettings settings, ScanCallback callback) {
if (callback != null) {
try {
callbacksMap.put(callback, settings);
updateRepeatingAlarm();
return true;
} catch (Exception e) { | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/SystemClock.java
// public class SystemClock implements Clock {
//
// /**
// * @return current time in milliseconds
// */
// @Override
// public long currentTimeMillis() {
// return System.currentTimeMillis();
// }
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// @Override
// @TargetApi(VERSION_CODES.JELLY_BEAN_MR1)
// public long elapsedRealtimeNanos() {
// return android.os.SystemClock.elapsedRealtimeNanos();
// }
// }
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/NoBluetoothLeScannerCompat.java
import android.app.AlarmManager;
import android.app.PendingIntent;
import android.content.Context;
import android.content.Intent;
import com.reelyactive.blesdk.support.ble.util.Logger;
import com.reelyactive.blesdk.support.ble.util.SystemClock;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.concurrent.ConcurrentHashMap;
package com.reelyactive.blesdk.support.ble;
/**
* Created by saiimons on 16-03-17.
*/
public class NoBluetoothLeScannerCompat extends BluetoothLeScannerCompat {
private final Map<ScanCallback, ScanSettings> callbacksMap = new ConcurrentHashMap<>();
public NoBluetoothLeScannerCompat(Context context, AlarmManager alarmManager) {
super(
new SystemClock(),
alarmManager,
PendingIntent.getBroadcast(
context,
0,
new Intent(context, ScanWakefulBroadcastReceiver.class).putExtra(ScanWakefulService.EXTRA_USE_LOLLIPOP_API, false), 0)
);
}
@Override
public boolean startScan(List<ScanFilter> filters, ScanSettings settings, ScanCallback callback) {
if (callback != null) {
try {
callbacksMap.put(callback, settings);
updateRepeatingAlarm();
return true;
} catch (Exception e) { | Logger.logError(e.getMessage(), e); |
reelyactive/ble-android-sdk | library/src/main/java/com/reelyactive/blesdk/support/ble/ScanWakefulService.java | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
| import android.app.IntentService;
import android.content.Intent;
import com.reelyactive.blesdk.support.ble.util.Logger; | package com.reelyactive.blesdk.support.ble;/*
* Copyright 2014 Google Inc. All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
/**
* The com.reelyactive.blesdk.support.ble.ScanWakefulService Class is called with a WakeLock held, and executes a single Bluetooth LE
* scan cycle. It then calls the {@link ScanWakefulBroadcastReceiver#completeWakefulIntent} with the
* same intent to release the associated WakeLock.
*/
public class ScanWakefulService extends IntentService {
public static final String EXTRA_USE_LOLLIPOP_API = "use_lollipop";
public ScanWakefulService() {
super("com.reelyactive.blesdk.support.ble.ScanWakefulService");
}
@Override
protected void onHandleIntent(Intent intent) {
if (intent == null) {
return;
}
// This method runs in a worker thread.
// At this point com.reelyactive.blesdk.support.ble.ScanWakefulBroadcastReceiver is still holding a WakeLock.
// We can do whatever we need to do in the code below.
// After the call to completeWakefulIntent the WakeLock is released. | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/ScanWakefulService.java
import android.app.IntentService;
import android.content.Intent;
import com.reelyactive.blesdk.support.ble.util.Logger;
package com.reelyactive.blesdk.support.ble;/*
* Copyright 2014 Google Inc. All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
/**
* The com.reelyactive.blesdk.support.ble.ScanWakefulService Class is called with a WakeLock held, and executes a single Bluetooth LE
* scan cycle. It then calls the {@link ScanWakefulBroadcastReceiver#completeWakefulIntent} with the
* same intent to release the associated WakeLock.
*/
public class ScanWakefulService extends IntentService {
public static final String EXTRA_USE_LOLLIPOP_API = "use_lollipop";
public ScanWakefulService() {
super("com.reelyactive.blesdk.support.ble.ScanWakefulService");
}
@Override
protected void onHandleIntent(Intent intent) {
if (intent == null) {
return;
}
// This method runs in a worker thread.
// At this point com.reelyactive.blesdk.support.ble.ScanWakefulBroadcastReceiver is still holding a WakeLock.
// We can do whatever we need to do in the code below.
// After the call to completeWakefulIntent the WakeLock is released. | Logger.logDebug("Running scancycle"); |
reelyactive/ble-android-sdk | library/src/main/java/com/reelyactive/blesdk/application/ReelyAwareActivity.java | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/ScanResult.java
// public final class ScanResult implements Parcelable {
// // Remote bluetooth device.
// private BluetoothDevice mDevice;
//
// // Scan record, including advertising data and scan response data.
// @Nullable
// private ScanRecord mScanRecord;
//
// // Received signal strength.
// private int mRssi;
//
// // Device timestamp when the result was last seen.
// private long mTimestampNanos;
//
// /**
// * Constructor of scan result.
// *
// * @param device Remote bluetooth device that is found.
// * @param scanRecord Scan record including both advertising data and scan response data.
// * @param rssi Received signal strength.
// * @param timestampNanos Device timestamp when the scan result was observed.
// */
// public ScanResult(BluetoothDevice device, ScanRecord scanRecord, int rssi,
// long timestampNanos) {
// mDevice = device;
// mScanRecord = scanRecord;
// mRssi = rssi;
// mTimestampNanos = timestampNanos;
// }
//
// private ScanResult(Parcel in) {
// readFromParcel(in);
// }
//
// @Override
// public void writeToParcel(Parcel dest, int flags) {
// if (mDevice != null) {
// dest.writeInt(1);
// mDevice.writeToParcel(dest, flags);
// } else {
// dest.writeInt(0);
// }
// if (mScanRecord != null) {
// dest.writeInt(1);
// dest.writeByteArray(mScanRecord.getBytes());
// } else {
// dest.writeInt(0);
// }
// dest.writeInt(mRssi);
// dest.writeLong(mTimestampNanos);
// }
//
// private void readFromParcel(Parcel in) {
// if (in.readInt() == 1) {
// mDevice = BluetoothDevice.CREATOR.createFromParcel(in);
// }
// if (in.readInt() == 1) {
// mScanRecord = ScanRecord.parseFromBytes(in.createByteArray());
// }
// mRssi = in.readInt();
// mTimestampNanos = in.readLong();
// }
//
// @Override
// public int describeContents() {
// return 0;
// }
//
// /**
// * Returns the remote bluetooth device identified by the bluetooth device address.
// */
// public BluetoothDevice getDevice() {
// return mDevice;
// }
//
// /**
// * Returns the scan record, which is a combination of advertisement and scan response.
// */
// @Nullable
// public ScanRecord getScanRecord() {
// return mScanRecord;
// }
//
// /**
// * Returns the received signal strength in dBm. The valid range is [-127, 127].
// */
// public int getRssi() {
// return mRssi;
// }
//
// /**
// * Returns timestamp since boot when the scan record was observed.
// */
// public long getTimestampNanos() {
// return mTimestampNanos;
// }
//
// @Override
// public int hashCode() {
// return Objects.hash(mDevice, mRssi, mScanRecord, mTimestampNanos);
// }
//
// @Override
// public boolean equals(Object obj) {
// if (this == obj) {
// return true;
// }
// if (obj == null || getClass() != obj.getClass()) {
// return false;
// }
// ScanResult other = (ScanResult) obj;
// return Objects.equals(mDevice, other.mDevice) && (mRssi == other.mRssi)
// && Objects.equals(mScanRecord, other.mScanRecord)
// && (mTimestampNanos == other.mTimestampNanos);
// }
//
// @Override
// public String toString() {
// return "com.reelyactive.blesdk.support.ble.ScanResult{" + "mDevice=" + mDevice + ", mScanRecord="
// + Objects.toString(mScanRecord) + ", mRssi=" + mRssi + ", mTimestampNanos="
// + mTimestampNanos + '}';
// }
//
// /**
// * @hide
// */
// public static final Creator<ScanResult> CREATOR = new Creator<ScanResult>() {
// @Override
// public ScanResult createFromParcel(Parcel source) {
// return new ScanResult(source);
// }
//
// @Override
// public ScanResult[] newArray(int size) {
// return new ScanResult[size];
// }
// };
//
// }
| import com.reelyactive.blesdk.support.ble.ScanResult; | package com.reelyactive.blesdk.application;
/**
* Implement this interface if you want your current activity to be notified when Reelceiver are detected.
*/
public interface ReelyAwareActivity {
public void onScanStarted();
public void onScanStopped();
| // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/ScanResult.java
// public final class ScanResult implements Parcelable {
// // Remote bluetooth device.
// private BluetoothDevice mDevice;
//
// // Scan record, including advertising data and scan response data.
// @Nullable
// private ScanRecord mScanRecord;
//
// // Received signal strength.
// private int mRssi;
//
// // Device timestamp when the result was last seen.
// private long mTimestampNanos;
//
// /**
// * Constructor of scan result.
// *
// * @param device Remote bluetooth device that is found.
// * @param scanRecord Scan record including both advertising data and scan response data.
// * @param rssi Received signal strength.
// * @param timestampNanos Device timestamp when the scan result was observed.
// */
// public ScanResult(BluetoothDevice device, ScanRecord scanRecord, int rssi,
// long timestampNanos) {
// mDevice = device;
// mScanRecord = scanRecord;
// mRssi = rssi;
// mTimestampNanos = timestampNanos;
// }
//
// private ScanResult(Parcel in) {
// readFromParcel(in);
// }
//
// @Override
// public void writeToParcel(Parcel dest, int flags) {
// if (mDevice != null) {
// dest.writeInt(1);
// mDevice.writeToParcel(dest, flags);
// } else {
// dest.writeInt(0);
// }
// if (mScanRecord != null) {
// dest.writeInt(1);
// dest.writeByteArray(mScanRecord.getBytes());
// } else {
// dest.writeInt(0);
// }
// dest.writeInt(mRssi);
// dest.writeLong(mTimestampNanos);
// }
//
// private void readFromParcel(Parcel in) {
// if (in.readInt() == 1) {
// mDevice = BluetoothDevice.CREATOR.createFromParcel(in);
// }
// if (in.readInt() == 1) {
// mScanRecord = ScanRecord.parseFromBytes(in.createByteArray());
// }
// mRssi = in.readInt();
// mTimestampNanos = in.readLong();
// }
//
// @Override
// public int describeContents() {
// return 0;
// }
//
// /**
// * Returns the remote bluetooth device identified by the bluetooth device address.
// */
// public BluetoothDevice getDevice() {
// return mDevice;
// }
//
// /**
// * Returns the scan record, which is a combination of advertisement and scan response.
// */
// @Nullable
// public ScanRecord getScanRecord() {
// return mScanRecord;
// }
//
// /**
// * Returns the received signal strength in dBm. The valid range is [-127, 127].
// */
// public int getRssi() {
// return mRssi;
// }
//
// /**
// * Returns timestamp since boot when the scan record was observed.
// */
// public long getTimestampNanos() {
// return mTimestampNanos;
// }
//
// @Override
// public int hashCode() {
// return Objects.hash(mDevice, mRssi, mScanRecord, mTimestampNanos);
// }
//
// @Override
// public boolean equals(Object obj) {
// if (this == obj) {
// return true;
// }
// if (obj == null || getClass() != obj.getClass()) {
// return false;
// }
// ScanResult other = (ScanResult) obj;
// return Objects.equals(mDevice, other.mDevice) && (mRssi == other.mRssi)
// && Objects.equals(mScanRecord, other.mScanRecord)
// && (mTimestampNanos == other.mTimestampNanos);
// }
//
// @Override
// public String toString() {
// return "com.reelyactive.blesdk.support.ble.ScanResult{" + "mDevice=" + mDevice + ", mScanRecord="
// + Objects.toString(mScanRecord) + ", mRssi=" + mRssi + ", mTimestampNanos="
// + mTimestampNanos + '}';
// }
//
// /**
// * @hide
// */
// public static final Creator<ScanResult> CREATOR = new Creator<ScanResult>() {
// @Override
// public ScanResult createFromParcel(Parcel source) {
// return new ScanResult(source);
// }
//
// @Override
// public ScanResult[] newArray(int size) {
// return new ScanResult[size];
// }
// };
//
// }
// Path: library/src/main/java/com/reelyactive/blesdk/application/ReelyAwareActivity.java
import com.reelyactive.blesdk.support.ble.ScanResult;
package com.reelyactive.blesdk.application;
/**
* Implement this interface if you want your current activity to be notified when Reelceiver are detected.
*/
public interface ReelyAwareActivity {
public void onScanStarted();
public void onScanStopped();
| public void onEnterRegion(ScanResult beacon); |
reelyactive/ble-android-sdk | library/src/main/java/com/reelyactive/blesdk/support/ble/JbBluetoothLeScannerCompat.java | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Clock.java
// public interface Clock {
//
// /**
// * @return current time in milliseconds
// */
// public long currentTimeMillis();
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// public long elapsedRealtimeNanos();
//
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/SystemClock.java
// public class SystemClock implements Clock {
//
// /**
// * @return current time in milliseconds
// */
// @Override
// public long currentTimeMillis() {
// return System.currentTimeMillis();
// }
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// @Override
// @TargetApi(VERSION_CODES.JELLY_BEAN_MR1)
// public long elapsedRealtimeNanos() {
// return android.os.SystemClock.elapsedRealtimeNanos();
// }
// }
| import android.annotation.TargetApi;
import android.app.AlarmManager;
import android.app.PendingIntent;
import android.bluetooth.BluetoothAdapter;
import android.bluetooth.BluetoothDevice;
import android.bluetooth.BluetoothManager;
import android.content.Context;
import android.content.Intent;
import android.os.Build;
import android.os.Handler;
import android.os.Looper;
import com.reelyactive.blesdk.support.ble.util.Clock;
import com.reelyactive.blesdk.support.ble.util.Logger;
import com.reelyactive.blesdk.support.ble.util.SystemClock;
import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.TimeUnit; | package com.reelyactive.blesdk.support.ble;/*
* Copyright 2014 Google Inc. All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
/**
* Implements Bluetooth LE scan related API on top of
* {@link android.os.Build.VERSION_CODES#JELLY_BEAN_MR2} and later.
* <p>
* This class delivers a callback on found, updated, and lost for devices matching a
* {@link ScanFilter} filter during scan cycles.
* <p>
* A scan cycle comprises a period when the Bluetooth Adapter is active and a period when the
* Bluetooth adapter is idle. Having an idle period is energy efficient for long lived scans.
* <p>
* This class can be accessed on multiple threads:
* <ul>
* <li> main thread (user) can call any of the BluetoothLeScanner APIs
* <li> IntentService worker thread can call {@link #onNewScanCycle()}
* <li> AIDL binder thread can call {@link #leScanCallback.onLeScan()}
* </ul>
*
* @see <a href="http://go/ble-glossary">BLE Glossary</a>
*/
@TargetApi(Build.VERSION_CODES.JELLY_BEAN_MR2)
class JbBluetoothLeScannerCompat extends BluetoothLeScannerCompat {
// Map of BD_ADDR->com.reelyactive.blesdk.support.ble.ScanResult for replay to new registrations.
// Entries are evicted after SCAN_LOST_CYCLES cycles.
/* @VisibleForTesting */ final Map<String, ScanResult> recentScanResults = new ConcurrentHashMap<>();
/* @VisibleForTesting */ final Map<ScanCallback, ScanClient> serialClients = new ConcurrentHashMap<>();
private final BluetoothAdapter bluetoothAdapter;
private BluetoothCrashResolver crashResolver;
private Handler mainHandler;
/**
* The Bluetooth LE callback which will be registered with the OS,
* to be fired on device discovery.
*/
private final BluetoothAdapter.LeScanCallback leScanCallback =
new BluetoothAdapter.LeScanCallback() {
/**
* Callback method called from the OS on each BLE device sighting.
* This method is invoked on the AIDL handler thread, so all methods
* called here must be synchronized.
*
* @param device The device discovered
* @param rssi The signal strength in dBm it was received at
* @param scanRecordBytes The raw byte payload buffer
*/
@Override
public void onLeScan(BluetoothDevice device, int rssi, byte[] scanRecordBytes) {
long currentTimeInNanos = TimeUnit.MILLISECONDS.toNanos(getClock().currentTimeMillis());
ScanResult result = new ScanResult(device, ScanRecord.parseFromBytes(scanRecordBytes), rssi,
currentTimeInNanos);
onScanResult(device.getAddress(), result);
if (crashResolver != null)
crashResolver.notifyScannedDevice(device, this);
}
};
/**
* Package constructor, called from {@link BluetoothLeScannerCompatProvider}.
*/
JbBluetoothLeScannerCompat(
Context context, BluetoothManager manager, AlarmManager alarmManager) { | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Clock.java
// public interface Clock {
//
// /**
// * @return current time in milliseconds
// */
// public long currentTimeMillis();
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// public long elapsedRealtimeNanos();
//
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/SystemClock.java
// public class SystemClock implements Clock {
//
// /**
// * @return current time in milliseconds
// */
// @Override
// public long currentTimeMillis() {
// return System.currentTimeMillis();
// }
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// @Override
// @TargetApi(VERSION_CODES.JELLY_BEAN_MR1)
// public long elapsedRealtimeNanos() {
// return android.os.SystemClock.elapsedRealtimeNanos();
// }
// }
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/JbBluetoothLeScannerCompat.java
import android.annotation.TargetApi;
import android.app.AlarmManager;
import android.app.PendingIntent;
import android.bluetooth.BluetoothAdapter;
import android.bluetooth.BluetoothDevice;
import android.bluetooth.BluetoothManager;
import android.content.Context;
import android.content.Intent;
import android.os.Build;
import android.os.Handler;
import android.os.Looper;
import com.reelyactive.blesdk.support.ble.util.Clock;
import com.reelyactive.blesdk.support.ble.util.Logger;
import com.reelyactive.blesdk.support.ble.util.SystemClock;
import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.TimeUnit;
package com.reelyactive.blesdk.support.ble;/*
* Copyright 2014 Google Inc. All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
/**
* Implements Bluetooth LE scan related API on top of
* {@link android.os.Build.VERSION_CODES#JELLY_BEAN_MR2} and later.
* <p>
* This class delivers a callback on found, updated, and lost for devices matching a
* {@link ScanFilter} filter during scan cycles.
* <p>
* A scan cycle comprises a period when the Bluetooth Adapter is active and a period when the
* Bluetooth adapter is idle. Having an idle period is energy efficient for long lived scans.
* <p>
* This class can be accessed on multiple threads:
* <ul>
* <li> main thread (user) can call any of the BluetoothLeScanner APIs
* <li> IntentService worker thread can call {@link #onNewScanCycle()}
* <li> AIDL binder thread can call {@link #leScanCallback.onLeScan()}
* </ul>
*
* @see <a href="http://go/ble-glossary">BLE Glossary</a>
*/
@TargetApi(Build.VERSION_CODES.JELLY_BEAN_MR2)
class JbBluetoothLeScannerCompat extends BluetoothLeScannerCompat {
// Map of BD_ADDR->com.reelyactive.blesdk.support.ble.ScanResult for replay to new registrations.
// Entries are evicted after SCAN_LOST_CYCLES cycles.
/* @VisibleForTesting */ final Map<String, ScanResult> recentScanResults = new ConcurrentHashMap<>();
/* @VisibleForTesting */ final Map<ScanCallback, ScanClient> serialClients = new ConcurrentHashMap<>();
private final BluetoothAdapter bluetoothAdapter;
private BluetoothCrashResolver crashResolver;
private Handler mainHandler;
/**
* The Bluetooth LE callback which will be registered with the OS,
* to be fired on device discovery.
*/
private final BluetoothAdapter.LeScanCallback leScanCallback =
new BluetoothAdapter.LeScanCallback() {
/**
* Callback method called from the OS on each BLE device sighting.
* This method is invoked on the AIDL handler thread, so all methods
* called here must be synchronized.
*
* @param device The device discovered
* @param rssi The signal strength in dBm it was received at
* @param scanRecordBytes The raw byte payload buffer
*/
@Override
public void onLeScan(BluetoothDevice device, int rssi, byte[] scanRecordBytes) {
long currentTimeInNanos = TimeUnit.MILLISECONDS.toNanos(getClock().currentTimeMillis());
ScanResult result = new ScanResult(device, ScanRecord.parseFromBytes(scanRecordBytes), rssi,
currentTimeInNanos);
onScanResult(device.getAddress(), result);
if (crashResolver != null)
crashResolver.notifyScannedDevice(device, this);
}
};
/**
* Package constructor, called from {@link BluetoothLeScannerCompatProvider}.
*/
JbBluetoothLeScannerCompat(
Context context, BluetoothManager manager, AlarmManager alarmManager) { | this(manager, alarmManager, new SystemClock(), |
reelyactive/ble-android-sdk | library/src/main/java/com/reelyactive/blesdk/support/ble/JbBluetoothLeScannerCompat.java | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Clock.java
// public interface Clock {
//
// /**
// * @return current time in milliseconds
// */
// public long currentTimeMillis();
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// public long elapsedRealtimeNanos();
//
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/SystemClock.java
// public class SystemClock implements Clock {
//
// /**
// * @return current time in milliseconds
// */
// @Override
// public long currentTimeMillis() {
// return System.currentTimeMillis();
// }
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// @Override
// @TargetApi(VERSION_CODES.JELLY_BEAN_MR1)
// public long elapsedRealtimeNanos() {
// return android.os.SystemClock.elapsedRealtimeNanos();
// }
// }
| import android.annotation.TargetApi;
import android.app.AlarmManager;
import android.app.PendingIntent;
import android.bluetooth.BluetoothAdapter;
import android.bluetooth.BluetoothDevice;
import android.bluetooth.BluetoothManager;
import android.content.Context;
import android.content.Intent;
import android.os.Build;
import android.os.Handler;
import android.os.Looper;
import com.reelyactive.blesdk.support.ble.util.Clock;
import com.reelyactive.blesdk.support.ble.util.Logger;
import com.reelyactive.blesdk.support.ble.util.SystemClock;
import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.TimeUnit; | @Override
public void onLeScan(BluetoothDevice device, int rssi, byte[] scanRecordBytes) {
long currentTimeInNanos = TimeUnit.MILLISECONDS.toNanos(getClock().currentTimeMillis());
ScanResult result = new ScanResult(device, ScanRecord.parseFromBytes(scanRecordBytes), rssi,
currentTimeInNanos);
onScanResult(device.getAddress(), result);
if (crashResolver != null)
crashResolver.notifyScannedDevice(device, this);
}
};
/**
* Package constructor, called from {@link BluetoothLeScannerCompatProvider}.
*/
JbBluetoothLeScannerCompat(
Context context, BluetoothManager manager, AlarmManager alarmManager) {
this(manager, alarmManager, new SystemClock(),
PendingIntent.getBroadcast(context, 0 /* requestCode */,
new Intent(context, ScanWakefulBroadcastReceiver.class).putExtra(ScanWakefulService.EXTRA_USE_LOLLIPOP_API, false), 0 /* flags */));
this.crashResolver = new BluetoothCrashResolver(context);
this.crashResolver.start();
this.mainHandler = new Handler(Looper.getMainLooper());
}
/**
* Testing constructor for the scanner.
*
* @VisibleForTesting
*/
JbBluetoothLeScannerCompat(BluetoothManager manager, AlarmManager alarmManager, | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Clock.java
// public interface Clock {
//
// /**
// * @return current time in milliseconds
// */
// public long currentTimeMillis();
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// public long elapsedRealtimeNanos();
//
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/SystemClock.java
// public class SystemClock implements Clock {
//
// /**
// * @return current time in milliseconds
// */
// @Override
// public long currentTimeMillis() {
// return System.currentTimeMillis();
// }
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// @Override
// @TargetApi(VERSION_CODES.JELLY_BEAN_MR1)
// public long elapsedRealtimeNanos() {
// return android.os.SystemClock.elapsedRealtimeNanos();
// }
// }
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/JbBluetoothLeScannerCompat.java
import android.annotation.TargetApi;
import android.app.AlarmManager;
import android.app.PendingIntent;
import android.bluetooth.BluetoothAdapter;
import android.bluetooth.BluetoothDevice;
import android.bluetooth.BluetoothManager;
import android.content.Context;
import android.content.Intent;
import android.os.Build;
import android.os.Handler;
import android.os.Looper;
import com.reelyactive.blesdk.support.ble.util.Clock;
import com.reelyactive.blesdk.support.ble.util.Logger;
import com.reelyactive.blesdk.support.ble.util.SystemClock;
import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.TimeUnit;
@Override
public void onLeScan(BluetoothDevice device, int rssi, byte[] scanRecordBytes) {
long currentTimeInNanos = TimeUnit.MILLISECONDS.toNanos(getClock().currentTimeMillis());
ScanResult result = new ScanResult(device, ScanRecord.parseFromBytes(scanRecordBytes), rssi,
currentTimeInNanos);
onScanResult(device.getAddress(), result);
if (crashResolver != null)
crashResolver.notifyScannedDevice(device, this);
}
};
/**
* Package constructor, called from {@link BluetoothLeScannerCompatProvider}.
*/
JbBluetoothLeScannerCompat(
Context context, BluetoothManager manager, AlarmManager alarmManager) {
this(manager, alarmManager, new SystemClock(),
PendingIntent.getBroadcast(context, 0 /* requestCode */,
new Intent(context, ScanWakefulBroadcastReceiver.class).putExtra(ScanWakefulService.EXTRA_USE_LOLLIPOP_API, false), 0 /* flags */));
this.crashResolver = new BluetoothCrashResolver(context);
this.crashResolver.start();
this.mainHandler = new Handler(Looper.getMainLooper());
}
/**
* Testing constructor for the scanner.
*
* @VisibleForTesting
*/
JbBluetoothLeScannerCompat(BluetoothManager manager, AlarmManager alarmManager, | Clock clock, PendingIntent alarmIntent) { |
reelyactive/ble-android-sdk | library/src/main/java/com/reelyactive/blesdk/support/ble/JbBluetoothLeScannerCompat.java | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Clock.java
// public interface Clock {
//
// /**
// * @return current time in milliseconds
// */
// public long currentTimeMillis();
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// public long elapsedRealtimeNanos();
//
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/SystemClock.java
// public class SystemClock implements Clock {
//
// /**
// * @return current time in milliseconds
// */
// @Override
// public long currentTimeMillis() {
// return System.currentTimeMillis();
// }
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// @Override
// @TargetApi(VERSION_CODES.JELLY_BEAN_MR1)
// public long elapsedRealtimeNanos() {
// return android.os.SystemClock.elapsedRealtimeNanos();
// }
// }
| import android.annotation.TargetApi;
import android.app.AlarmManager;
import android.app.PendingIntent;
import android.bluetooth.BluetoothAdapter;
import android.bluetooth.BluetoothDevice;
import android.bluetooth.BluetoothManager;
import android.content.Context;
import android.content.Intent;
import android.os.Build;
import android.os.Handler;
import android.os.Looper;
import com.reelyactive.blesdk.support.ble.util.Clock;
import com.reelyactive.blesdk.support.ble.util.Logger;
import com.reelyactive.blesdk.support.ble.util.SystemClock;
import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.TimeUnit; | long currentTimeInNanos = TimeUnit.MILLISECONDS.toNanos(getClock().currentTimeMillis());
ScanResult result = new ScanResult(device, ScanRecord.parseFromBytes(scanRecordBytes), rssi,
currentTimeInNanos);
onScanResult(device.getAddress(), result);
if (crashResolver != null)
crashResolver.notifyScannedDevice(device, this);
}
};
/**
* Package constructor, called from {@link BluetoothLeScannerCompatProvider}.
*/
JbBluetoothLeScannerCompat(
Context context, BluetoothManager manager, AlarmManager alarmManager) {
this(manager, alarmManager, new SystemClock(),
PendingIntent.getBroadcast(context, 0 /* requestCode */,
new Intent(context, ScanWakefulBroadcastReceiver.class).putExtra(ScanWakefulService.EXTRA_USE_LOLLIPOP_API, false), 0 /* flags */));
this.crashResolver = new BluetoothCrashResolver(context);
this.crashResolver.start();
this.mainHandler = new Handler(Looper.getMainLooper());
}
/**
* Testing constructor for the scanner.
*
* @VisibleForTesting
*/
JbBluetoothLeScannerCompat(BluetoothManager manager, AlarmManager alarmManager,
Clock clock, PendingIntent alarmIntent) {
super(clock, alarmManager, alarmIntent); | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Clock.java
// public interface Clock {
//
// /**
// * @return current time in milliseconds
// */
// public long currentTimeMillis();
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// public long elapsedRealtimeNanos();
//
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/SystemClock.java
// public class SystemClock implements Clock {
//
// /**
// * @return current time in milliseconds
// */
// @Override
// public long currentTimeMillis() {
// return System.currentTimeMillis();
// }
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// @Override
// @TargetApi(VERSION_CODES.JELLY_BEAN_MR1)
// public long elapsedRealtimeNanos() {
// return android.os.SystemClock.elapsedRealtimeNanos();
// }
// }
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/JbBluetoothLeScannerCompat.java
import android.annotation.TargetApi;
import android.app.AlarmManager;
import android.app.PendingIntent;
import android.bluetooth.BluetoothAdapter;
import android.bluetooth.BluetoothDevice;
import android.bluetooth.BluetoothManager;
import android.content.Context;
import android.content.Intent;
import android.os.Build;
import android.os.Handler;
import android.os.Looper;
import com.reelyactive.blesdk.support.ble.util.Clock;
import com.reelyactive.blesdk.support.ble.util.Logger;
import com.reelyactive.blesdk.support.ble.util.SystemClock;
import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.TimeUnit;
long currentTimeInNanos = TimeUnit.MILLISECONDS.toNanos(getClock().currentTimeMillis());
ScanResult result = new ScanResult(device, ScanRecord.parseFromBytes(scanRecordBytes), rssi,
currentTimeInNanos);
onScanResult(device.getAddress(), result);
if (crashResolver != null)
crashResolver.notifyScannedDevice(device, this);
}
};
/**
* Package constructor, called from {@link BluetoothLeScannerCompatProvider}.
*/
JbBluetoothLeScannerCompat(
Context context, BluetoothManager manager, AlarmManager alarmManager) {
this(manager, alarmManager, new SystemClock(),
PendingIntent.getBroadcast(context, 0 /* requestCode */,
new Intent(context, ScanWakefulBroadcastReceiver.class).putExtra(ScanWakefulService.EXTRA_USE_LOLLIPOP_API, false), 0 /* flags */));
this.crashResolver = new BluetoothCrashResolver(context);
this.crashResolver.start();
this.mainHandler = new Handler(Looper.getMainLooper());
}
/**
* Testing constructor for the scanner.
*
* @VisibleForTesting
*/
JbBluetoothLeScannerCompat(BluetoothManager manager, AlarmManager alarmManager,
Clock clock, PendingIntent alarmIntent) {
super(clock, alarmManager, alarmIntent); | Logger.logDebug("BLE 'JB' hardware access layer activated"); |
reelyactive/ble-android-sdk | library/src/main/java/com/reelyactive/blesdk/advertise/LBleAdvertiser.java | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/ScanResult.java
// public final class ScanResult implements Parcelable {
// // Remote bluetooth device.
// private BluetoothDevice mDevice;
//
// // Scan record, including advertising data and scan response data.
// @Nullable
// private ScanRecord mScanRecord;
//
// // Received signal strength.
// private int mRssi;
//
// // Device timestamp when the result was last seen.
// private long mTimestampNanos;
//
// /**
// * Constructor of scan result.
// *
// * @param device Remote bluetooth device that is found.
// * @param scanRecord Scan record including both advertising data and scan response data.
// * @param rssi Received signal strength.
// * @param timestampNanos Device timestamp when the scan result was observed.
// */
// public ScanResult(BluetoothDevice device, ScanRecord scanRecord, int rssi,
// long timestampNanos) {
// mDevice = device;
// mScanRecord = scanRecord;
// mRssi = rssi;
// mTimestampNanos = timestampNanos;
// }
//
// private ScanResult(Parcel in) {
// readFromParcel(in);
// }
//
// @Override
// public void writeToParcel(Parcel dest, int flags) {
// if (mDevice != null) {
// dest.writeInt(1);
// mDevice.writeToParcel(dest, flags);
// } else {
// dest.writeInt(0);
// }
// if (mScanRecord != null) {
// dest.writeInt(1);
// dest.writeByteArray(mScanRecord.getBytes());
// } else {
// dest.writeInt(0);
// }
// dest.writeInt(mRssi);
// dest.writeLong(mTimestampNanos);
// }
//
// private void readFromParcel(Parcel in) {
// if (in.readInt() == 1) {
// mDevice = BluetoothDevice.CREATOR.createFromParcel(in);
// }
// if (in.readInt() == 1) {
// mScanRecord = ScanRecord.parseFromBytes(in.createByteArray());
// }
// mRssi = in.readInt();
// mTimestampNanos = in.readLong();
// }
//
// @Override
// public int describeContents() {
// return 0;
// }
//
// /**
// * Returns the remote bluetooth device identified by the bluetooth device address.
// */
// public BluetoothDevice getDevice() {
// return mDevice;
// }
//
// /**
// * Returns the scan record, which is a combination of advertisement and scan response.
// */
// @Nullable
// public ScanRecord getScanRecord() {
// return mScanRecord;
// }
//
// /**
// * Returns the received signal strength in dBm. The valid range is [-127, 127].
// */
// public int getRssi() {
// return mRssi;
// }
//
// /**
// * Returns timestamp since boot when the scan record was observed.
// */
// public long getTimestampNanos() {
// return mTimestampNanos;
// }
//
// @Override
// public int hashCode() {
// return Objects.hash(mDevice, mRssi, mScanRecord, mTimestampNanos);
// }
//
// @Override
// public boolean equals(Object obj) {
// if (this == obj) {
// return true;
// }
// if (obj == null || getClass() != obj.getClass()) {
// return false;
// }
// ScanResult other = (ScanResult) obj;
// return Objects.equals(mDevice, other.mDevice) && (mRssi == other.mRssi)
// && Objects.equals(mScanRecord, other.mScanRecord)
// && (mTimestampNanos == other.mTimestampNanos);
// }
//
// @Override
// public String toString() {
// return "com.reelyactive.blesdk.support.ble.ScanResult{" + "mDevice=" + mDevice + ", mScanRecord="
// + Objects.toString(mScanRecord) + ", mRssi=" + mRssi + ", mTimestampNanos="
// + mTimestampNanos + '}';
// }
//
// /**
// * @hide
// */
// public static final Creator<ScanResult> CREATOR = new Creator<ScanResult>() {
// @Override
// public ScanResult createFromParcel(Parcel source) {
// return new ScanResult(source);
// }
//
// @Override
// public ScanResult[] newArray(int size) {
// return new ScanResult[size];
// }
// };
//
// }
| import android.annotation.TargetApi;
import android.bluetooth.BluetoothManager;
import android.bluetooth.le.AdvertiseCallback;
import android.bluetooth.le.AdvertiseData;
import android.bluetooth.le.AdvertiseSettings;
import android.bluetooth.le.BluetoothLeAdvertiser;
import android.content.Context;
import android.os.Build;
import android.os.ParcelUuid;
import com.reelyactive.blesdk.support.ble.ScanResult;
import java.util.List; | package com.reelyactive.blesdk.advertise;
/**
* Created by saiimons on 15-03-09.
*/
@TargetApi(Build.VERSION_CODES.LOLLIPOP)
public class LBleAdvertiser extends BleAdvertiser {
private final BluetoothLeAdvertiser advertiser;
private final Context context;
private final AdvertiseCallback callback = new AdvertiseCallback() {
@Override
public void onStartSuccess(AdvertiseSettings settingsInEffect) {
super.onStartSuccess(settingsInEffect);
}
@Override
public void onStartFailure(int errorCode) {
super.onStartFailure(errorCode);
}
};
public LBleAdvertiser(Context context, BluetoothManager manager) {
this.advertiser = manager.getAdapter().getBluetoothLeAdvertiser();
this.context = context;
}
@Override | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/ScanResult.java
// public final class ScanResult implements Parcelable {
// // Remote bluetooth device.
// private BluetoothDevice mDevice;
//
// // Scan record, including advertising data and scan response data.
// @Nullable
// private ScanRecord mScanRecord;
//
// // Received signal strength.
// private int mRssi;
//
// // Device timestamp when the result was last seen.
// private long mTimestampNanos;
//
// /**
// * Constructor of scan result.
// *
// * @param device Remote bluetooth device that is found.
// * @param scanRecord Scan record including both advertising data and scan response data.
// * @param rssi Received signal strength.
// * @param timestampNanos Device timestamp when the scan result was observed.
// */
// public ScanResult(BluetoothDevice device, ScanRecord scanRecord, int rssi,
// long timestampNanos) {
// mDevice = device;
// mScanRecord = scanRecord;
// mRssi = rssi;
// mTimestampNanos = timestampNanos;
// }
//
// private ScanResult(Parcel in) {
// readFromParcel(in);
// }
//
// @Override
// public void writeToParcel(Parcel dest, int flags) {
// if (mDevice != null) {
// dest.writeInt(1);
// mDevice.writeToParcel(dest, flags);
// } else {
// dest.writeInt(0);
// }
// if (mScanRecord != null) {
// dest.writeInt(1);
// dest.writeByteArray(mScanRecord.getBytes());
// } else {
// dest.writeInt(0);
// }
// dest.writeInt(mRssi);
// dest.writeLong(mTimestampNanos);
// }
//
// private void readFromParcel(Parcel in) {
// if (in.readInt() == 1) {
// mDevice = BluetoothDevice.CREATOR.createFromParcel(in);
// }
// if (in.readInt() == 1) {
// mScanRecord = ScanRecord.parseFromBytes(in.createByteArray());
// }
// mRssi = in.readInt();
// mTimestampNanos = in.readLong();
// }
//
// @Override
// public int describeContents() {
// return 0;
// }
//
// /**
// * Returns the remote bluetooth device identified by the bluetooth device address.
// */
// public BluetoothDevice getDevice() {
// return mDevice;
// }
//
// /**
// * Returns the scan record, which is a combination of advertisement and scan response.
// */
// @Nullable
// public ScanRecord getScanRecord() {
// return mScanRecord;
// }
//
// /**
// * Returns the received signal strength in dBm. The valid range is [-127, 127].
// */
// public int getRssi() {
// return mRssi;
// }
//
// /**
// * Returns timestamp since boot when the scan record was observed.
// */
// public long getTimestampNanos() {
// return mTimestampNanos;
// }
//
// @Override
// public int hashCode() {
// return Objects.hash(mDevice, mRssi, mScanRecord, mTimestampNanos);
// }
//
// @Override
// public boolean equals(Object obj) {
// if (this == obj) {
// return true;
// }
// if (obj == null || getClass() != obj.getClass()) {
// return false;
// }
// ScanResult other = (ScanResult) obj;
// return Objects.equals(mDevice, other.mDevice) && (mRssi == other.mRssi)
// && Objects.equals(mScanRecord, other.mScanRecord)
// && (mTimestampNanos == other.mTimestampNanos);
// }
//
// @Override
// public String toString() {
// return "com.reelyactive.blesdk.support.ble.ScanResult{" + "mDevice=" + mDevice + ", mScanRecord="
// + Objects.toString(mScanRecord) + ", mRssi=" + mRssi + ", mTimestampNanos="
// + mTimestampNanos + '}';
// }
//
// /**
// * @hide
// */
// public static final Creator<ScanResult> CREATOR = new Creator<ScanResult>() {
// @Override
// public ScanResult createFromParcel(Parcel source) {
// return new ScanResult(source);
// }
//
// @Override
// public ScanResult[] newArray(int size) {
// return new ScanResult[size];
// }
// };
//
// }
// Path: library/src/main/java/com/reelyactive/blesdk/advertise/LBleAdvertiser.java
import android.annotation.TargetApi;
import android.bluetooth.BluetoothManager;
import android.bluetooth.le.AdvertiseCallback;
import android.bluetooth.le.AdvertiseData;
import android.bluetooth.le.AdvertiseSettings;
import android.bluetooth.le.BluetoothLeAdvertiser;
import android.content.Context;
import android.os.Build;
import android.os.ParcelUuid;
import com.reelyactive.blesdk.support.ble.ScanResult;
import java.util.List;
package com.reelyactive.blesdk.advertise;
/**
* Created by saiimons on 15-03-09.
*/
@TargetApi(Build.VERSION_CODES.LOLLIPOP)
public class LBleAdvertiser extends BleAdvertiser {
private final BluetoothLeAdvertiser advertiser;
private final Context context;
private final AdvertiseCallback callback = new AdvertiseCallback() {
@Override
public void onStartSuccess(AdvertiseSettings settingsInEffect) {
super.onStartSuccess(settingsInEffect);
}
@Override
public void onStartFailure(int errorCode) {
super.onStartFailure(errorCode);
}
};
public LBleAdvertiser(Context context, BluetoothManager manager) {
this.advertiser = manager.getAdapter().getBluetoothLeAdvertiser();
this.context = context;
}
@Override | public void startAdvertising(String uuid, List<ScanResult> closestBeaconId, String fallbackUrl) { |
reelyactive/ble-android-sdk | library/src/main/java/com/reelyactive/blesdk/support/ble/LBluetoothLeScannerCompat.java | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Clock.java
// public interface Clock {
//
// /**
// * @return current time in milliseconds
// */
// public long currentTimeMillis();
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// public long elapsedRealtimeNanos();
//
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/SystemClock.java
// public class SystemClock implements Clock {
//
// /**
// * @return current time in milliseconds
// */
// @Override
// public long currentTimeMillis() {
// return System.currentTimeMillis();
// }
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// @Override
// @TargetApi(VERSION_CODES.JELLY_BEAN_MR1)
// public long elapsedRealtimeNanos() {
// return android.os.SystemClock.elapsedRealtimeNanos();
// }
// }
| import android.annotation.TargetApi;
import android.app.AlarmManager;
import android.app.PendingIntent;
import android.bluetooth.BluetoothAdapter;
import android.bluetooth.BluetoothManager;
import android.content.Context;
import android.content.Intent;
import android.os.Build;
import android.os.Handler;
import android.os.Looper;
import android.text.TextUtils;
import com.reelyactive.blesdk.support.ble.util.Clock;
import com.reelyactive.blesdk.support.ble.util.Logger;
import com.reelyactive.blesdk.support.ble.util.SystemClock;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.TimeUnit; | package com.reelyactive.blesdk.support.ble;
/*
* Copyright 2014 Google Inc. All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
/**
* Implements Bluetooth LE scan related API on top of {@link android.os.Build.VERSION_CODES#LOLLIPOP}
* and later.
*/
@TargetApi(Build.VERSION_CODES.LOLLIPOP)
class LBluetoothLeScannerCompat extends BluetoothLeScannerCompat {
private final Map<String, ScanResult> recentScanResults = new ConcurrentHashMap<>();
private final Map<ScanCallback, ScanClient> callbacksMap = new ConcurrentHashMap<>();
private final android.bluetooth.le.BluetoothLeScanner osScanner;
/**
* Package-protected constructor, used by {@link BluetoothLeScannerCompatProvider}.
* <p>
* Cannot be called from emulated devices that don't implement a BluetoothAdapter.
*/
LBluetoothLeScannerCompat(Context context, BluetoothManager manager, AlarmManager alarmManager) {
this(
manager,
alarmManager, | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Clock.java
// public interface Clock {
//
// /**
// * @return current time in milliseconds
// */
// public long currentTimeMillis();
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// public long elapsedRealtimeNanos();
//
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/SystemClock.java
// public class SystemClock implements Clock {
//
// /**
// * @return current time in milliseconds
// */
// @Override
// public long currentTimeMillis() {
// return System.currentTimeMillis();
// }
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// @Override
// @TargetApi(VERSION_CODES.JELLY_BEAN_MR1)
// public long elapsedRealtimeNanos() {
// return android.os.SystemClock.elapsedRealtimeNanos();
// }
// }
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/LBluetoothLeScannerCompat.java
import android.annotation.TargetApi;
import android.app.AlarmManager;
import android.app.PendingIntent;
import android.bluetooth.BluetoothAdapter;
import android.bluetooth.BluetoothManager;
import android.content.Context;
import android.content.Intent;
import android.os.Build;
import android.os.Handler;
import android.os.Looper;
import android.text.TextUtils;
import com.reelyactive.blesdk.support.ble.util.Clock;
import com.reelyactive.blesdk.support.ble.util.Logger;
import com.reelyactive.blesdk.support.ble.util.SystemClock;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.TimeUnit;
package com.reelyactive.blesdk.support.ble;
/*
* Copyright 2014 Google Inc. All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
/**
* Implements Bluetooth LE scan related API on top of {@link android.os.Build.VERSION_CODES#LOLLIPOP}
* and later.
*/
@TargetApi(Build.VERSION_CODES.LOLLIPOP)
class LBluetoothLeScannerCompat extends BluetoothLeScannerCompat {
private final Map<String, ScanResult> recentScanResults = new ConcurrentHashMap<>();
private final Map<ScanCallback, ScanClient> callbacksMap = new ConcurrentHashMap<>();
private final android.bluetooth.le.BluetoothLeScanner osScanner;
/**
* Package-protected constructor, used by {@link BluetoothLeScannerCompatProvider}.
* <p>
* Cannot be called from emulated devices that don't implement a BluetoothAdapter.
*/
LBluetoothLeScannerCompat(Context context, BluetoothManager manager, AlarmManager alarmManager) {
this(
manager,
alarmManager, | new SystemClock(), |
reelyactive/ble-android-sdk | library/src/main/java/com/reelyactive/blesdk/support/ble/LBluetoothLeScannerCompat.java | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Clock.java
// public interface Clock {
//
// /**
// * @return current time in milliseconds
// */
// public long currentTimeMillis();
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// public long elapsedRealtimeNanos();
//
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/SystemClock.java
// public class SystemClock implements Clock {
//
// /**
// * @return current time in milliseconds
// */
// @Override
// public long currentTimeMillis() {
// return System.currentTimeMillis();
// }
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// @Override
// @TargetApi(VERSION_CODES.JELLY_BEAN_MR1)
// public long elapsedRealtimeNanos() {
// return android.os.SystemClock.elapsedRealtimeNanos();
// }
// }
| import android.annotation.TargetApi;
import android.app.AlarmManager;
import android.app.PendingIntent;
import android.bluetooth.BluetoothAdapter;
import android.bluetooth.BluetoothManager;
import android.content.Context;
import android.content.Intent;
import android.os.Build;
import android.os.Handler;
import android.os.Looper;
import android.text.TextUtils;
import com.reelyactive.blesdk.support.ble.util.Clock;
import com.reelyactive.blesdk.support.ble.util.Logger;
import com.reelyactive.blesdk.support.ble.util.SystemClock;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.TimeUnit; | package com.reelyactive.blesdk.support.ble;
/*
* Copyright 2014 Google Inc. All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
/**
* Implements Bluetooth LE scan related API on top of {@link android.os.Build.VERSION_CODES#LOLLIPOP}
* and later.
*/
@TargetApi(Build.VERSION_CODES.LOLLIPOP)
class LBluetoothLeScannerCompat extends BluetoothLeScannerCompat {
private final Map<String, ScanResult> recentScanResults = new ConcurrentHashMap<>();
private final Map<ScanCallback, ScanClient> callbacksMap = new ConcurrentHashMap<>();
private final android.bluetooth.le.BluetoothLeScanner osScanner;
/**
* Package-protected constructor, used by {@link BluetoothLeScannerCompatProvider}.
* <p>
* Cannot be called from emulated devices that don't implement a BluetoothAdapter.
*/
LBluetoothLeScannerCompat(Context context, BluetoothManager manager, AlarmManager alarmManager) {
this(
manager,
alarmManager,
new SystemClock(),
PendingIntent.getBroadcast(
context,
0 /* requestCode */,
new Intent(context, ScanWakefulBroadcastReceiver.class).putExtra(ScanWakefulService.EXTRA_USE_LOLLIPOP_API, true),
0 /* flags */
)
);
}
LBluetoothLeScannerCompat(BluetoothManager manager, AlarmManager alarmManager, | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Clock.java
// public interface Clock {
//
// /**
// * @return current time in milliseconds
// */
// public long currentTimeMillis();
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// public long elapsedRealtimeNanos();
//
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/SystemClock.java
// public class SystemClock implements Clock {
//
// /**
// * @return current time in milliseconds
// */
// @Override
// public long currentTimeMillis() {
// return System.currentTimeMillis();
// }
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// @Override
// @TargetApi(VERSION_CODES.JELLY_BEAN_MR1)
// public long elapsedRealtimeNanos() {
// return android.os.SystemClock.elapsedRealtimeNanos();
// }
// }
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/LBluetoothLeScannerCompat.java
import android.annotation.TargetApi;
import android.app.AlarmManager;
import android.app.PendingIntent;
import android.bluetooth.BluetoothAdapter;
import android.bluetooth.BluetoothManager;
import android.content.Context;
import android.content.Intent;
import android.os.Build;
import android.os.Handler;
import android.os.Looper;
import android.text.TextUtils;
import com.reelyactive.blesdk.support.ble.util.Clock;
import com.reelyactive.blesdk.support.ble.util.Logger;
import com.reelyactive.blesdk.support.ble.util.SystemClock;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.TimeUnit;
package com.reelyactive.blesdk.support.ble;
/*
* Copyright 2014 Google Inc. All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
/**
* Implements Bluetooth LE scan related API on top of {@link android.os.Build.VERSION_CODES#LOLLIPOP}
* and later.
*/
@TargetApi(Build.VERSION_CODES.LOLLIPOP)
class LBluetoothLeScannerCompat extends BluetoothLeScannerCompat {
private final Map<String, ScanResult> recentScanResults = new ConcurrentHashMap<>();
private final Map<ScanCallback, ScanClient> callbacksMap = new ConcurrentHashMap<>();
private final android.bluetooth.le.BluetoothLeScanner osScanner;
/**
* Package-protected constructor, used by {@link BluetoothLeScannerCompatProvider}.
* <p>
* Cannot be called from emulated devices that don't implement a BluetoothAdapter.
*/
LBluetoothLeScannerCompat(Context context, BluetoothManager manager, AlarmManager alarmManager) {
this(
manager,
alarmManager,
new SystemClock(),
PendingIntent.getBroadcast(
context,
0 /* requestCode */,
new Intent(context, ScanWakefulBroadcastReceiver.class).putExtra(ScanWakefulService.EXTRA_USE_LOLLIPOP_API, true),
0 /* flags */
)
);
}
LBluetoothLeScannerCompat(BluetoothManager manager, AlarmManager alarmManager, | Clock clock, PendingIntent alarmIntent) { |
reelyactive/ble-android-sdk | library/src/main/java/com/reelyactive/blesdk/support/ble/LBluetoothLeScannerCompat.java | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Clock.java
// public interface Clock {
//
// /**
// * @return current time in milliseconds
// */
// public long currentTimeMillis();
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// public long elapsedRealtimeNanos();
//
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/SystemClock.java
// public class SystemClock implements Clock {
//
// /**
// * @return current time in milliseconds
// */
// @Override
// public long currentTimeMillis() {
// return System.currentTimeMillis();
// }
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// @Override
// @TargetApi(VERSION_CODES.JELLY_BEAN_MR1)
// public long elapsedRealtimeNanos() {
// return android.os.SystemClock.elapsedRealtimeNanos();
// }
// }
| import android.annotation.TargetApi;
import android.app.AlarmManager;
import android.app.PendingIntent;
import android.bluetooth.BluetoothAdapter;
import android.bluetooth.BluetoothManager;
import android.content.Context;
import android.content.Intent;
import android.os.Build;
import android.os.Handler;
import android.os.Looper;
import android.text.TextUtils;
import com.reelyactive.blesdk.support.ble.util.Clock;
import com.reelyactive.blesdk.support.ble.util.Logger;
import com.reelyactive.blesdk.support.ble.util.SystemClock;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.TimeUnit; | package com.reelyactive.blesdk.support.ble;
/*
* Copyright 2014 Google Inc. All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
/**
* Implements Bluetooth LE scan related API on top of {@link android.os.Build.VERSION_CODES#LOLLIPOP}
* and later.
*/
@TargetApi(Build.VERSION_CODES.LOLLIPOP)
class LBluetoothLeScannerCompat extends BluetoothLeScannerCompat {
private final Map<String, ScanResult> recentScanResults = new ConcurrentHashMap<>();
private final Map<ScanCallback, ScanClient> callbacksMap = new ConcurrentHashMap<>();
private final android.bluetooth.le.BluetoothLeScanner osScanner;
/**
* Package-protected constructor, used by {@link BluetoothLeScannerCompatProvider}.
* <p>
* Cannot be called from emulated devices that don't implement a BluetoothAdapter.
*/
LBluetoothLeScannerCompat(Context context, BluetoothManager manager, AlarmManager alarmManager) {
this(
manager,
alarmManager,
new SystemClock(),
PendingIntent.getBroadcast(
context,
0 /* requestCode */,
new Intent(context, ScanWakefulBroadcastReceiver.class).putExtra(ScanWakefulService.EXTRA_USE_LOLLIPOP_API, true),
0 /* flags */
)
);
}
LBluetoothLeScannerCompat(BluetoothManager manager, AlarmManager alarmManager,
Clock clock, PendingIntent alarmIntent) {
super(clock, alarmManager, alarmIntent); | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Clock.java
// public interface Clock {
//
// /**
// * @return current time in milliseconds
// */
// public long currentTimeMillis();
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// public long elapsedRealtimeNanos();
//
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/SystemClock.java
// public class SystemClock implements Clock {
//
// /**
// * @return current time in milliseconds
// */
// @Override
// public long currentTimeMillis() {
// return System.currentTimeMillis();
// }
//
// /**
// * @return time since the device was booted, in nanoseconds
// */
// @Override
// @TargetApi(VERSION_CODES.JELLY_BEAN_MR1)
// public long elapsedRealtimeNanos() {
// return android.os.SystemClock.elapsedRealtimeNanos();
// }
// }
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/LBluetoothLeScannerCompat.java
import android.annotation.TargetApi;
import android.app.AlarmManager;
import android.app.PendingIntent;
import android.bluetooth.BluetoothAdapter;
import android.bluetooth.BluetoothManager;
import android.content.Context;
import android.content.Intent;
import android.os.Build;
import android.os.Handler;
import android.os.Looper;
import android.text.TextUtils;
import com.reelyactive.blesdk.support.ble.util.Clock;
import com.reelyactive.blesdk.support.ble.util.Logger;
import com.reelyactive.blesdk.support.ble.util.SystemClock;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.TimeUnit;
package com.reelyactive.blesdk.support.ble;
/*
* Copyright 2014 Google Inc. All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
/**
* Implements Bluetooth LE scan related API on top of {@link android.os.Build.VERSION_CODES#LOLLIPOP}
* and later.
*/
@TargetApi(Build.VERSION_CODES.LOLLIPOP)
class LBluetoothLeScannerCompat extends BluetoothLeScannerCompat {
private final Map<String, ScanResult> recentScanResults = new ConcurrentHashMap<>();
private final Map<ScanCallback, ScanClient> callbacksMap = new ConcurrentHashMap<>();
private final android.bluetooth.le.BluetoothLeScanner osScanner;
/**
* Package-protected constructor, used by {@link BluetoothLeScannerCompatProvider}.
* <p>
* Cannot be called from emulated devices that don't implement a BluetoothAdapter.
*/
LBluetoothLeScannerCompat(Context context, BluetoothManager manager, AlarmManager alarmManager) {
this(
manager,
alarmManager,
new SystemClock(),
PendingIntent.getBroadcast(
context,
0 /* requestCode */,
new Intent(context, ScanWakefulBroadcastReceiver.class).putExtra(ScanWakefulService.EXTRA_USE_LOLLIPOP_API, true),
0 /* flags */
)
);
}
LBluetoothLeScannerCompat(BluetoothManager manager, AlarmManager alarmManager,
Clock clock, PendingIntent alarmIntent) {
super(clock, alarmManager, alarmIntent); | Logger.logDebug("BLE 'L' hardware access layer activated"); |
reelyactive/ble-android-sdk | example_app/src/main/java/com/reelyactive/blescanner/BleScanResultAdapter.java | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/ScanResult.java
// public final class ScanResult implements Parcelable {
// // Remote bluetooth device.
// private BluetoothDevice mDevice;
//
// // Scan record, including advertising data and scan response data.
// @Nullable
// private ScanRecord mScanRecord;
//
// // Received signal strength.
// private int mRssi;
//
// // Device timestamp when the result was last seen.
// private long mTimestampNanos;
//
// /**
// * Constructor of scan result.
// *
// * @param device Remote bluetooth device that is found.
// * @param scanRecord Scan record including both advertising data and scan response data.
// * @param rssi Received signal strength.
// * @param timestampNanos Device timestamp when the scan result was observed.
// */
// public ScanResult(BluetoothDevice device, ScanRecord scanRecord, int rssi,
// long timestampNanos) {
// mDevice = device;
// mScanRecord = scanRecord;
// mRssi = rssi;
// mTimestampNanos = timestampNanos;
// }
//
// private ScanResult(Parcel in) {
// readFromParcel(in);
// }
//
// @Override
// public void writeToParcel(Parcel dest, int flags) {
// if (mDevice != null) {
// dest.writeInt(1);
// mDevice.writeToParcel(dest, flags);
// } else {
// dest.writeInt(0);
// }
// if (mScanRecord != null) {
// dest.writeInt(1);
// dest.writeByteArray(mScanRecord.getBytes());
// } else {
// dest.writeInt(0);
// }
// dest.writeInt(mRssi);
// dest.writeLong(mTimestampNanos);
// }
//
// private void readFromParcel(Parcel in) {
// if (in.readInt() == 1) {
// mDevice = BluetoothDevice.CREATOR.createFromParcel(in);
// }
// if (in.readInt() == 1) {
// mScanRecord = ScanRecord.parseFromBytes(in.createByteArray());
// }
// mRssi = in.readInt();
// mTimestampNanos = in.readLong();
// }
//
// @Override
// public int describeContents() {
// return 0;
// }
//
// /**
// * Returns the remote bluetooth device identified by the bluetooth device address.
// */
// public BluetoothDevice getDevice() {
// return mDevice;
// }
//
// /**
// * Returns the scan record, which is a combination of advertisement and scan response.
// */
// @Nullable
// public ScanRecord getScanRecord() {
// return mScanRecord;
// }
//
// /**
// * Returns the received signal strength in dBm. The valid range is [-127, 127].
// */
// public int getRssi() {
// return mRssi;
// }
//
// /**
// * Returns timestamp since boot when the scan record was observed.
// */
// public long getTimestampNanos() {
// return mTimestampNanos;
// }
//
// @Override
// public int hashCode() {
// return Objects.hash(mDevice, mRssi, mScanRecord, mTimestampNanos);
// }
//
// @Override
// public boolean equals(Object obj) {
// if (this == obj) {
// return true;
// }
// if (obj == null || getClass() != obj.getClass()) {
// return false;
// }
// ScanResult other = (ScanResult) obj;
// return Objects.equals(mDevice, other.mDevice) && (mRssi == other.mRssi)
// && Objects.equals(mScanRecord, other.mScanRecord)
// && (mTimestampNanos == other.mTimestampNanos);
// }
//
// @Override
// public String toString() {
// return "com.reelyactive.blesdk.support.ble.ScanResult{" + "mDevice=" + mDevice + ", mScanRecord="
// + Objects.toString(mScanRecord) + ", mRssi=" + mRssi + ", mTimestampNanos="
// + mTimestampNanos + '}';
// }
//
// /**
// * @hide
// */
// public static final Creator<ScanResult> CREATOR = new Creator<ScanResult>() {
// @Override
// public ScanResult createFromParcel(Parcel source) {
// return new ScanResult(source);
// }
//
// @Override
// public ScanResult[] newArray(int size) {
// return new ScanResult[size];
// }
// };
//
// }
| import android.content.Context;
import android.view.LayoutInflater;
import android.view.View;
import android.view.ViewGroup;
import android.widget.BaseAdapter;
import android.widget.TextView;
import com.reelyactive.blesdk.support.ble.ScanResult;
import java.util.HashMap; | package com.reelyactive.blescanner;
public class BleScanResultAdapter extends BaseAdapter {
private final Context mContext; | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/ScanResult.java
// public final class ScanResult implements Parcelable {
// // Remote bluetooth device.
// private BluetoothDevice mDevice;
//
// // Scan record, including advertising data and scan response data.
// @Nullable
// private ScanRecord mScanRecord;
//
// // Received signal strength.
// private int mRssi;
//
// // Device timestamp when the result was last seen.
// private long mTimestampNanos;
//
// /**
// * Constructor of scan result.
// *
// * @param device Remote bluetooth device that is found.
// * @param scanRecord Scan record including both advertising data and scan response data.
// * @param rssi Received signal strength.
// * @param timestampNanos Device timestamp when the scan result was observed.
// */
// public ScanResult(BluetoothDevice device, ScanRecord scanRecord, int rssi,
// long timestampNanos) {
// mDevice = device;
// mScanRecord = scanRecord;
// mRssi = rssi;
// mTimestampNanos = timestampNanos;
// }
//
// private ScanResult(Parcel in) {
// readFromParcel(in);
// }
//
// @Override
// public void writeToParcel(Parcel dest, int flags) {
// if (mDevice != null) {
// dest.writeInt(1);
// mDevice.writeToParcel(dest, flags);
// } else {
// dest.writeInt(0);
// }
// if (mScanRecord != null) {
// dest.writeInt(1);
// dest.writeByteArray(mScanRecord.getBytes());
// } else {
// dest.writeInt(0);
// }
// dest.writeInt(mRssi);
// dest.writeLong(mTimestampNanos);
// }
//
// private void readFromParcel(Parcel in) {
// if (in.readInt() == 1) {
// mDevice = BluetoothDevice.CREATOR.createFromParcel(in);
// }
// if (in.readInt() == 1) {
// mScanRecord = ScanRecord.parseFromBytes(in.createByteArray());
// }
// mRssi = in.readInt();
// mTimestampNanos = in.readLong();
// }
//
// @Override
// public int describeContents() {
// return 0;
// }
//
// /**
// * Returns the remote bluetooth device identified by the bluetooth device address.
// */
// public BluetoothDevice getDevice() {
// return mDevice;
// }
//
// /**
// * Returns the scan record, which is a combination of advertisement and scan response.
// */
// @Nullable
// public ScanRecord getScanRecord() {
// return mScanRecord;
// }
//
// /**
// * Returns the received signal strength in dBm. The valid range is [-127, 127].
// */
// public int getRssi() {
// return mRssi;
// }
//
// /**
// * Returns timestamp since boot when the scan record was observed.
// */
// public long getTimestampNanos() {
// return mTimestampNanos;
// }
//
// @Override
// public int hashCode() {
// return Objects.hash(mDevice, mRssi, mScanRecord, mTimestampNanos);
// }
//
// @Override
// public boolean equals(Object obj) {
// if (this == obj) {
// return true;
// }
// if (obj == null || getClass() != obj.getClass()) {
// return false;
// }
// ScanResult other = (ScanResult) obj;
// return Objects.equals(mDevice, other.mDevice) && (mRssi == other.mRssi)
// && Objects.equals(mScanRecord, other.mScanRecord)
// && (mTimestampNanos == other.mTimestampNanos);
// }
//
// @Override
// public String toString() {
// return "com.reelyactive.blesdk.support.ble.ScanResult{" + "mDevice=" + mDevice + ", mScanRecord="
// + Objects.toString(mScanRecord) + ", mRssi=" + mRssi + ", mTimestampNanos="
// + mTimestampNanos + '}';
// }
//
// /**
// * @hide
// */
// public static final Creator<ScanResult> CREATOR = new Creator<ScanResult>() {
// @Override
// public ScanResult createFromParcel(Parcel source) {
// return new ScanResult(source);
// }
//
// @Override
// public ScanResult[] newArray(int size) {
// return new ScanResult[size];
// }
// };
//
// }
// Path: example_app/src/main/java/com/reelyactive/blescanner/BleScanResultAdapter.java
import android.content.Context;
import android.view.LayoutInflater;
import android.view.View;
import android.view.ViewGroup;
import android.widget.BaseAdapter;
import android.widget.TextView;
import com.reelyactive.blesdk.support.ble.ScanResult;
import java.util.HashMap;
package com.reelyactive.blescanner;
public class BleScanResultAdapter extends BaseAdapter {
private final Context mContext; | private HashMap<String, ScanResult> items; |
reelyactive/ble-android-sdk | example_app/src/main/java/com/reelyactive/blescanner/ReelyAwareScanActivity.java | // Path: library/src/main/java/com/reelyactive/blesdk/application/ReelyAwareActivity.java
// public interface ReelyAwareActivity {
// public void onScanStarted();
//
// public void onScanStopped();
//
// public void onEnterRegion(ScanResult beacon);
//
// public void onLeaveRegion(ScanResult beacon);
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/ScanResult.java
// public final class ScanResult implements Parcelable {
// // Remote bluetooth device.
// private BluetoothDevice mDevice;
//
// // Scan record, including advertising data and scan response data.
// @Nullable
// private ScanRecord mScanRecord;
//
// // Received signal strength.
// private int mRssi;
//
// // Device timestamp when the result was last seen.
// private long mTimestampNanos;
//
// /**
// * Constructor of scan result.
// *
// * @param device Remote bluetooth device that is found.
// * @param scanRecord Scan record including both advertising data and scan response data.
// * @param rssi Received signal strength.
// * @param timestampNanos Device timestamp when the scan result was observed.
// */
// public ScanResult(BluetoothDevice device, ScanRecord scanRecord, int rssi,
// long timestampNanos) {
// mDevice = device;
// mScanRecord = scanRecord;
// mRssi = rssi;
// mTimestampNanos = timestampNanos;
// }
//
// private ScanResult(Parcel in) {
// readFromParcel(in);
// }
//
// @Override
// public void writeToParcel(Parcel dest, int flags) {
// if (mDevice != null) {
// dest.writeInt(1);
// mDevice.writeToParcel(dest, flags);
// } else {
// dest.writeInt(0);
// }
// if (mScanRecord != null) {
// dest.writeInt(1);
// dest.writeByteArray(mScanRecord.getBytes());
// } else {
// dest.writeInt(0);
// }
// dest.writeInt(mRssi);
// dest.writeLong(mTimestampNanos);
// }
//
// private void readFromParcel(Parcel in) {
// if (in.readInt() == 1) {
// mDevice = BluetoothDevice.CREATOR.createFromParcel(in);
// }
// if (in.readInt() == 1) {
// mScanRecord = ScanRecord.parseFromBytes(in.createByteArray());
// }
// mRssi = in.readInt();
// mTimestampNanos = in.readLong();
// }
//
// @Override
// public int describeContents() {
// return 0;
// }
//
// /**
// * Returns the remote bluetooth device identified by the bluetooth device address.
// */
// public BluetoothDevice getDevice() {
// return mDevice;
// }
//
// /**
// * Returns the scan record, which is a combination of advertisement and scan response.
// */
// @Nullable
// public ScanRecord getScanRecord() {
// return mScanRecord;
// }
//
// /**
// * Returns the received signal strength in dBm. The valid range is [-127, 127].
// */
// public int getRssi() {
// return mRssi;
// }
//
// /**
// * Returns timestamp since boot when the scan record was observed.
// */
// public long getTimestampNanos() {
// return mTimestampNanos;
// }
//
// @Override
// public int hashCode() {
// return Objects.hash(mDevice, mRssi, mScanRecord, mTimestampNanos);
// }
//
// @Override
// public boolean equals(Object obj) {
// if (this == obj) {
// return true;
// }
// if (obj == null || getClass() != obj.getClass()) {
// return false;
// }
// ScanResult other = (ScanResult) obj;
// return Objects.equals(mDevice, other.mDevice) && (mRssi == other.mRssi)
// && Objects.equals(mScanRecord, other.mScanRecord)
// && (mTimestampNanos == other.mTimestampNanos);
// }
//
// @Override
// public String toString() {
// return "com.reelyactive.blesdk.support.ble.ScanResult{" + "mDevice=" + mDevice + ", mScanRecord="
// + Objects.toString(mScanRecord) + ", mRssi=" + mRssi + ", mTimestampNanos="
// + mTimestampNanos + '}';
// }
//
// /**
// * @hide
// */
// public static final Creator<ScanResult> CREATOR = new Creator<ScanResult>() {
// @Override
// public ScanResult createFromParcel(Parcel source) {
// return new ScanResult(source);
// }
//
// @Override
// public ScanResult[] newArray(int size) {
// return new ScanResult[size];
// }
// };
//
// }
| import android.Manifest;
import android.content.pm.PackageManager;
import android.os.Bundle;
import android.support.design.widget.Snackbar;
import android.support.v4.app.ActivityCompat;
import android.support.v7.app.AppCompatActivity;
import android.view.View;
import android.widget.ListView;
import com.reelyactive.blesdk.application.ReelyAwareActivity;
import com.reelyactive.blesdk.support.ble.ScanResult; | Snackbar
.make((View) list.getParent(), R.string.location_permission, Snackbar.LENGTH_INDEFINITE)
.setAction(
R.string.ok,
new View.OnClickListener() {
@Override
public void onClick(View v) {
ActivityCompat.requestPermissions(ReelyAwareScanActivity.this, new String[]{Manifest.permission.ACCESS_COARSE_LOCATION}, REQUEST_CODE_LOCATION);
}
}
).show();
}
break;
default:
super.onRequestPermissionsResult(requestCode, permissions, grantResults);
break;
}
}
@Override
public void onScanStarted() {
}
@Override
public void onScanStopped() {
}
@Override | // Path: library/src/main/java/com/reelyactive/blesdk/application/ReelyAwareActivity.java
// public interface ReelyAwareActivity {
// public void onScanStarted();
//
// public void onScanStopped();
//
// public void onEnterRegion(ScanResult beacon);
//
// public void onLeaveRegion(ScanResult beacon);
// }
//
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/ScanResult.java
// public final class ScanResult implements Parcelable {
// // Remote bluetooth device.
// private BluetoothDevice mDevice;
//
// // Scan record, including advertising data and scan response data.
// @Nullable
// private ScanRecord mScanRecord;
//
// // Received signal strength.
// private int mRssi;
//
// // Device timestamp when the result was last seen.
// private long mTimestampNanos;
//
// /**
// * Constructor of scan result.
// *
// * @param device Remote bluetooth device that is found.
// * @param scanRecord Scan record including both advertising data and scan response data.
// * @param rssi Received signal strength.
// * @param timestampNanos Device timestamp when the scan result was observed.
// */
// public ScanResult(BluetoothDevice device, ScanRecord scanRecord, int rssi,
// long timestampNanos) {
// mDevice = device;
// mScanRecord = scanRecord;
// mRssi = rssi;
// mTimestampNanos = timestampNanos;
// }
//
// private ScanResult(Parcel in) {
// readFromParcel(in);
// }
//
// @Override
// public void writeToParcel(Parcel dest, int flags) {
// if (mDevice != null) {
// dest.writeInt(1);
// mDevice.writeToParcel(dest, flags);
// } else {
// dest.writeInt(0);
// }
// if (mScanRecord != null) {
// dest.writeInt(1);
// dest.writeByteArray(mScanRecord.getBytes());
// } else {
// dest.writeInt(0);
// }
// dest.writeInt(mRssi);
// dest.writeLong(mTimestampNanos);
// }
//
// private void readFromParcel(Parcel in) {
// if (in.readInt() == 1) {
// mDevice = BluetoothDevice.CREATOR.createFromParcel(in);
// }
// if (in.readInt() == 1) {
// mScanRecord = ScanRecord.parseFromBytes(in.createByteArray());
// }
// mRssi = in.readInt();
// mTimestampNanos = in.readLong();
// }
//
// @Override
// public int describeContents() {
// return 0;
// }
//
// /**
// * Returns the remote bluetooth device identified by the bluetooth device address.
// */
// public BluetoothDevice getDevice() {
// return mDevice;
// }
//
// /**
// * Returns the scan record, which is a combination of advertisement and scan response.
// */
// @Nullable
// public ScanRecord getScanRecord() {
// return mScanRecord;
// }
//
// /**
// * Returns the received signal strength in dBm. The valid range is [-127, 127].
// */
// public int getRssi() {
// return mRssi;
// }
//
// /**
// * Returns timestamp since boot when the scan record was observed.
// */
// public long getTimestampNanos() {
// return mTimestampNanos;
// }
//
// @Override
// public int hashCode() {
// return Objects.hash(mDevice, mRssi, mScanRecord, mTimestampNanos);
// }
//
// @Override
// public boolean equals(Object obj) {
// if (this == obj) {
// return true;
// }
// if (obj == null || getClass() != obj.getClass()) {
// return false;
// }
// ScanResult other = (ScanResult) obj;
// return Objects.equals(mDevice, other.mDevice) && (mRssi == other.mRssi)
// && Objects.equals(mScanRecord, other.mScanRecord)
// && (mTimestampNanos == other.mTimestampNanos);
// }
//
// @Override
// public String toString() {
// return "com.reelyactive.blesdk.support.ble.ScanResult{" + "mDevice=" + mDevice + ", mScanRecord="
// + Objects.toString(mScanRecord) + ", mRssi=" + mRssi + ", mTimestampNanos="
// + mTimestampNanos + '}';
// }
//
// /**
// * @hide
// */
// public static final Creator<ScanResult> CREATOR = new Creator<ScanResult>() {
// @Override
// public ScanResult createFromParcel(Parcel source) {
// return new ScanResult(source);
// }
//
// @Override
// public ScanResult[] newArray(int size) {
// return new ScanResult[size];
// }
// };
//
// }
// Path: example_app/src/main/java/com/reelyactive/blescanner/ReelyAwareScanActivity.java
import android.Manifest;
import android.content.pm.PackageManager;
import android.os.Bundle;
import android.support.design.widget.Snackbar;
import android.support.v4.app.ActivityCompat;
import android.support.v7.app.AppCompatActivity;
import android.view.View;
import android.widget.ListView;
import com.reelyactive.blesdk.application.ReelyAwareActivity;
import com.reelyactive.blesdk.support.ble.ScanResult;
Snackbar
.make((View) list.getParent(), R.string.location_permission, Snackbar.LENGTH_INDEFINITE)
.setAction(
R.string.ok,
new View.OnClickListener() {
@Override
public void onClick(View v) {
ActivityCompat.requestPermissions(ReelyAwareScanActivity.this, new String[]{Manifest.permission.ACCESS_COARSE_LOCATION}, REQUEST_CODE_LOCATION);
}
}
).show();
}
break;
default:
super.onRequestPermissionsResult(requestCode, permissions, grantResults);
break;
}
}
@Override
public void onScanStarted() {
}
@Override
public void onScanStopped() {
}
@Override | public void onEnterRegion(ScanResult beacon) { |
reelyactive/ble-android-sdk | library/src/main/java/com/reelyactive/blesdk/support/ble/ScanRecord.java | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
| import java.util.List;
import java.util.Map;
import android.os.ParcelUuid;
import android.support.annotation.Nullable;
import android.util.SparseArray;
import com.reelyactive.blesdk.support.ble.util.Logger;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap; | byte[] serviceDataUuidBytes = extractBytes(scanRecord, currentPos,
serviceUuidLength);
ParcelUuid serviceDataUuid = BluetoothUuid.parseUuidFrom(
serviceDataUuidBytes);
byte[] serviceDataArray = extractBytes(scanRecord,
currentPos + serviceUuidLength, dataLength - serviceUuidLength);
serviceData.put(serviceDataUuid, serviceDataArray);
break;
case DATA_TYPE_MANUFACTURER_SPECIFIC_DATA:
// The first two bytes of the manufacturer specific data are
// manufacturer ids in little endian.
int manufacturerId = ((scanRecord[currentPos + 1] & 0xFF) << 8)
+ (scanRecord[currentPos] & 0xFF);
byte[] manufacturerDataBytes = extractBytes(scanRecord, currentPos + 2,
dataLength - 2);
manufacturerData.put(manufacturerId, manufacturerDataBytes);
break;
default:
// Just ignore, we don't handle such data type.
break;
}
currentPos += dataLength;
}
if (serviceUuids.isEmpty()) {
serviceUuids = null;
}
return new ScanRecord(serviceUuids, manufacturerData, serviceData,
advertiseFlag, txPowerLevel, localName, scanRecord);
} catch (Exception e) { | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/ScanRecord.java
import java.util.List;
import java.util.Map;
import android.os.ParcelUuid;
import android.support.annotation.Nullable;
import android.util.SparseArray;
import com.reelyactive.blesdk.support.ble.util.Logger;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
byte[] serviceDataUuidBytes = extractBytes(scanRecord, currentPos,
serviceUuidLength);
ParcelUuid serviceDataUuid = BluetoothUuid.parseUuidFrom(
serviceDataUuidBytes);
byte[] serviceDataArray = extractBytes(scanRecord,
currentPos + serviceUuidLength, dataLength - serviceUuidLength);
serviceData.put(serviceDataUuid, serviceDataArray);
break;
case DATA_TYPE_MANUFACTURER_SPECIFIC_DATA:
// The first two bytes of the manufacturer specific data are
// manufacturer ids in little endian.
int manufacturerId = ((scanRecord[currentPos + 1] & 0xFF) << 8)
+ (scanRecord[currentPos] & 0xFF);
byte[] manufacturerDataBytes = extractBytes(scanRecord, currentPos + 2,
dataLength - 2);
manufacturerData.put(manufacturerId, manufacturerDataBytes);
break;
default:
// Just ignore, we don't handle such data type.
break;
}
currentPos += dataLength;
}
if (serviceUuids.isEmpty()) {
serviceUuids = null;
}
return new ScanRecord(serviceUuids, manufacturerData, serviceData,
advertiseFlag, txPowerLevel, localName, scanRecord);
} catch (Exception e) { | Logger.logError("unable to parse scan record: " + Arrays.toString(scanRecord), e); |
reelyactive/ble-android-sdk | library/src/main/java/com/reelyactive/blesdk/support/ble/ScanWakefulBroadcastReceiver.java | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
| import android.content.Context;
import android.content.Intent;
import android.support.v4.content.WakefulBroadcastReceiver;
import com.reelyactive.blesdk.support.ble.util.Logger; | package com.reelyactive.blesdk.support.ble;/*
* Copyright 2014 Google Inc. All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
/**
* com.reelyactive.blesdk.support.ble.ScanWakefulBroadcastReceiver initiates the Bluetooth LE scan by calling
* {@link ScanWakefulService} after acquiring a WakeLock. On completion {@link ScanWakefulService}
* releases the WakeLock.
* <p/>
* This WakefulBroadcastReceiver is invoked by a pending intent through the alarm manager.
*/
public class ScanWakefulBroadcastReceiver extends WakefulBroadcastReceiver {
@Override
public void onReceive(Context context, Intent intent) { | // Path: library/src/main/java/com/reelyactive/blesdk/support/ble/util/Logger.java
// public class Logger {
//
// public static final String TAG = "BleScanCompatLib";
//
// public static void logVerbose(String message) {
// if (Log.isLoggable(TAG, Log.VERBOSE)) {
// Log.v(TAG, message);
// }
// }
//
// public static void logWarning(String message) {
// if (Log.isLoggable(TAG, Log.WARN)) {
// Log.w(TAG, message);
// }
// }
//
// public static void logDebug(String message) {
// if (Log.isLoggable(TAG, Log.DEBUG)) {
// Log.d(TAG, message);
// }
// }
//
// public static void logInfo(String message) {
// if (Log.isLoggable(TAG, Log.INFO)) {
// Log.i(TAG, message);
// }
// }
//
// public static void logError(String message, Exception... e) {
// if (Log.isLoggable(TAG, Log.ERROR)) {
// if (e == null || e.length == 0) {
// Log.e(TAG, message);
// } else {
// Log.e(TAG, message, e[0]);
// }
// }
// }
// }
// Path: library/src/main/java/com/reelyactive/blesdk/support/ble/ScanWakefulBroadcastReceiver.java
import android.content.Context;
import android.content.Intent;
import android.support.v4.content.WakefulBroadcastReceiver;
import com.reelyactive.blesdk.support.ble.util.Logger;
package com.reelyactive.blesdk.support.ble;/*
* Copyright 2014 Google Inc. All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
/**
* com.reelyactive.blesdk.support.ble.ScanWakefulBroadcastReceiver initiates the Bluetooth LE scan by calling
* {@link ScanWakefulService} after acquiring a WakeLock. On completion {@link ScanWakefulService}
* releases the WakeLock.
* <p/>
* This WakefulBroadcastReceiver is invoked by a pending intent through the alarm manager.
*/
public class ScanWakefulBroadcastReceiver extends WakefulBroadcastReceiver {
@Override
public void onReceive(Context context, Intent intent) { | Logger.logDebug("Alarm triggered"); |
mguetlein/CheS-Mapper | src/main/java/org/chesmapper/view/gui/GUIControler.java | // Path: src/main/java/org/chesmapper/view/cluster/Clustering.java
// public interface Clustering extends CompoundGroupWithProperties
// {
// void addListener(PropertyChangeListener propertyChangeListener);
//
// int getNumClusters();
//
// int numClusters();
//
// List<Cluster> getClusters();
//
// boolean isClusterActive();
//
// boolean isClusterWatched();
//
// Cluster getCluster(int i);
//
// int indexOf(Cluster cluster);
//
// Cluster getActiveCluster();
//
// Cluster getWatchedCluster();
//
// int getActiveClusterIdx();
//
// int getWatchedClusterIdx();
//
// boolean isCompoundActive();
//
// boolean isCompoundWatched();
//
// boolean isCompoundActive(Compound c);
//
// Compound[] getActiveCompounds();
//
// Compound getActiveCompound();
//
// int[] getActiveCompoundsJmolIdx();
//
// Compound getWatchedCompound();
//
// Compound[] getWatchedCompounds();
//
// int[] getWatchedCompoundsJmolIdx();
//
// Cluster getClusterForCompound(Compound c);
//
// List<CompoundProperty> selectPropertiesAndFeaturesWithDialog(String title, CompoundProperty preselected,
// boolean addSmiles, boolean addEmbeddingStress, boolean addActivityCliffs, boolean addDistanceTo);
//
// List<CompoundProperty> getPropertiesAndFeatures();
//
// List<CompoundProperty> getProperties();
//
// List<CompoundProperty> getFeatures();
//
// List<Compound> getCompounds(boolean includingMultiClusteredCompounds);
//
// Cluster getUniqueClusterForCompounds(Compound[] c);
//
// String getOrigLocalPath();
//
// String getOrigSDFile();
//
// String getSDFile();
//
// boolean isClusterAlgorithmDisjoint();
//
// String getClusterAlgorithm();
//
// int getClusterIndexForCompound(Compound m);
//
// List<CompoundData> getCompounds();
//
// void chooseClustersToExport(CompoundProperty compoundDescriptor);
//
// void chooseCompoundsToExport(CompoundProperty compoundDescriptor);
//
// Double[] getDoubleValues(NumericProperty p);
//
// String[] getStringValues(NominalProperty p, Compound m);
//
// String getSummaryStringValue(CompoundProperty p, boolean b);
//
// int numMissingValues(CompoundProperty p);
//
// String getName();
//
// Double getNormalizedLogDoubleValue(CompoundPropertyOwner m, NumericProperty p);
//
// Double getNormalizedDoubleValue(CompoundPropertyOwner m, NumericProperty p);
//
// double getSpecificity(Compound compound, CompoundProperty p);
//
// double getSpecificity(Cluster cluster, CompoundProperty p);
//
// double getSpecificity(CompoundSelection sel, CompoundProperty p);
//
// int getNumCompounds(boolean includingMultiClusteredCompounds);
//
// int getNumUnfilteredCompounds(boolean includingMultiClusteredCompounds);
//
// String getEmbedAlgorithm();
//
// String getEmbedQuality();
//
// List<CompoundProperty> getAdditionalProperties();
//
// CorrelationProperty getEmbeddingQualityProperty();
//
// EqualPositionProperty getEqualPosProperty();
//
// Compound getCompoundWithJmolIndex(int convertRowIndexToModel);
//
// int numDistinctValues(CompoundProperty p);
//
// public void addSelectionListener(SelectionListener l);
//
// public abstract static class SelectionListener
// {
// public void clusterActiveChanged(Cluster c)
// {
// }
//
// public void clusterWatchedChanged(Cluster c)
// {
// }
//
// public void compoundActiveChanged(Compound c[])
// {
// }
//
// public void compoundWatchedChanged(Compound c[])
// {
// }
// }
//
// boolean isBMBFRealEndpointDataset(boolean b);
//
// CompoundProperty addDistanceToCompoundFeature(Compound c);
//
// CompoundProperty addSALIFeatures(CompoundProperty c);
//
// void predict();
//
// void addPredictionFeature(CompoundProperty clazz, PredictionResult p);
//
// NumericProperty addLogFeature(NumericProperty p);
//
// public CompoundSelection getCompoundSelection(Compound[] c);
//
// boolean isRandomEmbedding();
//
// CompoundProperty getHighlightProperty();
//
// Color getHighlightColorText();
//
// Double getFeatureDistance(int origIndex, int origIndex2);
//
// boolean isSkippingRedundantFeatures();
//
// boolean isBigDataMode();
//
// void computeAppDomain();
//
// boolean doCheSMappingWarningsExist();
//
// void showCheSMappingWarnings();
//
// }
| import java.beans.PropertyChangeListener;
import javax.swing.JComponent;
import javax.swing.JPopupMenu;
import org.chesmapper.view.cluster.Clustering;
import org.mg.javalib.gui.Blockable;
import org.mg.javalib.gui.property.Property;
| package org.chesmapper.view.gui;
public interface GUIControler extends Blockable
{
| // Path: src/main/java/org/chesmapper/view/cluster/Clustering.java
// public interface Clustering extends CompoundGroupWithProperties
// {
// void addListener(PropertyChangeListener propertyChangeListener);
//
// int getNumClusters();
//
// int numClusters();
//
// List<Cluster> getClusters();
//
// boolean isClusterActive();
//
// boolean isClusterWatched();
//
// Cluster getCluster(int i);
//
// int indexOf(Cluster cluster);
//
// Cluster getActiveCluster();
//
// Cluster getWatchedCluster();
//
// int getActiveClusterIdx();
//
// int getWatchedClusterIdx();
//
// boolean isCompoundActive();
//
// boolean isCompoundWatched();
//
// boolean isCompoundActive(Compound c);
//
// Compound[] getActiveCompounds();
//
// Compound getActiveCompound();
//
// int[] getActiveCompoundsJmolIdx();
//
// Compound getWatchedCompound();
//
// Compound[] getWatchedCompounds();
//
// int[] getWatchedCompoundsJmolIdx();
//
// Cluster getClusterForCompound(Compound c);
//
// List<CompoundProperty> selectPropertiesAndFeaturesWithDialog(String title, CompoundProperty preselected,
// boolean addSmiles, boolean addEmbeddingStress, boolean addActivityCliffs, boolean addDistanceTo);
//
// List<CompoundProperty> getPropertiesAndFeatures();
//
// List<CompoundProperty> getProperties();
//
// List<CompoundProperty> getFeatures();
//
// List<Compound> getCompounds(boolean includingMultiClusteredCompounds);
//
// Cluster getUniqueClusterForCompounds(Compound[] c);
//
// String getOrigLocalPath();
//
// String getOrigSDFile();
//
// String getSDFile();
//
// boolean isClusterAlgorithmDisjoint();
//
// String getClusterAlgorithm();
//
// int getClusterIndexForCompound(Compound m);
//
// List<CompoundData> getCompounds();
//
// void chooseClustersToExport(CompoundProperty compoundDescriptor);
//
// void chooseCompoundsToExport(CompoundProperty compoundDescriptor);
//
// Double[] getDoubleValues(NumericProperty p);
//
// String[] getStringValues(NominalProperty p, Compound m);
//
// String getSummaryStringValue(CompoundProperty p, boolean b);
//
// int numMissingValues(CompoundProperty p);
//
// String getName();
//
// Double getNormalizedLogDoubleValue(CompoundPropertyOwner m, NumericProperty p);
//
// Double getNormalizedDoubleValue(CompoundPropertyOwner m, NumericProperty p);
//
// double getSpecificity(Compound compound, CompoundProperty p);
//
// double getSpecificity(Cluster cluster, CompoundProperty p);
//
// double getSpecificity(CompoundSelection sel, CompoundProperty p);
//
// int getNumCompounds(boolean includingMultiClusteredCompounds);
//
// int getNumUnfilteredCompounds(boolean includingMultiClusteredCompounds);
//
// String getEmbedAlgorithm();
//
// String getEmbedQuality();
//
// List<CompoundProperty> getAdditionalProperties();
//
// CorrelationProperty getEmbeddingQualityProperty();
//
// EqualPositionProperty getEqualPosProperty();
//
// Compound getCompoundWithJmolIndex(int convertRowIndexToModel);
//
// int numDistinctValues(CompoundProperty p);
//
// public void addSelectionListener(SelectionListener l);
//
// public abstract static class SelectionListener
// {
// public void clusterActiveChanged(Cluster c)
// {
// }
//
// public void clusterWatchedChanged(Cluster c)
// {
// }
//
// public void compoundActiveChanged(Compound c[])
// {
// }
//
// public void compoundWatchedChanged(Compound c[])
// {
// }
// }
//
// boolean isBMBFRealEndpointDataset(boolean b);
//
// CompoundProperty addDistanceToCompoundFeature(Compound c);
//
// CompoundProperty addSALIFeatures(CompoundProperty c);
//
// void predict();
//
// void addPredictionFeature(CompoundProperty clazz, PredictionResult p);
//
// NumericProperty addLogFeature(NumericProperty p);
//
// public CompoundSelection getCompoundSelection(Compound[] c);
//
// boolean isRandomEmbedding();
//
// CompoundProperty getHighlightProperty();
//
// Color getHighlightColorText();
//
// Double getFeatureDistance(int origIndex, int origIndex2);
//
// boolean isSkippingRedundantFeatures();
//
// boolean isBigDataMode();
//
// void computeAppDomain();
//
// boolean doCheSMappingWarningsExist();
//
// void showCheSMappingWarnings();
//
// }
// Path: src/main/java/org/chesmapper/view/gui/GUIControler.java
import java.beans.PropertyChangeListener;
import javax.swing.JComponent;
import javax.swing.JPopupMenu;
import org.chesmapper.view.cluster.Clustering;
import org.mg.javalib.gui.Blockable;
import org.mg.javalib.gui.property.Property;
package org.chesmapper.view.gui;
public interface GUIControler extends Blockable
{
| public void updateTitle(Clustering c);
|
mguetlein/CheS-Mapper | src/main/java/org/chesmapper/view/gui/ColorEditor.java | // Path: src/main/java/org/chesmapper/view/cluster/Clustering.java
// public interface Clustering extends CompoundGroupWithProperties
// {
// void addListener(PropertyChangeListener propertyChangeListener);
//
// int getNumClusters();
//
// int numClusters();
//
// List<Cluster> getClusters();
//
// boolean isClusterActive();
//
// boolean isClusterWatched();
//
// Cluster getCluster(int i);
//
// int indexOf(Cluster cluster);
//
// Cluster getActiveCluster();
//
// Cluster getWatchedCluster();
//
// int getActiveClusterIdx();
//
// int getWatchedClusterIdx();
//
// boolean isCompoundActive();
//
// boolean isCompoundWatched();
//
// boolean isCompoundActive(Compound c);
//
// Compound[] getActiveCompounds();
//
// Compound getActiveCompound();
//
// int[] getActiveCompoundsJmolIdx();
//
// Compound getWatchedCompound();
//
// Compound[] getWatchedCompounds();
//
// int[] getWatchedCompoundsJmolIdx();
//
// Cluster getClusterForCompound(Compound c);
//
// List<CompoundProperty> selectPropertiesAndFeaturesWithDialog(String title, CompoundProperty preselected,
// boolean addSmiles, boolean addEmbeddingStress, boolean addActivityCliffs, boolean addDistanceTo);
//
// List<CompoundProperty> getPropertiesAndFeatures();
//
// List<CompoundProperty> getProperties();
//
// List<CompoundProperty> getFeatures();
//
// List<Compound> getCompounds(boolean includingMultiClusteredCompounds);
//
// Cluster getUniqueClusterForCompounds(Compound[] c);
//
// String getOrigLocalPath();
//
// String getOrigSDFile();
//
// String getSDFile();
//
// boolean isClusterAlgorithmDisjoint();
//
// String getClusterAlgorithm();
//
// int getClusterIndexForCompound(Compound m);
//
// List<CompoundData> getCompounds();
//
// void chooseClustersToExport(CompoundProperty compoundDescriptor);
//
// void chooseCompoundsToExport(CompoundProperty compoundDescriptor);
//
// Double[] getDoubleValues(NumericProperty p);
//
// String[] getStringValues(NominalProperty p, Compound m);
//
// String getSummaryStringValue(CompoundProperty p, boolean b);
//
// int numMissingValues(CompoundProperty p);
//
// String getName();
//
// Double getNormalizedLogDoubleValue(CompoundPropertyOwner m, NumericProperty p);
//
// Double getNormalizedDoubleValue(CompoundPropertyOwner m, NumericProperty p);
//
// double getSpecificity(Compound compound, CompoundProperty p);
//
// double getSpecificity(Cluster cluster, CompoundProperty p);
//
// double getSpecificity(CompoundSelection sel, CompoundProperty p);
//
// int getNumCompounds(boolean includingMultiClusteredCompounds);
//
// int getNumUnfilteredCompounds(boolean includingMultiClusteredCompounds);
//
// String getEmbedAlgorithm();
//
// String getEmbedQuality();
//
// List<CompoundProperty> getAdditionalProperties();
//
// CorrelationProperty getEmbeddingQualityProperty();
//
// EqualPositionProperty getEqualPosProperty();
//
// Compound getCompoundWithJmolIndex(int convertRowIndexToModel);
//
// int numDistinctValues(CompoundProperty p);
//
// public void addSelectionListener(SelectionListener l);
//
// public abstract static class SelectionListener
// {
// public void clusterActiveChanged(Cluster c)
// {
// }
//
// public void clusterWatchedChanged(Cluster c)
// {
// }
//
// public void compoundActiveChanged(Compound c[])
// {
// }
//
// public void compoundWatchedChanged(Compound c[])
// {
// }
// }
//
// boolean isBMBFRealEndpointDataset(boolean b);
//
// CompoundProperty addDistanceToCompoundFeature(Compound c);
//
// CompoundProperty addSALIFeatures(CompoundProperty c);
//
// void predict();
//
// void addPredictionFeature(CompoundProperty clazz, PredictionResult p);
//
// NumericProperty addLogFeature(NumericProperty p);
//
// public CompoundSelection getCompoundSelection(Compound[] c);
//
// boolean isRandomEmbedding();
//
// CompoundProperty getHighlightProperty();
//
// Color getHighlightColorText();
//
// Double getFeatureDistance(int origIndex, int origIndex2);
//
// boolean isSkippingRedundantFeatures();
//
// boolean isBigDataMode();
//
// void computeAppDomain();
//
// boolean doCheSMappingWarningsExist();
//
// void showCheSMappingWarnings();
//
// }
| import java.awt.BorderLayout;
import java.awt.Window;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.JButton;
import javax.swing.JDialog;
import javax.swing.JPanel;
import javax.swing.JTabbedPane;
import javax.swing.border.EmptyBorder;
import org.chesmapper.map.main.Settings;
import org.chesmapper.view.cluster.Clustering;
import com.jgoodies.forms.factories.ButtonBarFactory; | package org.chesmapper.view.gui;
public class ColorEditor extends JDialog
{
ViewControler viewControler;
boolean okPressed = false;
ColorEditorPanel panels[];
| // Path: src/main/java/org/chesmapper/view/cluster/Clustering.java
// public interface Clustering extends CompoundGroupWithProperties
// {
// void addListener(PropertyChangeListener propertyChangeListener);
//
// int getNumClusters();
//
// int numClusters();
//
// List<Cluster> getClusters();
//
// boolean isClusterActive();
//
// boolean isClusterWatched();
//
// Cluster getCluster(int i);
//
// int indexOf(Cluster cluster);
//
// Cluster getActiveCluster();
//
// Cluster getWatchedCluster();
//
// int getActiveClusterIdx();
//
// int getWatchedClusterIdx();
//
// boolean isCompoundActive();
//
// boolean isCompoundWatched();
//
// boolean isCompoundActive(Compound c);
//
// Compound[] getActiveCompounds();
//
// Compound getActiveCompound();
//
// int[] getActiveCompoundsJmolIdx();
//
// Compound getWatchedCompound();
//
// Compound[] getWatchedCompounds();
//
// int[] getWatchedCompoundsJmolIdx();
//
// Cluster getClusterForCompound(Compound c);
//
// List<CompoundProperty> selectPropertiesAndFeaturesWithDialog(String title, CompoundProperty preselected,
// boolean addSmiles, boolean addEmbeddingStress, boolean addActivityCliffs, boolean addDistanceTo);
//
// List<CompoundProperty> getPropertiesAndFeatures();
//
// List<CompoundProperty> getProperties();
//
// List<CompoundProperty> getFeatures();
//
// List<Compound> getCompounds(boolean includingMultiClusteredCompounds);
//
// Cluster getUniqueClusterForCompounds(Compound[] c);
//
// String getOrigLocalPath();
//
// String getOrigSDFile();
//
// String getSDFile();
//
// boolean isClusterAlgorithmDisjoint();
//
// String getClusterAlgorithm();
//
// int getClusterIndexForCompound(Compound m);
//
// List<CompoundData> getCompounds();
//
// void chooseClustersToExport(CompoundProperty compoundDescriptor);
//
// void chooseCompoundsToExport(CompoundProperty compoundDescriptor);
//
// Double[] getDoubleValues(NumericProperty p);
//
// String[] getStringValues(NominalProperty p, Compound m);
//
// String getSummaryStringValue(CompoundProperty p, boolean b);
//
// int numMissingValues(CompoundProperty p);
//
// String getName();
//
// Double getNormalizedLogDoubleValue(CompoundPropertyOwner m, NumericProperty p);
//
// Double getNormalizedDoubleValue(CompoundPropertyOwner m, NumericProperty p);
//
// double getSpecificity(Compound compound, CompoundProperty p);
//
// double getSpecificity(Cluster cluster, CompoundProperty p);
//
// double getSpecificity(CompoundSelection sel, CompoundProperty p);
//
// int getNumCompounds(boolean includingMultiClusteredCompounds);
//
// int getNumUnfilteredCompounds(boolean includingMultiClusteredCompounds);
//
// String getEmbedAlgorithm();
//
// String getEmbedQuality();
//
// List<CompoundProperty> getAdditionalProperties();
//
// CorrelationProperty getEmbeddingQualityProperty();
//
// EqualPositionProperty getEqualPosProperty();
//
// Compound getCompoundWithJmolIndex(int convertRowIndexToModel);
//
// int numDistinctValues(CompoundProperty p);
//
// public void addSelectionListener(SelectionListener l);
//
// public abstract static class SelectionListener
// {
// public void clusterActiveChanged(Cluster c)
// {
// }
//
// public void clusterWatchedChanged(Cluster c)
// {
// }
//
// public void compoundActiveChanged(Compound c[])
// {
// }
//
// public void compoundWatchedChanged(Compound c[])
// {
// }
// }
//
// boolean isBMBFRealEndpointDataset(boolean b);
//
// CompoundProperty addDistanceToCompoundFeature(Compound c);
//
// CompoundProperty addSALIFeatures(CompoundProperty c);
//
// void predict();
//
// void addPredictionFeature(CompoundProperty clazz, PredictionResult p);
//
// NumericProperty addLogFeature(NumericProperty p);
//
// public CompoundSelection getCompoundSelection(Compound[] c);
//
// boolean isRandomEmbedding();
//
// CompoundProperty getHighlightProperty();
//
// Color getHighlightColorText();
//
// Double getFeatureDistance(int origIndex, int origIndex2);
//
// boolean isSkippingRedundantFeatures();
//
// boolean isBigDataMode();
//
// void computeAppDomain();
//
// boolean doCheSMappingWarningsExist();
//
// void showCheSMappingWarnings();
//
// }
// Path: src/main/java/org/chesmapper/view/gui/ColorEditor.java
import java.awt.BorderLayout;
import java.awt.Window;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.JButton;
import javax.swing.JDialog;
import javax.swing.JPanel;
import javax.swing.JTabbedPane;
import javax.swing.border.EmptyBorder;
import org.chesmapper.map.main.Settings;
import org.chesmapper.view.cluster.Clustering;
import com.jgoodies.forms.factories.ButtonBarFactory;
package org.chesmapper.view.gui;
public class ColorEditor extends JDialog
{
ViewControler viewControler;
boolean okPressed = false;
ColorEditorPanel panels[];
| public ColorEditor(Window owner, String title, ViewControler viewControler, Clustering clustering) |
mguetlein/CheS-Mapper | src/test/java/org/chesmapper/test/util/SwingTestUtil.java | // Path: src/main/java/org/chesmapper/view/gui/swing/ComponentFactory.java
// public static class ClickableLabel extends JLabel
// {
// public ClickableLabel(String text, ImageIcon icon, int horizontalAlignment)
// {
// super(text, icon, horizontalAlignment);
// }
//
// Boolean myEnabled = null;
//
// public void setEnabled(boolean enabled)
// {
// myEnabled = enabled;
// updateUI();
// }
//
// public void addActionListener(final ActionListener l)
// {
// addMouseListener(new MouseAdapter()
// {
// @Override
// public void mousePressed(MouseEvent e)
// {
// if (myEnabled == null || myEnabled)
// l.actionPerformed(new ActionEvent(ClickableLabel.this, 0, "button clicked"));
// }
// });
// }
// }
| import java.awt.Component;
import java.awt.Container;
import java.awt.Frame;
import java.awt.Point;
import java.awt.Robot;
import java.awt.Window;
import java.awt.event.InputEvent;
import java.awt.event.KeyEvent;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import javax.swing.AbstractButton;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JDialog;
import javax.swing.JFileChooser;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
import javax.swing.JPopupMenu;
import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
import javax.swing.JSpinner;
import javax.swing.JTextField;
import javax.swing.SwingConstants;
import javax.swing.text.JTextComponent;
import org.chesmapper.view.gui.swing.ComponentFactory.ClickableLabel;
import org.junit.Assert;
import org.mg.javalib.gui.BlockableFrame;
import org.mg.javalib.gui.Selector;
import org.mg.javalib.util.ScreenUtil;
import org.mg.javalib.util.SwingUtil;
import org.mg.javalib.util.ThreadUtil; | public static JPopupMenu getOnlyPopupMenu(Container owner)
{
return (JPopupMenu) getOnlyComponent(owner, JPopupMenu.class);
}
public static Selector<?, ?> getOnlySelector(Container owner)
{
return (Selector<?, ?>) getOnlyComponent(owner, Selector.class);
}
public static JSpinner getOnlySpinner(Container owner)
{
return (JSpinner) getOnlyComponent(owner, JSpinner.class);
}
public static JCheckBox getOnlyCheckBox(Container owner)
{
return (JCheckBox) getOnlyComponent(owner, JCheckBox.class);
}
public static JComboBox<?> getOnlyComboBox(Container owner)
{
return getOnlyComboBox(owner, false);
}
public static JComboBox<?> getOnlyComboBox(Container owner, boolean onlyVisible)
{
return (JComboBox<?>) getOnlyComponent(owner, JComboBox.class, onlyVisible);
}
| // Path: src/main/java/org/chesmapper/view/gui/swing/ComponentFactory.java
// public static class ClickableLabel extends JLabel
// {
// public ClickableLabel(String text, ImageIcon icon, int horizontalAlignment)
// {
// super(text, icon, horizontalAlignment);
// }
//
// Boolean myEnabled = null;
//
// public void setEnabled(boolean enabled)
// {
// myEnabled = enabled;
// updateUI();
// }
//
// public void addActionListener(final ActionListener l)
// {
// addMouseListener(new MouseAdapter()
// {
// @Override
// public void mousePressed(MouseEvent e)
// {
// if (myEnabled == null || myEnabled)
// l.actionPerformed(new ActionEvent(ClickableLabel.this, 0, "button clicked"));
// }
// });
// }
// }
// Path: src/test/java/org/chesmapper/test/util/SwingTestUtil.java
import java.awt.Component;
import java.awt.Container;
import java.awt.Frame;
import java.awt.Point;
import java.awt.Robot;
import java.awt.Window;
import java.awt.event.InputEvent;
import java.awt.event.KeyEvent;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import javax.swing.AbstractButton;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JDialog;
import javax.swing.JFileChooser;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
import javax.swing.JPopupMenu;
import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
import javax.swing.JSpinner;
import javax.swing.JTextField;
import javax.swing.SwingConstants;
import javax.swing.text.JTextComponent;
import org.chesmapper.view.gui.swing.ComponentFactory.ClickableLabel;
import org.junit.Assert;
import org.mg.javalib.gui.BlockableFrame;
import org.mg.javalib.gui.Selector;
import org.mg.javalib.util.ScreenUtil;
import org.mg.javalib.util.SwingUtil;
import org.mg.javalib.util.ThreadUtil;
public static JPopupMenu getOnlyPopupMenu(Container owner)
{
return (JPopupMenu) getOnlyComponent(owner, JPopupMenu.class);
}
public static Selector<?, ?> getOnlySelector(Container owner)
{
return (Selector<?, ?>) getOnlyComponent(owner, Selector.class);
}
public static JSpinner getOnlySpinner(Container owner)
{
return (JSpinner) getOnlyComponent(owner, JSpinner.class);
}
public static JCheckBox getOnlyCheckBox(Container owner)
{
return (JCheckBox) getOnlyComponent(owner, JCheckBox.class);
}
public static JComboBox<?> getOnlyComboBox(Container owner)
{
return getOnlyComboBox(owner, false);
}
public static JComboBox<?> getOnlyComboBox(Container owner, boolean onlyVisible)
{
return (JComboBox<?>) getOnlyComponent(owner, JComboBox.class, onlyVisible);
}
| public static ClickableLabel getVisibleClickableLabel(Container owner, final int swingConstantOrientation) |
mguetlein/CheS-Mapper | src/main/java/org/chesmapper/view/gui/swing/ComponentFactory.java | // Path: src/main/java/org/chesmapper/view/gui/ViewControler.java
// public enum Style
// {
// wireframe, ballsAndSticks, dots
// }
| import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.Insets;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.image.BufferedImage;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.lang.reflect.Array;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import javax.swing.Icon;
import javax.swing.ImageIcon;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.JScrollBar;
import javax.swing.JScrollPane;
import javax.swing.JSlider;
import javax.swing.JTable;
import javax.swing.JTextArea;
import javax.swing.JTextField;
import javax.swing.ScrollPaneConstants;
import javax.swing.SwingConstants;
import javax.swing.SwingUtilities;
import javax.swing.border.CompoundBorder;
import javax.swing.border.EmptyBorder;
import javax.swing.border.EtchedBorder;
import javax.swing.border.LineBorder;
import javax.swing.plaf.basic.BasicArrowButton;
import javax.swing.plaf.basic.BasicComboBoxUI;
import javax.swing.plaf.basic.BasicComboPopup;
import javax.swing.plaf.basic.BasicScrollBarUI;
import javax.swing.plaf.basic.BasicSliderUI;
import javax.swing.plaf.basic.ComboPopup;
import javax.swing.table.DefaultTableCellRenderer;
import javax.swing.table.DefaultTableColumnModel;
import javax.swing.table.DefaultTableModel;
import javax.swing.table.TableCellRenderer;
import javax.swing.table.TableColumn;
import org.chesmapper.map.main.ScreenSetup;
import org.chesmapper.map.main.Settings;
import org.chesmapper.view.gui.LaunchCheSMapper;
import org.chesmapper.view.gui.ViewControler.Style;
import org.mg.javalib.gui.BorderImageIcon;
import org.mg.javalib.gui.DescriptionListCellRenderer;
import org.mg.javalib.gui.LinkButton;
import org.mg.javalib.gui.SimpleImageIcon;
import org.mg.javalib.gui.StringImageIcon;
import org.mg.javalib.util.ColorUtil;
import org.mg.javalib.util.SwingUtil;
| public static JCheckBox createViewCheckBox(String text)
{
JCheckBox c = new JCheckBox(text)
{
public void updateUI()
{
super.updateUI();
setForeground(FOREGROUND);
setFont(getFont().deriveFont((float) ScreenSetup.INSTANCE.getFontSize()));
}
};
c.setFocusable(false);
return c;
}
// public static JRadioButton createViewRadioButton(String text)
// {
// JRadioButton r = new JRadioButton(text)
// {
// public void updateUI()
// {
// super.updateUI();
// setForeground(FOREGROUND);
// }
// };
// return r;
// }
public static class StyleButton extends JRadioButton
{
| // Path: src/main/java/org/chesmapper/view/gui/ViewControler.java
// public enum Style
// {
// wireframe, ballsAndSticks, dots
// }
// Path: src/main/java/org/chesmapper/view/gui/swing/ComponentFactory.java
import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.Insets;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.image.BufferedImage;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.lang.reflect.Array;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import javax.swing.Icon;
import javax.swing.ImageIcon;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.JScrollBar;
import javax.swing.JScrollPane;
import javax.swing.JSlider;
import javax.swing.JTable;
import javax.swing.JTextArea;
import javax.swing.JTextField;
import javax.swing.ScrollPaneConstants;
import javax.swing.SwingConstants;
import javax.swing.SwingUtilities;
import javax.swing.border.CompoundBorder;
import javax.swing.border.EmptyBorder;
import javax.swing.border.EtchedBorder;
import javax.swing.border.LineBorder;
import javax.swing.plaf.basic.BasicArrowButton;
import javax.swing.plaf.basic.BasicComboBoxUI;
import javax.swing.plaf.basic.BasicComboPopup;
import javax.swing.plaf.basic.BasicScrollBarUI;
import javax.swing.plaf.basic.BasicSliderUI;
import javax.swing.plaf.basic.ComboPopup;
import javax.swing.table.DefaultTableCellRenderer;
import javax.swing.table.DefaultTableColumnModel;
import javax.swing.table.DefaultTableModel;
import javax.swing.table.TableCellRenderer;
import javax.swing.table.TableColumn;
import org.chesmapper.map.main.ScreenSetup;
import org.chesmapper.map.main.Settings;
import org.chesmapper.view.gui.LaunchCheSMapper;
import org.chesmapper.view.gui.ViewControler.Style;
import org.mg.javalib.gui.BorderImageIcon;
import org.mg.javalib.gui.DescriptionListCellRenderer;
import org.mg.javalib.gui.LinkButton;
import org.mg.javalib.gui.SimpleImageIcon;
import org.mg.javalib.gui.StringImageIcon;
import org.mg.javalib.util.ColorUtil;
import org.mg.javalib.util.SwingUtil;
public static JCheckBox createViewCheckBox(String text)
{
JCheckBox c = new JCheckBox(text)
{
public void updateUI()
{
super.updateUI();
setForeground(FOREGROUND);
setFont(getFont().deriveFont((float) ScreenSetup.INSTANCE.getFontSize()));
}
};
c.setFocusable(false);
return c;
}
// public static JRadioButton createViewRadioButton(String text)
// {
// JRadioButton r = new JRadioButton(text)
// {
// public void updateUI()
// {
// super.updateUI();
// setForeground(FOREGROUND);
// }
// };
// return r;
// }
public static class StyleButton extends JRadioButton
{
| public Style style;
|
OfficeDev/O365-Android-Snippets | app/src/main/java/com/microsoft/office365/snippetapp/helpers/BaseUserStory.java | // Path: app/src/main/java/com/microsoft/office365/snippetapp/AndroidSnippetsApplication.java
// public class AndroidSnippetsApplication extends Application {
//
// private static AndroidSnippetsApplication mAndroidSnippetsApplication;
//
// @Override
// public void onCreate() {
// super.onCreate();
// mAndroidSnippetsApplication = this;
// }
//
// public static AndroidSnippetsApplication getApplication() {
// return mAndroidSnippetsApplication;
// }
// }
//
// Path: app/src/main/java/com/microsoft/office365/snippetapp/Interfaces/OnUseCaseStatusChangedListener.java
// public interface OnUseCaseStatusChangedListener {
//
// void onUseCaseStatusChanged();
// }
| import android.content.res.AssetFileDescriptor;
import android.util.Log;
import android.view.View;
import com.microsoft.fileservices.odata.SharePointClient;
import com.microsoft.office365.snippetapp.AndroidSnippetsApplication;
import com.microsoft.office365.snippetapp.Interfaces.OnUseCaseStatusChangedListener;
import com.microsoft.outlookservices.odata.OutlookClient;
import java.io.ByteArrayOutputStream;
import java.io.FileInputStream;
import java.io.IOException; | /*
* Copyright (c) Microsoft. All rights reserved. Licensed under the MIT license. See full license at the bottom of this file.
*/
package com.microsoft.office365.snippetapp.helpers;
public abstract class BaseUserStory {
private boolean mIsExecuting = false;
private View mUpdateView;
private OutlookClient mO365MailClient;
private SharePointClient mO365MyFilesClient;
private String mMailResourceId; | // Path: app/src/main/java/com/microsoft/office365/snippetapp/AndroidSnippetsApplication.java
// public class AndroidSnippetsApplication extends Application {
//
// private static AndroidSnippetsApplication mAndroidSnippetsApplication;
//
// @Override
// public void onCreate() {
// super.onCreate();
// mAndroidSnippetsApplication = this;
// }
//
// public static AndroidSnippetsApplication getApplication() {
// return mAndroidSnippetsApplication;
// }
// }
//
// Path: app/src/main/java/com/microsoft/office365/snippetapp/Interfaces/OnUseCaseStatusChangedListener.java
// public interface OnUseCaseStatusChangedListener {
//
// void onUseCaseStatusChanged();
// }
// Path: app/src/main/java/com/microsoft/office365/snippetapp/helpers/BaseUserStory.java
import android.content.res.AssetFileDescriptor;
import android.util.Log;
import android.view.View;
import com.microsoft.fileservices.odata.SharePointClient;
import com.microsoft.office365.snippetapp.AndroidSnippetsApplication;
import com.microsoft.office365.snippetapp.Interfaces.OnUseCaseStatusChangedListener;
import com.microsoft.outlookservices.odata.OutlookClient;
import java.io.ByteArrayOutputStream;
import java.io.FileInputStream;
import java.io.IOException;
/*
* Copyright (c) Microsoft. All rights reserved. Licensed under the MIT license. See full license at the bottom of this file.
*/
package com.microsoft.office365.snippetapp.helpers;
public abstract class BaseUserStory {
private boolean mIsExecuting = false;
private View mUpdateView;
private OutlookClient mO365MailClient;
private SharePointClient mO365MyFilesClient;
private String mMailResourceId; | private OnUseCaseStatusChangedListener mUseCaseStatusChangedListener; |
OfficeDev/O365-Android-Snippets | app/src/main/java/com/microsoft/office365/snippetapp/helpers/BaseUserStory.java | // Path: app/src/main/java/com/microsoft/office365/snippetapp/AndroidSnippetsApplication.java
// public class AndroidSnippetsApplication extends Application {
//
// private static AndroidSnippetsApplication mAndroidSnippetsApplication;
//
// @Override
// public void onCreate() {
// super.onCreate();
// mAndroidSnippetsApplication = this;
// }
//
// public static AndroidSnippetsApplication getApplication() {
// return mAndroidSnippetsApplication;
// }
// }
//
// Path: app/src/main/java/com/microsoft/office365/snippetapp/Interfaces/OnUseCaseStatusChangedListener.java
// public interface OnUseCaseStatusChangedListener {
//
// void onUseCaseStatusChanged();
// }
| import android.content.res.AssetFileDescriptor;
import android.util.Log;
import android.view.View;
import com.microsoft.fileservices.odata.SharePointClient;
import com.microsoft.office365.snippetapp.AndroidSnippetsApplication;
import com.microsoft.office365.snippetapp.Interfaces.OnUseCaseStatusChangedListener;
import com.microsoft.outlookservices.odata.OutlookClient;
import java.io.ByteArrayOutputStream;
import java.io.FileInputStream;
import java.io.IOException; | public String getFilesFoldersResourceId() {
return mFilesFoldersResourceId;
}
public void setFilesFoldersResourceId(String filesFoldersResourceId) {
this.mFilesFoldersResourceId = filesFoldersResourceId;
}
public void setUseCaseStatusChangedListener(OnUseCaseStatusChangedListener listener) {
mUseCaseStatusChangedListener = listener;
}
protected abstract String execute();
public abstract String getDescription();
public boolean getGroupingFlag() {
return mGroupingFlag;
}
public void setGroupingFlag(boolean groupingFlag) {
mGroupingFlag = groupingFlag;
}
protected String getId() {
return java.util.UUID.randomUUID().toString();
}
protected String getStringResource(int resourceToGet) { | // Path: app/src/main/java/com/microsoft/office365/snippetapp/AndroidSnippetsApplication.java
// public class AndroidSnippetsApplication extends Application {
//
// private static AndroidSnippetsApplication mAndroidSnippetsApplication;
//
// @Override
// public void onCreate() {
// super.onCreate();
// mAndroidSnippetsApplication = this;
// }
//
// public static AndroidSnippetsApplication getApplication() {
// return mAndroidSnippetsApplication;
// }
// }
//
// Path: app/src/main/java/com/microsoft/office365/snippetapp/Interfaces/OnUseCaseStatusChangedListener.java
// public interface OnUseCaseStatusChangedListener {
//
// void onUseCaseStatusChanged();
// }
// Path: app/src/main/java/com/microsoft/office365/snippetapp/helpers/BaseUserStory.java
import android.content.res.AssetFileDescriptor;
import android.util.Log;
import android.view.View;
import com.microsoft.fileservices.odata.SharePointClient;
import com.microsoft.office365.snippetapp.AndroidSnippetsApplication;
import com.microsoft.office365.snippetapp.Interfaces.OnUseCaseStatusChangedListener;
import com.microsoft.outlookservices.odata.OutlookClient;
import java.io.ByteArrayOutputStream;
import java.io.FileInputStream;
import java.io.IOException;
public String getFilesFoldersResourceId() {
return mFilesFoldersResourceId;
}
public void setFilesFoldersResourceId(String filesFoldersResourceId) {
this.mFilesFoldersResourceId = filesFoldersResourceId;
}
public void setUseCaseStatusChangedListener(OnUseCaseStatusChangedListener listener) {
mUseCaseStatusChangedListener = listener;
}
protected abstract String execute();
public abstract String getDescription();
public boolean getGroupingFlag() {
return mGroupingFlag;
}
public void setGroupingFlag(boolean groupingFlag) {
mGroupingFlag = groupingFlag;
}
protected String getId() {
return java.util.UUID.randomUUID().toString();
}
protected String getStringResource(int resourceToGet) { | return AndroidSnippetsApplication |
OfficeDev/O365-Android-Snippets | app/src/main/java/com/microsoft/office365/snippetapp/OperationListAdapter.java | // Path: app/src/main/java/com/microsoft/office365/snippetapp/helpers/BaseUserStory.java
// public abstract class BaseUserStory {
//
// private boolean mIsExecuting = false;
// private View mUpdateView;
// private OutlookClient mO365MailClient;
// private SharePointClient mO365MyFilesClient;
// private String mMailResourceId;
// private OnUseCaseStatusChangedListener mUseCaseStatusChangedListener;
// private String mFilesFoldersResourceId;
// boolean mGroupingFlag = false;
//
// public String getFilesFoldersResourceId() {
// return mFilesFoldersResourceId;
// }
//
// public void setFilesFoldersResourceId(String filesFoldersResourceId) {
// this.mFilesFoldersResourceId = filesFoldersResourceId;
// }
//
// public void setUseCaseStatusChangedListener(OnUseCaseStatusChangedListener listener) {
// mUseCaseStatusChangedListener = listener;
// }
//
// protected abstract String execute();
//
// public abstract String getDescription();
//
//
// public boolean getGroupingFlag() {
// return mGroupingFlag;
// }
//
// public void setGroupingFlag(boolean groupingFlag) {
// mGroupingFlag = groupingFlag;
// }
//
// protected String getId() {
// return java.util.UUID.randomUUID().toString();
// }
//
// protected String getStringResource(int resourceToGet) {
// return AndroidSnippetsApplication
// .getApplication()
// .getApplicationContext()
// .getString(resourceToGet);
// }
//
// protected String FormatException(Exception exception, String storyDescription) {
// exception.printStackTrace();
// String formattedException = APIErrorMessageHelper.getErrorMessage(exception.getMessage());
// Log.e(storyDescription, formattedException);
// return StoryResultFormatter.wrapResult(
// storyDescription + ": "
// + formattedException
// , false
// );
//
// }
//
// public byte[] getDrawableResource(int resourceToGet) {
//
// //Get the photo from the resource/drawable folder as a raw image
// final AssetFileDescriptor raw = AndroidSnippetsApplication
// .getApplication()
// .getApplicationContext()
// .getResources()
// .openRawResourceFd(resourceToGet);
//
// //Load raw image into a buffer
// final ByteArrayOutputStream buffer = new ByteArrayOutputStream();
// try {
// final FileInputStream is = raw.createInputStream();
// int nRead;
//
// //Read 16kb at a time
// final byte[] data = new byte[16384];
//
// while ((nRead = is.read(data, 0, data.length)) != -1) {
// buffer.write(data, 0, nRead);
// }
//
// buffer.flush();
//
// } catch (IOException e) {
// e.printStackTrace();
// }
// return buffer.toByteArray();
//
// }
//
// public View getUIResultView() {
// return mUpdateView;
// }
//
// public void setUIResultView(View view) {
// mUpdateView = view;
// }
//
// public String getO365MailResourceId() {
// return mMailResourceId;
// }
//
// public void setO365MailResourceId(String resourceId) {
// mMailResourceId = resourceId;
// }
//
// public OutlookClient getO365MailClient() {
// AuthenticationController
// .getInstance()
// .setResourceId(
// this.getO365MailResourceId());
//
// return mO365MailClient;
// }
//
// public void setO365MailClient(OutlookClient client) {
//
// mO365MailClient = client;
// }
//
// public SharePointClient getO365MyFilesClient() {
// return mO365MyFilesClient;
// }
//
// public void setO365MyFilesClient(SharePointClient client) {
// mO365MyFilesClient = client;
// }
//
// private void notifyStatusChange() {
// if (null != mUseCaseStatusChangedListener) {
// mUseCaseStatusChangedListener.onUseCaseStatusChanged();
// }
// }
//
// public final void onPreExecute() {
// mIsExecuting = true;
// notifyStatusChange();
// }
//
// public final void onPostExecute() {
// mIsExecuting = false;
// notifyStatusChange();
// }
//
// public final boolean isExecuting() {
// return mIsExecuting;
// }
//
// @Override
// public String toString() {
// return this.getDescription();
// }
//
//
// }
| import android.app.Activity;
import android.view.LayoutInflater;
import android.view.View;
import android.view.ViewGroup;
import android.widget.BaseAdapter;
import android.widget.TextView;
import com.microsoft.office365.snippetapp.helpers.BaseUserStory;
import java.util.List; | /*
* Copyright (c) Microsoft. All rights reserved. Licensed under the MIT license. See full license at the bottom of this file.
*/
package com.microsoft.office365.snippetapp;
class OperationListAdapter extends BaseAdapter {
protected LayoutInflater mLayoutInflater; | // Path: app/src/main/java/com/microsoft/office365/snippetapp/helpers/BaseUserStory.java
// public abstract class BaseUserStory {
//
// private boolean mIsExecuting = false;
// private View mUpdateView;
// private OutlookClient mO365MailClient;
// private SharePointClient mO365MyFilesClient;
// private String mMailResourceId;
// private OnUseCaseStatusChangedListener mUseCaseStatusChangedListener;
// private String mFilesFoldersResourceId;
// boolean mGroupingFlag = false;
//
// public String getFilesFoldersResourceId() {
// return mFilesFoldersResourceId;
// }
//
// public void setFilesFoldersResourceId(String filesFoldersResourceId) {
// this.mFilesFoldersResourceId = filesFoldersResourceId;
// }
//
// public void setUseCaseStatusChangedListener(OnUseCaseStatusChangedListener listener) {
// mUseCaseStatusChangedListener = listener;
// }
//
// protected abstract String execute();
//
// public abstract String getDescription();
//
//
// public boolean getGroupingFlag() {
// return mGroupingFlag;
// }
//
// public void setGroupingFlag(boolean groupingFlag) {
// mGroupingFlag = groupingFlag;
// }
//
// protected String getId() {
// return java.util.UUID.randomUUID().toString();
// }
//
// protected String getStringResource(int resourceToGet) {
// return AndroidSnippetsApplication
// .getApplication()
// .getApplicationContext()
// .getString(resourceToGet);
// }
//
// protected String FormatException(Exception exception, String storyDescription) {
// exception.printStackTrace();
// String formattedException = APIErrorMessageHelper.getErrorMessage(exception.getMessage());
// Log.e(storyDescription, formattedException);
// return StoryResultFormatter.wrapResult(
// storyDescription + ": "
// + formattedException
// , false
// );
//
// }
//
// public byte[] getDrawableResource(int resourceToGet) {
//
// //Get the photo from the resource/drawable folder as a raw image
// final AssetFileDescriptor raw = AndroidSnippetsApplication
// .getApplication()
// .getApplicationContext()
// .getResources()
// .openRawResourceFd(resourceToGet);
//
// //Load raw image into a buffer
// final ByteArrayOutputStream buffer = new ByteArrayOutputStream();
// try {
// final FileInputStream is = raw.createInputStream();
// int nRead;
//
// //Read 16kb at a time
// final byte[] data = new byte[16384];
//
// while ((nRead = is.read(data, 0, data.length)) != -1) {
// buffer.write(data, 0, nRead);
// }
//
// buffer.flush();
//
// } catch (IOException e) {
// e.printStackTrace();
// }
// return buffer.toByteArray();
//
// }
//
// public View getUIResultView() {
// return mUpdateView;
// }
//
// public void setUIResultView(View view) {
// mUpdateView = view;
// }
//
// public String getO365MailResourceId() {
// return mMailResourceId;
// }
//
// public void setO365MailResourceId(String resourceId) {
// mMailResourceId = resourceId;
// }
//
// public OutlookClient getO365MailClient() {
// AuthenticationController
// .getInstance()
// .setResourceId(
// this.getO365MailResourceId());
//
// return mO365MailClient;
// }
//
// public void setO365MailClient(OutlookClient client) {
//
// mO365MailClient = client;
// }
//
// public SharePointClient getO365MyFilesClient() {
// return mO365MyFilesClient;
// }
//
// public void setO365MyFilesClient(SharePointClient client) {
// mO365MyFilesClient = client;
// }
//
// private void notifyStatusChange() {
// if (null != mUseCaseStatusChangedListener) {
// mUseCaseStatusChangedListener.onUseCaseStatusChanged();
// }
// }
//
// public final void onPreExecute() {
// mIsExecuting = true;
// notifyStatusChange();
// }
//
// public final void onPostExecute() {
// mIsExecuting = false;
// notifyStatusChange();
// }
//
// public final boolean isExecuting() {
// return mIsExecuting;
// }
//
// @Override
// public String toString() {
// return this.getDescription();
// }
//
//
// }
// Path: app/src/main/java/com/microsoft/office365/snippetapp/OperationListAdapter.java
import android.app.Activity;
import android.view.LayoutInflater;
import android.view.View;
import android.view.ViewGroup;
import android.widget.BaseAdapter;
import android.widget.TextView;
import com.microsoft.office365.snippetapp.helpers.BaseUserStory;
import java.util.List;
/*
* Copyright (c) Microsoft. All rights reserved. Licensed under the MIT license. See full license at the bottom of this file.
*/
package com.microsoft.office365.snippetapp;
class OperationListAdapter extends BaseAdapter {
protected LayoutInflater mLayoutInflater; | protected List<BaseUserStory> mBaseStoryList; |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/ngs/FragmentLengthDistributionByGene.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Iterator;
import org.apache.commons.math3.stat.Frequency;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader; | package edu.unc.genomics.ngs;
/**
* Calculate the fragment length distribution for fragments overlapping each
* gene
*
* @author timpalpant
*
*/
public class FragmentLengthDistributionByGene extends CommandLineTool {
private static final Logger log = Logger.getLogger(FragmentLengthDistributionByGene.class);
| // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/ngs/FragmentLengthDistributionByGene.java
import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Iterator;
import org.apache.commons.math3.stat.Frequency;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
package edu.unc.genomics.ngs;
/**
* Calculate the fragment length distribution for fragments overlapping each
* gene
*
* @author timpalpant
*
*/
public class FragmentLengthDistributionByGene extends CommandLineTool {
private static final Logger log = Logger.getLogger(FragmentLengthDistributionByGene.class);
| @Parameter(names = { "-i", "--input" }, description = "Input file (reads)", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/nucleosomes/IntervalEntropy.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException; | package edu.unc.genomics.ngs;
/**
* For each interval, compute the mean/min/max/total/coverage of data in a (Big)Wig file over that interval.
* @author timpalpant
*
*/
public class IntervalEntropy extends CommandLineTool {
private static final Logger log = Logger.getLogger(IntervalStats.class);
@Parameter(description = "Input files", required = true)
public List<String> inputFiles = new ArrayList<>();
@Parameter(names = {"-l", "--loci"}, description = "Loci file (Bed)", | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/nucleosomes/IntervalEntropy.java
import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
package edu.unc.genomics.ngs;
/**
* For each interval, compute the mean/min/max/total/coverage of data in a (Big)Wig file over that interval.
* @author timpalpant
*
*/
public class IntervalEntropy extends CommandLineTool {
private static final Logger log = Logger.getLogger(IntervalStats.class);
@Parameter(description = "Input files", required = true)
public List<String> inputFiles = new ArrayList<>();
@Parameter(names = {"-l", "--loci"}, description = "Loci file (Bed)", | required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/converters/InterpolateDiscontinuousData.java | // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.IOException;
import java.nio.file.Path;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.genomics.ReadablePathValidator; | package edu.unc.genomics.converters;
/**
* Interpolates missing values (NaN) in a Wig file to create a continuous track
* Useful for making microarray data continuous
*
* @author timpalpant
*
*/
public class InterpolateDiscontinuousData extends WigMathTool {
private static final Logger log = Logger.getLogger(InterpolateDiscontinuousData.class);
| // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/converters/InterpolateDiscontinuousData.java
import java.io.IOException;
import java.nio.file.Path;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.genomics.ReadablePathValidator;
package edu.unc.genomics.converters;
/**
* Interpolates missing values (NaN) in a Wig file to create a continuous track
* Useful for making microarray data continuous
*
* @author timpalpant
*
*/
public class InterpolateDiscontinuousData extends WigMathTool {
private static final Logger log = Logger.getLogger(InterpolateDiscontinuousData.class);
| @Parameter(names = { "-i", "--input" }, description = "Input file (Wig)", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/wigmath/ZScore.java | // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
| import java.io.IOException;
import java.nio.file.Path;
import java.util.HashMap;
import java.util.Map;
import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException; | package edu.unc.genomics.wigmath;
/**
* Z-score the values in a Wig file: calculate normal scores =
* (value-mean)/stdev
*
* @author timpalpant
*
*/
public class ZScore extends WigMathTool {
private static final Logger log = Logger.getLogger(ZScore.class);
| // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
// Path: src/edu/unc/genomics/wigmath/ZScore.java
import java.io.IOException;
import java.nio.file.Path;
import java.util.HashMap;
import java.util.Map;
import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
package edu.unc.genomics.wigmath;
/**
* Z-score the values in a Wig file: calculate normal scores =
* (value-mean)/stdev
*
* @author timpalpant
*
*/
public class ZScore extends WigMathTool {
private static final Logger log = Logger.getLogger(ZScore.class);
| @Parameter(names = { "-i", "--input" }, description = "Input file", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/nucleosomes/DynaPro.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.IOException;
import java.nio.file.Path;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.ucsc.genome.TrackHeader;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Contig;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.genomics.io.WigFileWriter; | package edu.unc.genomics.nucleosomes;
/**
* Solve single-particle hard-rod statistical equilibria with the DynaPro
* algorithm See Morozov AV, et al. (2009) Using DNA mechanics to predict in
* vitro nucleosome positions and formation energies. Nucleic Acids Res 37:
* 4707-4722
*
* @author timpalpant
*
*/
public class DynaPro extends CommandLineTool {
private static final Logger log = Logger.getLogger(DynaPro.class);
| // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/nucleosomes/DynaPro.java
import java.io.IOException;
import java.nio.file.Path;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.ucsc.genome.TrackHeader;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Contig;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.genomics.io.WigFileWriter;
package edu.unc.genomics.nucleosomes;
/**
* Solve single-particle hard-rod statistical equilibria with the DynaPro
* algorithm See Morozov AV, et al. (2009) Using DNA mechanics to predict in
* vitro nucleosome positions and formation energies. Nucleic Acids Res 37:
* 4707-4722
*
* @author timpalpant
*
*/
public class DynaPro extends CommandLineTool {
private static final Logger log = Logger.getLogger(DynaPro.class);
| @Parameter(names = { "-i", "--input" }, description = "Energy landscape", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/nucleosomes/DynaPro.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.IOException;
import java.nio.file.Path;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.ucsc.genome.TrackHeader;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Contig;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.genomics.io.WigFileWriter; | if (scale != null) {
for (int i = 0; i < energy.length; i++) {
energy[i] *= scale;
}
}
// Compute the probabilities
float[] forward = new float[energy.length];
for (int i = nucleosomeSize; i < energy.length; i++) {
double factor = 1 + Math.exp(forward[i - nucleosomeSize] - forward[i - 1] - energy[i - nucleosomeSize]);
forward[i] = (float) (forward[i - 1] + Math.log(factor));
}
float[] backward = new float[energy.length];
for (int i = energy.length - nucleosomeSize - 1; i > 0; i--) {
double factor = 1 + Math.exp(backward[i + nucleosomeSize] - backward[i + 1] - energy[i - 1]);
backward[i] = (float) (backward[i + 1] + Math.log(factor));
}
float[] p = new float[energy.length];
for (int i = 0; i < energy.length - nucleosomeSize; i++) {
p[i] = (float) Math.exp(forward[i] - energy[i] + backward[i + nucleosomeSize] - backward[1]);
}
// Write the chromosome to output
writer.write(new Contig(chr, start, stop, p));
}
} catch (WigFileException e) {
log.error("Error getting data from Wig file");
e.printStackTrace(); | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/nucleosomes/DynaPro.java
import java.io.IOException;
import java.nio.file.Path;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.ucsc.genome.TrackHeader;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Contig;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.genomics.io.WigFileWriter;
if (scale != null) {
for (int i = 0; i < energy.length; i++) {
energy[i] *= scale;
}
}
// Compute the probabilities
float[] forward = new float[energy.length];
for (int i = nucleosomeSize; i < energy.length; i++) {
double factor = 1 + Math.exp(forward[i - nucleosomeSize] - forward[i - 1] - energy[i - nucleosomeSize]);
forward[i] = (float) (forward[i - 1] + Math.log(factor));
}
float[] backward = new float[energy.length];
for (int i = energy.length - nucleosomeSize - 1; i > 0; i--) {
double factor = 1 + Math.exp(backward[i + nucleosomeSize] - backward[i + 1] - energy[i - 1]);
backward[i] = (float) (backward[i + 1] + Math.log(factor));
}
float[] p = new float[energy.length];
for (int i = 0; i < energy.length - nucleosomeSize; i++) {
p[i] = (float) Math.exp(forward[i] - energy[i] + backward[i + nucleosomeSize] - backward[1]);
}
// Write the chromosome to output
writer.write(new Contig(chr, start, stop, p));
}
} catch (WigFileException e) {
log.error("Error getting data from Wig file");
e.printStackTrace(); | throw new CommandLineToolException("Error getting data from Wig file"); |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/visualization/IntervalAverager.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.BedEntry;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.BedFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException; | package edu.unc.genomics.visualization;
/**
* Aggregate and average genomic signal for a set of aligned intervals
*
* @author timpalpant
*
*/
public class IntervalAverager extends CommandLineTool {
private static final Logger log = Logger.getLogger(IntervalAverager.class);
@Parameter(description = "Input files", required = true)
public List<String> inputFiles = new ArrayList<String>(); | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/visualization/IntervalAverager.java
import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.BedEntry;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.BedFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
package edu.unc.genomics.visualization;
/**
* Aggregate and average genomic signal for a set of aligned intervals
*
* @author timpalpant
*
*/
public class IntervalAverager extends CommandLineTool {
private static final Logger log = Logger.getLogger(IntervalAverager.class);
@Parameter(description = "Input files", required = true)
public List<String> inputFiles = new ArrayList<String>(); | @Parameter(names = { "-l", "--loci" }, description = "Loci file (Bed)", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/visualization/IntervalAverager.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.BedEntry;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.BedFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException; | package edu.unc.genomics.visualization;
/**
* Aggregate and average genomic signal for a set of aligned intervals
*
* @author timpalpant
*
*/
public class IntervalAverager extends CommandLineTool {
private static final Logger log = Logger.getLogger(IntervalAverager.class);
@Parameter(description = "Input files", required = true)
public List<String> inputFiles = new ArrayList<String>();
@Parameter(names = { "-l", "--loci" }, description = "Loci file (Bed)", required = true, validateWith = ReadablePathValidator.class)
public Path lociFile;
@Parameter(names = { "-o", "--output" }, description = "Output file (matrix2png format)", required = true)
public Path outputFile;
private List<WigFileReader> wigs = new ArrayList<>();
private int numFiles;
private List<BedEntry> loci;
@Override
public void run() throws IOException {
log.debug("Initializing input files");
for (String inputFile : inputFiles) {
try {
WigFileReader wig = WigFileReader.autodetect(Paths.get(inputFile));
wigs.add(wig);
} catch (IOException e) {
log.error("IOError initializing input Wig file: " + inputFile);
e.printStackTrace(); | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/visualization/IntervalAverager.java
import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.BedEntry;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.BedFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
package edu.unc.genomics.visualization;
/**
* Aggregate and average genomic signal for a set of aligned intervals
*
* @author timpalpant
*
*/
public class IntervalAverager extends CommandLineTool {
private static final Logger log = Logger.getLogger(IntervalAverager.class);
@Parameter(description = "Input files", required = true)
public List<String> inputFiles = new ArrayList<String>();
@Parameter(names = { "-l", "--loci" }, description = "Loci file (Bed)", required = true, validateWith = ReadablePathValidator.class)
public Path lociFile;
@Parameter(names = { "-o", "--output" }, description = "Output file (matrix2png format)", required = true)
public Path outputFile;
private List<WigFileReader> wigs = new ArrayList<>();
private int numFiles;
private List<BedEntry> loci;
@Override
public void run() throws IOException {
log.debug("Initializing input files");
for (String inputFile : inputFiles) {
try {
WigFileReader wig = WigFileReader.autodetect(Paths.get(inputFile));
wigs.add(wig);
} catch (IOException e) {
log.error("IOError initializing input Wig file: " + inputFile);
e.printStackTrace(); | throw new CommandLineToolException(e.getMessage()); |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/wigmath/Scale.java | // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
| import java.io.IOException;
import java.nio.file.Path;
import java.util.HashMap;
import java.util.Map;
import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException; | package edu.unc.genomics.wigmath;
/**
* Scale a Wig file by a constant, or normalize to its mean value
*
* @author timpalpant
*
*/
public class Scale extends WigMathTool {
private static final Logger log = Logger.getLogger(Scale.class);
| // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
// Path: src/edu/unc/genomics/wigmath/Scale.java
import java.io.IOException;
import java.nio.file.Path;
import java.util.HashMap;
import java.util.Map;
import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
package edu.unc.genomics.wigmath;
/**
* Scale a Wig file by a constant, or normalize to its mean value
*
* @author timpalpant
*
*/
public class Scale extends WigMathTool {
private static final Logger log = Logger.getLogger(Scale.class);
| @Parameter(names = { "-i", "--input" }, description = "Input file", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/visualization/MatrixAligner.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Arrays;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.BedEntry;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.BedFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException; | package edu.unc.genomics.visualization;
/**
* Align data from a Wig file into a matrix for making a heatmap with matrix2png
*
* @author timpalpant
*
*/
public class MatrixAligner extends CommandLineTool {
private static final Logger log = Logger.getLogger(MatrixAligner.class);
| // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/visualization/MatrixAligner.java
import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Arrays;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.BedEntry;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.BedFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
package edu.unc.genomics.visualization;
/**
* Align data from a Wig file into a matrix for making a heatmap with matrix2png
*
* @author timpalpant
*
*/
public class MatrixAligner extends CommandLineTool {
private static final Logger log = Logger.getLogger(MatrixAligner.class);
| @Parameter(names = { "-i", "--input" }, description = "Input file (Wig)", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/visualization/MatrixAligner.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Arrays;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.BedEntry;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.BedFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException; | package edu.unc.genomics.visualization;
/**
* Align data from a Wig file into a matrix for making a heatmap with matrix2png
*
* @author timpalpant
*
*/
public class MatrixAligner extends CommandLineTool {
private static final Logger log = Logger.getLogger(MatrixAligner.class);
@Parameter(names = { "-i", "--input" }, description = "Input file (Wig)", required = true, validateWith = ReadablePathValidator.class)
public Path inputFile;
@Parameter(names = { "-l", "--loci" }, description = "Loci file (Bed)", required = true, validateWith = ReadablePathValidator.class)
public Path lociFile;
@Parameter(names = { "-m", "--max" }, description = "Truncate width (base pairs)")
public Integer maxWidth;
@Parameter(names = { "-o", "--output" }, description = "Output file (matrix2png format)", required = true)
public Path outputFile;
private List<BedEntry> loci;
@Override
public void run() throws IOException {
log.debug("Loading alignment intervals");
try (BedFileReader bed = new BedFileReader(lociFile)) {
loci = bed.loadAll();
}
// Compute the matrix dimensions
int leftMax = Integer.MIN_VALUE;
int rightMax = Integer.MIN_VALUE;
for (BedEntry entry : loci) {
if (entry.getValue() == null) { | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/visualization/MatrixAligner.java
import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Arrays;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.BedEntry;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.BedFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
package edu.unc.genomics.visualization;
/**
* Align data from a Wig file into a matrix for making a heatmap with matrix2png
*
* @author timpalpant
*
*/
public class MatrixAligner extends CommandLineTool {
private static final Logger log = Logger.getLogger(MatrixAligner.class);
@Parameter(names = { "-i", "--input" }, description = "Input file (Wig)", required = true, validateWith = ReadablePathValidator.class)
public Path inputFile;
@Parameter(names = { "-l", "--loci" }, description = "Loci file (Bed)", required = true, validateWith = ReadablePathValidator.class)
public Path lociFile;
@Parameter(names = { "-m", "--max" }, description = "Truncate width (base pairs)")
public Integer maxWidth;
@Parameter(names = { "-o", "--output" }, description = "Output file (matrix2png format)", required = true)
public Path outputFile;
private List<BedEntry> loci;
@Override
public void run() throws IOException {
log.debug("Loading alignment intervals");
try (BedFileReader bed = new BedFileReader(lociFile)) {
loci = bed.loadAll();
}
// Compute the matrix dimensions
int leftMax = Integer.MIN_VALUE;
int rightMax = Integer.MIN_VALUE;
for (BedEntry entry : loci) {
if (entry.getValue() == null) { | throw new CommandLineToolException("You must specify an alignment point for each interval in column 5"); |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/nucleosomes/Phasogram.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.IOException;
import java.io.PrintWriter;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException; | package edu.unc.genomics.nucleosomes;
/**
* Make a histogram of phase counts from sequencing data to identify
* periodicities. See Valouev A, et al. (2011) Determinants of nucleosome
* organization in primary human cells. Nature 474: 516-520
*
* @author timpalpant
*
*/
public class Phasogram extends CommandLineTool {
private static final Logger log = Logger.getLogger(Phasogram.class);
| // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/nucleosomes/Phasogram.java
import java.io.IOException;
import java.io.PrintWriter;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
package edu.unc.genomics.nucleosomes;
/**
* Make a histogram of phase counts from sequencing data to identify
* periodicities. See Valouev A, et al. (2011) Determinants of nucleosome
* organization in primary human cells. Nature 474: 516-520
*
* @author timpalpant
*
*/
public class Phasogram extends CommandLineTool {
private static final Logger log = Logger.getLogger(Phasogram.class);
| @Parameter(names = { "-i", "--input" }, description = "Input wig file (read counts)", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/nucleosomes/Phasogram.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.IOException;
import java.io.PrintWriter;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException; | @Parameter(names = { "-o", "--output" }, description = "Output file (histogram)", required = true)
public Path outputFile;
public void run() throws IOException {
double[] phaseCounts = new double[maxPhase + 1];
// Process each chromosome in the input file
try (WigFileReader reader = WigFileReader.autodetect(inputFile)) {
for (String chr : reader.chromosomes()) {
log.debug("Processing chromosome " + chr);
int start = reader.getChrStart(chr);
while (start < reader.getChrStop(chr)) {
int stop = Math.min(start + DEFAULT_CHUNK_SIZE - 1, reader.getChrStop(chr));
log.debug("Processing chunk " + chr + ":" + start + "-" + stop);
int paddedStop = Math.min(stop + maxPhase, reader.getChrStop(chr));
try {
float[] data = reader.query(chr, start, paddedStop).getValues();
for (int i = 0; i < data.length - maxPhase; i++) {
if (!Float.isNaN(data[i]) && !Float.isInfinite(data[i])) {
for (int j = 0; j <= maxPhase; j++) {
if (!Float.isNaN(data[i + j]) && !Float.isInfinite(data[i + j])) {
phaseCounts[j] += data[i] * data[i + j];
}
}
}
}
} catch (WigFileException e) {
log.fatal("Error querying data from Wig file!");
e.printStackTrace(); | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/nucleosomes/Phasogram.java
import java.io.IOException;
import java.io.PrintWriter;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
@Parameter(names = { "-o", "--output" }, description = "Output file (histogram)", required = true)
public Path outputFile;
public void run() throws IOException {
double[] phaseCounts = new double[maxPhase + 1];
// Process each chromosome in the input file
try (WigFileReader reader = WigFileReader.autodetect(inputFile)) {
for (String chr : reader.chromosomes()) {
log.debug("Processing chromosome " + chr);
int start = reader.getChrStart(chr);
while (start < reader.getChrStop(chr)) {
int stop = Math.min(start + DEFAULT_CHUNK_SIZE - 1, reader.getChrStop(chr));
log.debug("Processing chunk " + chr + ":" + start + "-" + stop);
int paddedStop = Math.min(stop + maxPhase, reader.getChrStop(chr));
try {
float[] data = reader.query(chr, start, paddedStop).getValues();
for (int i = 0; i < data.length - maxPhase; i++) {
if (!Float.isNaN(data[i]) && !Float.isInfinite(data[i])) {
for (int j = 0; j <= maxPhase; j++) {
if (!Float.isNaN(data[i + j]) && !Float.isInfinite(data[i + j])) {
phaseCounts[j] += data[i] * data[i + j];
}
}
}
}
} catch (WigFileException e) {
log.fatal("Error querying data from Wig file!");
e.printStackTrace(); | throw new CommandLineToolException("Error querying data from Wig file!"); |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/wigmath/Divide.java | // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
| import java.io.IOException;
import java.nio.file.Path;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException; | package edu.unc.genomics.wigmath;
/**
* Divide two (Big)Wig files base pair by base pair
*
* @author timpalpant
*
*/
public class Divide extends WigMathTool {
private static final Logger log = Logger.getLogger(Divide.class);
| // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
// Path: src/edu/unc/genomics/wigmath/Divide.java
import java.io.IOException;
import java.nio.file.Path;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
package edu.unc.genomics.wigmath;
/**
* Divide two (Big)Wig files base pair by base pair
*
* @author timpalpant
*
*/
public class Divide extends WigMathTool {
private static final Logger log = Logger.getLogger(Divide.class);
| @Parameter(names = { "-n", "--numerator" }, description = "Dividend / Numerator (file 1)", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/wigmath/Summary.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/genomics/ngs/Autocorrelation.java
// public class Autocorrelation extends CommandLineTool {
//
// private static final Logger log = Logger.getLogger(Autocorrelation.class);
//
// @Parameter(names = { "-i", "--input" }, description = "Input file", required = true, validateWith = ReadablePathValidator.class)
// public Path inputFile;
// @Parameter(names = { "-l", "--loci" }, description = "Genomic loci (Bed format)", required = true, validateWith = ReadablePathValidator.class)
// public Path lociFile;
// @Parameter(names = { "-o", "--output" }, description = "Output file", required = true)
// public Path outputFile;
// @Parameter(names = { "-m", "--max" }, description = "Autocorrelation limit (bp)")
// public int limit = 200;
//
// @Override
// public void run() throws IOException {
// try (WigFileReader wig = WigFileReader.autodetect(inputFile);
// IntervalFileReader<? extends Interval> loci = IntervalFileReader.autodetect(lociFile);
// BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
// log.debug("Computing autocorrelation for each window");
// int skipped = 0;
// for (Interval interval : loci) {
// float[] data;
// try {
// data = wig.query(interval).getValues();
// } catch (IOException | WigFileException e) {
// log.debug("Skipping interval: " + interval.toString());
// skipped++;
// continue;
// }
//
// // Compute the autocorrelation
// float[] auto = FFTUtils.autocovariance(data, limit);
//
// // Write to output
// writer.write(interval.toBed());
// for (int i = 0; i < auto.length; i++) {
// writer.write("\t" + auto[i]);
// }
// writer.newLine();
// }
//
// log.info("Skipped " + skipped + " intervals");
// }
// }
//
// public static void main(String[] args) {
// new Autocorrelation().instanceMain(args);
// }
// }
| import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.genomics.ngs.Autocorrelation; | package edu.unc.genomics.wigmath;
/**
* Output a summary of a (Big)Wig file with information about the chromosomes,
* contigs, and statistics about the data.
*
* @author timpalpant
*
*/
public class Summary extends CommandLineTool {
private static final Logger log = Logger.getLogger(Autocorrelation.class);
| // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/genomics/ngs/Autocorrelation.java
// public class Autocorrelation extends CommandLineTool {
//
// private static final Logger log = Logger.getLogger(Autocorrelation.class);
//
// @Parameter(names = { "-i", "--input" }, description = "Input file", required = true, validateWith = ReadablePathValidator.class)
// public Path inputFile;
// @Parameter(names = { "-l", "--loci" }, description = "Genomic loci (Bed format)", required = true, validateWith = ReadablePathValidator.class)
// public Path lociFile;
// @Parameter(names = { "-o", "--output" }, description = "Output file", required = true)
// public Path outputFile;
// @Parameter(names = { "-m", "--max" }, description = "Autocorrelation limit (bp)")
// public int limit = 200;
//
// @Override
// public void run() throws IOException {
// try (WigFileReader wig = WigFileReader.autodetect(inputFile);
// IntervalFileReader<? extends Interval> loci = IntervalFileReader.autodetect(lociFile);
// BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
// log.debug("Computing autocorrelation for each window");
// int skipped = 0;
// for (Interval interval : loci) {
// float[] data;
// try {
// data = wig.query(interval).getValues();
// } catch (IOException | WigFileException e) {
// log.debug("Skipping interval: " + interval.toString());
// skipped++;
// continue;
// }
//
// // Compute the autocorrelation
// float[] auto = FFTUtils.autocovariance(data, limit);
//
// // Write to output
// writer.write(interval.toBed());
// for (int i = 0; i < auto.length; i++) {
// writer.write("\t" + auto[i]);
// }
// writer.newLine();
// }
//
// log.info("Skipped " + skipped + " intervals");
// }
// }
//
// public static void main(String[] args) {
// new Autocorrelation().instanceMain(args);
// }
// }
// Path: src/edu/unc/genomics/wigmath/Summary.java
import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.genomics.ngs.Autocorrelation;
package edu.unc.genomics.wigmath;
/**
* Output a summary of a (Big)Wig file with information about the chromosomes,
* contigs, and statistics about the data.
*
* @author timpalpant
*
*/
public class Summary extends CommandLineTool {
private static final Logger log = Logger.getLogger(Autocorrelation.class);
| @Parameter(names = { "-i", "--input" }, description = "Input file", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/ngs/SplitReads.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.IOException;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
import edu.unc.genomics.io.IntervalFileWriter; | package edu.unc.genomics.ngs;
/**
* This tool splits sequencing reads into bins
*
* @author timpalpant
*
*/
public class SplitReads extends CommandLineTool {
private static final Logger log = Logger.getLogger(SplitReads.class);
| // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/ngs/SplitReads.java
import java.io.IOException;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
import edu.unc.genomics.io.IntervalFileWriter;
package edu.unc.genomics.ngs;
/**
* This tool splits sequencing reads into bins
*
* @author timpalpant
*
*/
public class SplitReads extends CommandLineTool {
private static final Logger log = Logger.getLogger(SplitReads.class);
| @Parameter(names = { "-i", "--input" }, required = true, description = "Input file", validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/wigmath/Subtract.java | // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
| import java.io.IOException;
import java.nio.file.Path;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException; | package edu.unc.genomics.wigmath;
/**
* Subtract two (Big)Wig files
*
* @author timpalpant
*
*/
public class Subtract extends WigMathTool {
private static final Logger log = Logger.getLogger(Subtract.class);
| // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
// Path: src/edu/unc/genomics/wigmath/Subtract.java
import java.io.IOException;
import java.nio.file.Path;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
package edu.unc.genomics.wigmath;
/**
* Subtract two (Big)Wig files
*
* @author timpalpant
*
*/
public class Subtract extends WigMathTool {
private static final Logger log = Logger.getLogger(Subtract.class);
| @Parameter(names = { "-m", "--minuend" }, description = "Minuend (top - file 1)", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/ngs/FindAbsoluteMaxima.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/utils/ArrayUtils.java
// public class ArrayUtils {
//
// /**
// * Get the index of the maximum (largest) value in an array In the event of a
// * tie, the first index is returned
// *
// * @param x
// * a vector of values
// * @return the index of the largest element in x
// */
// public static int maxIndex(float[] x) {
// float maxValue = -Float.MAX_VALUE;
// int maxIndex = -1;
// for (int i = 0; i < x.length; i++) {
// if (x[i] > maxValue) {
// maxValue = x[i];
// maxIndex = i;
// }
// }
//
// return maxIndex;
// }
//
// public static float[] mapToFloat(int[] data) {
// float[] ret = new float[data.length];
// for (int i = 0; i < data.length; i++) {
// ret[i] = data[i];
// }
// return ret;
// }
//
// public static int[] mapToInt(float[] data) {
// int[] ret = new int[data.length];
// for (int i = 0; i < data.length; i++) {
// ret[i] = (int) data[i];
// }
// return ret;
// }
// }
| import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.utils.ArrayUtils; | package edu.unc.genomics.ngs;
/**
* For a set of intervals, this tool finds the location of the largest value in
* a Wig file for each interval.
*
* @author timpalpant
*
*/
public class FindAbsoluteMaxima extends CommandLineTool {
private static final Logger log = Logger.getLogger(FindAbsoluteMaxima.class);
@Parameter(description = "Input files", required = true)
public List<String> inputFiles = new ArrayList<String>(); | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/utils/ArrayUtils.java
// public class ArrayUtils {
//
// /**
// * Get the index of the maximum (largest) value in an array In the event of a
// * tie, the first index is returned
// *
// * @param x
// * a vector of values
// * @return the index of the largest element in x
// */
// public static int maxIndex(float[] x) {
// float maxValue = -Float.MAX_VALUE;
// int maxIndex = -1;
// for (int i = 0; i < x.length; i++) {
// if (x[i] > maxValue) {
// maxValue = x[i];
// maxIndex = i;
// }
// }
//
// return maxIndex;
// }
//
// public static float[] mapToFloat(int[] data) {
// float[] ret = new float[data.length];
// for (int i = 0; i < data.length; i++) {
// ret[i] = data[i];
// }
// return ret;
// }
//
// public static int[] mapToInt(float[] data) {
// int[] ret = new int[data.length];
// for (int i = 0; i < data.length; i++) {
// ret[i] = (int) data[i];
// }
// return ret;
// }
// }
// Path: src/edu/unc/genomics/ngs/FindAbsoluteMaxima.java
import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.utils.ArrayUtils;
package edu.unc.genomics.ngs;
/**
* For a set of intervals, this tool finds the location of the largest value in
* a Wig file for each interval.
*
* @author timpalpant
*
*/
public class FindAbsoluteMaxima extends CommandLineTool {
private static final Logger log = Logger.getLogger(FindAbsoluteMaxima.class);
@Parameter(description = "Input files", required = true)
public List<String> inputFiles = new ArrayList<String>(); | @Parameter(names = { "-l", "--loci" }, description = "Loci file (Bed)", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/ngs/FindAbsoluteMaxima.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/utils/ArrayUtils.java
// public class ArrayUtils {
//
// /**
// * Get the index of the maximum (largest) value in an array In the event of a
// * tie, the first index is returned
// *
// * @param x
// * a vector of values
// * @return the index of the largest element in x
// */
// public static int maxIndex(float[] x) {
// float maxValue = -Float.MAX_VALUE;
// int maxIndex = -1;
// for (int i = 0; i < x.length; i++) {
// if (x[i] > maxValue) {
// maxValue = x[i];
// maxIndex = i;
// }
// }
//
// return maxIndex;
// }
//
// public static float[] mapToFloat(int[] data) {
// float[] ret = new float[data.length];
// for (int i = 0; i < data.length; i++) {
// ret[i] = data[i];
// }
// return ret;
// }
//
// public static int[] mapToInt(float[] data) {
// int[] ret = new int[data.length];
// for (int i = 0; i < data.length; i++) {
// ret[i] = (int) data[i];
// }
// return ret;
// }
// }
| import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.utils.ArrayUtils; | @Parameter(names = { "-o", "--output" }, description = "Output file", required = true)
public Path outputFile;
private List<WigFileReader> wigs = new ArrayList<>();
@Override
public void run() throws IOException {
log.debug("Initializing input Wig file(s)");
for (String inputFile : inputFiles) {
wigs.add(WigFileReader.autodetect(Paths.get(inputFile)));
}
log.debug("Initializing output file");
int count = 0, skipped = 0;
try (IntervalFileReader<? extends Interval> reader = IntervalFileReader.autodetect(lociFile);
BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
writer.write("#Chr\tStart\tStop\tID\tValue\tStrand");
for (String inputFile : inputFiles) {
Path p = Paths.get(inputFile);
writer.write("\t" + p.getFileName().toString());
}
writer.newLine();
log.debug("Iterating over all intervals and finding maxima");
for (Interval interval : reader) {
writer.write(interval.toBed());
for (WigFileReader wig : wigs) {
try {
float[] data = wig.query(interval).getValues();
int dir = interval.isWatson() ? 1 : -1; | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/utils/ArrayUtils.java
// public class ArrayUtils {
//
// /**
// * Get the index of the maximum (largest) value in an array In the event of a
// * tie, the first index is returned
// *
// * @param x
// * a vector of values
// * @return the index of the largest element in x
// */
// public static int maxIndex(float[] x) {
// float maxValue = -Float.MAX_VALUE;
// int maxIndex = -1;
// for (int i = 0; i < x.length; i++) {
// if (x[i] > maxValue) {
// maxValue = x[i];
// maxIndex = i;
// }
// }
//
// return maxIndex;
// }
//
// public static float[] mapToFloat(int[] data) {
// float[] ret = new float[data.length];
// for (int i = 0; i < data.length; i++) {
// ret[i] = data[i];
// }
// return ret;
// }
//
// public static int[] mapToInt(float[] data) {
// int[] ret = new int[data.length];
// for (int i = 0; i < data.length; i++) {
// ret[i] = (int) data[i];
// }
// return ret;
// }
// }
// Path: src/edu/unc/genomics/ngs/FindAbsoluteMaxima.java
import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.utils.ArrayUtils;
@Parameter(names = { "-o", "--output" }, description = "Output file", required = true)
public Path outputFile;
private List<WigFileReader> wigs = new ArrayList<>();
@Override
public void run() throws IOException {
log.debug("Initializing input Wig file(s)");
for (String inputFile : inputFiles) {
wigs.add(WigFileReader.autodetect(Paths.get(inputFile)));
}
log.debug("Initializing output file");
int count = 0, skipped = 0;
try (IntervalFileReader<? extends Interval> reader = IntervalFileReader.autodetect(lociFile);
BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
writer.write("#Chr\tStart\tStop\tID\tValue\tStrand");
for (String inputFile : inputFiles) {
Path p = Paths.get(inputFile);
writer.write("\t" + p.getFileName().toString());
}
writer.newLine();
log.debug("Iterating over all intervals and finding maxima");
for (Interval interval : reader) {
writer.write(interval.toBed());
for (WigFileReader wig : wigs) {
try {
float[] data = wig.query(interval).getValues();
int dir = interval.isWatson() ? 1 : -1; | int maxima = interval.getStart() + dir * ArrayUtils.maxIndex(data); |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/ngs/IntervalStats.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/utils/WigStatistic.java
// public enum WigStatistic {
// COVERAGE("coverage"), TOTAL("total"), MEAN("mean"), MIN("min"), MAX("max");
//
// private String name;
//
// WigStatistic(final String name) {
// this.name = name;
// }
//
// public static WigStatistic fromName(final String name) {
// for (WigStatistic dsm : WigStatistic.values()) {
// if (dsm.getName().equalsIgnoreCase(name)) {
// return dsm;
// }
// }
//
// return null;
// }
//
// /**
// * @return the name
// */
// public String getName() {
// return name;
// }
// }
| import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.utils.WigStatistic; | package edu.unc.genomics.ngs;
/**
* For each interval, compute the mean/min/max/total/coverage of data in a
* (Big)Wig file over that interval.
*
* @author timpalpant
*
*/
public class IntervalStats extends CommandLineTool {
private static final Logger log = Logger.getLogger(IntervalStats.class);
@Parameter(description = "Input files", required = true)
public List<String> inputFiles = new ArrayList<>(); | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/utils/WigStatistic.java
// public enum WigStatistic {
// COVERAGE("coverage"), TOTAL("total"), MEAN("mean"), MIN("min"), MAX("max");
//
// private String name;
//
// WigStatistic(final String name) {
// this.name = name;
// }
//
// public static WigStatistic fromName(final String name) {
// for (WigStatistic dsm : WigStatistic.values()) {
// if (dsm.getName().equalsIgnoreCase(name)) {
// return dsm;
// }
// }
//
// return null;
// }
//
// /**
// * @return the name
// */
// public String getName() {
// return name;
// }
// }
// Path: src/edu/unc/genomics/ngs/IntervalStats.java
import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.utils.WigStatistic;
package edu.unc.genomics.ngs;
/**
* For each interval, compute the mean/min/max/total/coverage of data in a
* (Big)Wig file over that interval.
*
* @author timpalpant
*
*/
public class IntervalStats extends CommandLineTool {
private static final Logger log = Logger.getLogger(IntervalStats.class);
@Parameter(description = "Input files", required = true)
public List<String> inputFiles = new ArrayList<>(); | @Parameter(names = { "-l", "--loci" }, description = "Loci file (Bed)", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/wigmath/ExtractRegion.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.Contig;
import edu.unc.genomics.Interval;
import edu.unc.genomics.io.WigFileException;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileWriter; | package edu.unc.genomics.wigmath;
/**
* Extracts the values from a (Big)Wig file for a given interval
*
* @author timpalpant
*
*/
public class ExtractRegion extends CommandLineTool {
private static final Logger log = Logger.getLogger(ExtractRegion.class);
| // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/wigmath/ExtractRegion.java
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.Contig;
import edu.unc.genomics.Interval;
import edu.unc.genomics.io.WigFileException;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileWriter;
package edu.unc.genomics.wigmath;
/**
* Extracts the values from a (Big)Wig file for a given interval
*
* @author timpalpant
*
*/
public class ExtractRegion extends CommandLineTool {
private static final Logger log = Logger.getLogger(ExtractRegion.class);
| @Parameter(names = { "-i", "--input" }, description = "Input file (BigWig/Wig)", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/wigmath/ExtractRegion.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.Contig;
import edu.unc.genomics.Interval;
import edu.unc.genomics.io.WigFileException;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileWriter; | package edu.unc.genomics.wigmath;
/**
* Extracts the values from a (Big)Wig file for a given interval
*
* @author timpalpant
*
*/
public class ExtractRegion extends CommandLineTool {
private static final Logger log = Logger.getLogger(ExtractRegion.class);
@Parameter(names = { "-i", "--input" }, description = "Input file (BigWig/Wig)", required = true, validateWith = ReadablePathValidator.class)
public Path inputFile;
@Parameter(names = { "-c", "--chr" }, description = "Chromosome", required = true)
public String chr;
@Parameter(names = { "-s", "--start" }, description = "Start base pair")
public int start = -1;
@Parameter(names = { "-e", "--stop" }, description = "Stop base pair")
public int stop = -1;
@Parameter(names = { "--chunk" }, description = "Size to chunk each chromosome into when processing (bp)")
public int chunkSize = DEFAULT_CHUNK_SIZE;
@Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
public boolean fixedStep = false;
@Parameter(names = { "-o", "--output" }, description = "Output file (wig)", required = true)
public Path outputFile;
@Override
public void run() throws IOException {
try (WigFileReader reader = WigFileReader.autodetect(inputFile)) {
if (!reader.includes(chr)) { | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/wigmath/ExtractRegion.java
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.Contig;
import edu.unc.genomics.Interval;
import edu.unc.genomics.io.WigFileException;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileWriter;
package edu.unc.genomics.wigmath;
/**
* Extracts the values from a (Big)Wig file for a given interval
*
* @author timpalpant
*
*/
public class ExtractRegion extends CommandLineTool {
private static final Logger log = Logger.getLogger(ExtractRegion.class);
@Parameter(names = { "-i", "--input" }, description = "Input file (BigWig/Wig)", required = true, validateWith = ReadablePathValidator.class)
public Path inputFile;
@Parameter(names = { "-c", "--chr" }, description = "Chromosome", required = true)
public String chr;
@Parameter(names = { "-s", "--start" }, description = "Start base pair")
public int start = -1;
@Parameter(names = { "-e", "--stop" }, description = "Stop base pair")
public int stop = -1;
@Parameter(names = { "--chunk" }, description = "Size to chunk each chromosome into when processing (bp)")
public int chunkSize = DEFAULT_CHUNK_SIZE;
@Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
public boolean fixedStep = false;
@Parameter(names = { "-o", "--output" }, description = "Output file (wig)", required = true)
public Path outputFile;
@Override
public void run() throws IOException {
try (WigFileReader reader = WigFileReader.autodetect(inputFile)) {
if (!reader.includes(chr)) { | throw new CommandLineToolException("Wig file does not contain chromosome " + chr); |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/wigmath/Average.java | // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
| import java.io.IOException;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException; | package edu.unc.genomics.wigmath;
/**
* Average multiple Wig files base pair by base pair
*
* @author timpalpant
*
*/
public class Average extends WigMathTool {
private static final Logger log = Logger.getLogger(Average.class);
@Parameter(description = "Input files", required = true)
public List<String> inputFiles = new ArrayList<String>();
@Override
public void setup() {
if (inputFiles.size() < 2) { | // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
// Path: src/edu/unc/genomics/wigmath/Average.java
import java.io.IOException;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
package edu.unc.genomics.wigmath;
/**
* Average multiple Wig files base pair by base pair
*
* @author timpalpant
*
*/
public class Average extends WigMathTool {
private static final Logger log = Logger.getLogger(Average.class);
@Parameter(description = "Input files", required = true)
public List<String> inputFiles = new ArrayList<String>();
@Override
public void setup() {
if (inputFiles.size() < 2) { | throw new CommandLineToolException("No reason to average < 2 files."); |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/wigmath/Multiply.java | // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
| import java.io.IOException;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException; | package edu.unc.genomics.wigmath;
/**
* Multiply (Big)Wig files base pair by base pair
*
* @author timpalpant
*
*/
public class Multiply extends WigMathTool {
private static final Logger log = Logger.getLogger(Multiply.class);
@Parameter(description = "Input files", required = true)
public List<String> inputFiles = new ArrayList<String>();
@Override
public void setup() {
log.debug("Initializing input files");
for (String inputFile : inputFiles) {
try {
addInputFile(WigFileReader.autodetect(Paths.get(inputFile)));
} catch (IOException e) { | // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
// Path: src/edu/unc/genomics/wigmath/Multiply.java
import java.io.IOException;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
package edu.unc.genomics.wigmath;
/**
* Multiply (Big)Wig files base pair by base pair
*
* @author timpalpant
*
*/
public class Multiply extends WigMathTool {
private static final Logger log = Logger.getLogger(Multiply.class);
@Parameter(description = "Input files", required = true)
public List<String> inputFiles = new ArrayList<String>();
@Override
public void setup() {
log.debug("Initializing input files");
for (String inputFile : inputFiles) {
try {
addInputFile(WigFileReader.autodetect(Paths.get(inputFile)));
} catch (IOException e) { | throw new CommandLineToolException(e); |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/wigmath/Downsample.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/utils/WigStatistic.java
// public enum WigStatistic {
// COVERAGE("coverage"), TOTAL("total"), MEAN("mean"), MIN("min"), MAX("max");
//
// private String name;
//
// WigStatistic(final String name) {
// this.name = name;
// }
//
// public static WigStatistic fromName(final String name) {
// for (WigStatistic dsm : WigStatistic.values()) {
// if (dsm.getName().equalsIgnoreCase(name)) {
// return dsm;
// }
// }
//
// return null;
// }
//
// /**
// * @return the name
// */
// public String getName() {
// return name;
// }
// }
| import java.io.IOException;
import java.io.PrintWriter;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.ucsc.genome.TrackHeader;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.utils.WigStatistic; | package edu.unc.genomics.wigmath;
/**
* Downsample a high-resolution Wig file into larger windows so that it has
* smaller file size
*
* @author timpalpant
*
*/
public class Downsample extends CommandLineTool {
private static final Logger log = Logger.getLogger(Downsample.class);
| // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/utils/WigStatistic.java
// public enum WigStatistic {
// COVERAGE("coverage"), TOTAL("total"), MEAN("mean"), MIN("min"), MAX("max");
//
// private String name;
//
// WigStatistic(final String name) {
// this.name = name;
// }
//
// public static WigStatistic fromName(final String name) {
// for (WigStatistic dsm : WigStatistic.values()) {
// if (dsm.getName().equalsIgnoreCase(name)) {
// return dsm;
// }
// }
//
// return null;
// }
//
// /**
// * @return the name
// */
// public String getName() {
// return name;
// }
// }
// Path: src/edu/unc/genomics/wigmath/Downsample.java
import java.io.IOException;
import java.io.PrintWriter;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.ucsc.genome.TrackHeader;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.utils.WigStatistic;
package edu.unc.genomics.wigmath;
/**
* Downsample a high-resolution Wig file into larger windows so that it has
* smaller file size
*
* @author timpalpant
*
*/
public class Downsample extends CommandLineTool {
private static final Logger log = Logger.getLogger(Downsample.class);
| @Parameter(names = { "-i", "--input" }, description = "Input file", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/wigmath/Downsample.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/utils/WigStatistic.java
// public enum WigStatistic {
// COVERAGE("coverage"), TOTAL("total"), MEAN("mean"), MIN("min"), MAX("max");
//
// private String name;
//
// WigStatistic(final String name) {
// this.name = name;
// }
//
// public static WigStatistic fromName(final String name) {
// for (WigStatistic dsm : WigStatistic.values()) {
// if (dsm.getName().equalsIgnoreCase(name)) {
// return dsm;
// }
// }
//
// return null;
// }
//
// /**
// * @return the name
// */
// public String getName() {
// return name;
// }
// }
| import java.io.IOException;
import java.io.PrintWriter;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.ucsc.genome.TrackHeader;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.utils.WigStatistic; | package edu.unc.genomics.wigmath;
/**
* Downsample a high-resolution Wig file into larger windows so that it has
* smaller file size
*
* @author timpalpant
*
*/
public class Downsample extends CommandLineTool {
private static final Logger log = Logger.getLogger(Downsample.class);
@Parameter(names = { "-i", "--input" }, description = "Input file", required = true, validateWith = ReadablePathValidator.class)
public Path inputFile;
@Parameter(names = { "-w", "--window" }, description = "Window size (bp)")
public int windowSize = 100;
@Parameter(names = { "-m", "--metric" }, description = "Downsampling metric (coverage/total/mean/min/max)")
public String metric = "mean";
@Parameter(names = { "-o", "--output" }, description = "Output file", required = true)
public Path outputFile;
@Override
public void run() throws IOException { | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/utils/WigStatistic.java
// public enum WigStatistic {
// COVERAGE("coverage"), TOTAL("total"), MEAN("mean"), MIN("min"), MAX("max");
//
// private String name;
//
// WigStatistic(final String name) {
// this.name = name;
// }
//
// public static WigStatistic fromName(final String name) {
// for (WigStatistic dsm : WigStatistic.values()) {
// if (dsm.getName().equalsIgnoreCase(name)) {
// return dsm;
// }
// }
//
// return null;
// }
//
// /**
// * @return the name
// */
// public String getName() {
// return name;
// }
// }
// Path: src/edu/unc/genomics/wigmath/Downsample.java
import java.io.IOException;
import java.io.PrintWriter;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.ucsc.genome.TrackHeader;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.utils.WigStatistic;
package edu.unc.genomics.wigmath;
/**
* Downsample a high-resolution Wig file into larger windows so that it has
* smaller file size
*
* @author timpalpant
*
*/
public class Downsample extends CommandLineTool {
private static final Logger log = Logger.getLogger(Downsample.class);
@Parameter(names = { "-i", "--input" }, description = "Input file", required = true, validateWith = ReadablePathValidator.class)
public Path inputFile;
@Parameter(names = { "-w", "--window" }, description = "Window size (bp)")
public int windowSize = 100;
@Parameter(names = { "-m", "--metric" }, description = "Downsampling metric (coverage/total/mean/min/max)")
public String metric = "mean";
@Parameter(names = { "-o", "--output" }, description = "Output file", required = true)
public Path outputFile;
@Override
public void run() throws IOException { | WigStatistic dsm = WigStatistic.fromName(metric); |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/wigmath/Downsample.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/utils/WigStatistic.java
// public enum WigStatistic {
// COVERAGE("coverage"), TOTAL("total"), MEAN("mean"), MIN("min"), MAX("max");
//
// private String name;
//
// WigStatistic(final String name) {
// this.name = name;
// }
//
// public static WigStatistic fromName(final String name) {
// for (WigStatistic dsm : WigStatistic.values()) {
// if (dsm.getName().equalsIgnoreCase(name)) {
// return dsm;
// }
// }
//
// return null;
// }
//
// /**
// * @return the name
// */
// public String getName() {
// return name;
// }
// }
| import java.io.IOException;
import java.io.PrintWriter;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.ucsc.genome.TrackHeader;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.utils.WigStatistic; | package edu.unc.genomics.wigmath;
/**
* Downsample a high-resolution Wig file into larger windows so that it has
* smaller file size
*
* @author timpalpant
*
*/
public class Downsample extends CommandLineTool {
private static final Logger log = Logger.getLogger(Downsample.class);
@Parameter(names = { "-i", "--input" }, description = "Input file", required = true, validateWith = ReadablePathValidator.class)
public Path inputFile;
@Parameter(names = { "-w", "--window" }, description = "Window size (bp)")
public int windowSize = 100;
@Parameter(names = { "-m", "--metric" }, description = "Downsampling metric (coverage/total/mean/min/max)")
public String metric = "mean";
@Parameter(names = { "-o", "--output" }, description = "Output file", required = true)
public Path outputFile;
@Override
public void run() throws IOException {
WigStatistic dsm = WigStatistic.fromName(metric);
if (dsm == null) {
log.error("Unknown downsampling metric: " + metric); | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/utils/WigStatistic.java
// public enum WigStatistic {
// COVERAGE("coverage"), TOTAL("total"), MEAN("mean"), MIN("min"), MAX("max");
//
// private String name;
//
// WigStatistic(final String name) {
// this.name = name;
// }
//
// public static WigStatistic fromName(final String name) {
// for (WigStatistic dsm : WigStatistic.values()) {
// if (dsm.getName().equalsIgnoreCase(name)) {
// return dsm;
// }
// }
//
// return null;
// }
//
// /**
// * @return the name
// */
// public String getName() {
// return name;
// }
// }
// Path: src/edu/unc/genomics/wigmath/Downsample.java
import java.io.IOException;
import java.io.PrintWriter;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.ucsc.genome.TrackHeader;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.utils.WigStatistic;
package edu.unc.genomics.wigmath;
/**
* Downsample a high-resolution Wig file into larger windows so that it has
* smaller file size
*
* @author timpalpant
*
*/
public class Downsample extends CommandLineTool {
private static final Logger log = Logger.getLogger(Downsample.class);
@Parameter(names = { "-i", "--input" }, description = "Input file", required = true, validateWith = ReadablePathValidator.class)
public Path inputFile;
@Parameter(names = { "-w", "--window" }, description = "Window size (bp)")
public int windowSize = 100;
@Parameter(names = { "-m", "--metric" }, description = "Downsampling metric (coverage/total/mean/min/max)")
public String metric = "mean";
@Parameter(names = { "-o", "--output" }, description = "Output file", required = true)
public Path outputFile;
@Override
public void run() throws IOException {
WigStatistic dsm = WigStatistic.fromName(metric);
if (dsm == null) {
log.error("Unknown downsampling metric: " + metric); | throw new CommandLineToolException("Unknown downsampling metric: " + metric |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/wigmath/MovingEntropy.java | // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
| import java.io.IOException;
import java.nio.file.Path;
import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException; | package edu.unc.genomics.wigmath;
/**
* Smooth a (Big)Wig file with a moving average filter
* @author timpalpant
*
*/
public class MovingEntropy extends WigMathTool {
@Parameter(names = {"-i", "--input"}, description = "Input file", | // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
// Path: src/edu/unc/genomics/wigmath/MovingEntropy.java
import java.io.IOException;
import java.nio.file.Path;
import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
package edu.unc.genomics.wigmath;
/**
* Smooth a (Big)Wig file with a moving average filter
* @author timpalpant
*
*/
public class MovingEntropy extends WigMathTool {
@Parameter(names = {"-i", "--input"}, description = "Input file", | required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/converters/FastqIlluminaToSanger.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.IOException;
import java.io.PrintWriter;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import net.sf.picard.fastq.FastqReader;
import net.sf.picard.fastq.FastqRecord;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.ReadablePathValidator; | package edu.unc.genomics.converters;
/**
* Converts a FASTQ file with Illumina quality scores (Phred+64) to Sanger
* quality scores (Phred+33)
*
* @author timpalpant
*
*/
public class FastqIlluminaToSanger extends CommandLineTool {
private static final Logger log = Logger.getLogger(FastqIlluminaToSanger.class);
| // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/converters/FastqIlluminaToSanger.java
import java.io.IOException;
import java.io.PrintWriter;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import net.sf.picard.fastq.FastqReader;
import net.sf.picard.fastq.FastqRecord;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.ReadablePathValidator;
package edu.unc.genomics.converters;
/**
* Converts a FASTQ file with Illumina quality scores (Phred+64) to Sanger
* quality scores (Phred+33)
*
* @author timpalpant
*
*/
public class FastqIlluminaToSanger extends CommandLineTool {
private static final Logger log = Logger.getLogger(FastqIlluminaToSanger.class);
| @Parameter(names = { "-i", "--input" }, description = "Input file (FASTQ, Illumina)", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/ngs/FindOutlierRegions.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.IOException;
import java.nio.file.Path;
import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.BedGraphFileWriter;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException; | package edu.unc.genomics.ngs;
/**
* Finds regions of a Wig file that differ significantly from the mean, such as
* CNVs or deletions.
*
* @author timpalpant
*
*/
public class FindOutlierRegions extends CommandLineTool {
private static final Logger log = Logger.getLogger(FindOutlierRegions.class);
| // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/ngs/FindOutlierRegions.java
import java.io.IOException;
import java.nio.file.Path;
import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.BedGraphFileWriter;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
package edu.unc.genomics.ngs;
/**
* Finds regions of a Wig file that differ significantly from the mean, such as
* CNVs or deletions.
*
* @author timpalpant
*
*/
public class FindOutlierRegions extends CommandLineTool {
private static final Logger log = Logger.getLogger(FindOutlierRegions.class);
| @Parameter(names = { "-i", "--input" }, description = "Input file", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/dna/DNAPropertyCalculator.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/utils/Samtools.java
// public class Samtools {
//
// private static final Logger log = Logger.getLogger(Samtools.class);
//
// /**
// * Index a FASTA file with 'samtools faidx'
// *
// * @param p
// * the FASTA file to index
// * @throws Exception
// * if the index is not created successfully
// */
// public static void indexFasta(Path p) throws Exception {
// log.debug("Attempting to generate FASTA index by calling 'samtools faidx'");
//
// try {
// Process proc = new ProcessBuilder("samtools", "faidx", p.toString()).start();
// proc.waitFor();
// } catch (Exception e) {
// log.error("Error attempting to call 'samtools faidx'. Is samtools available in the PATH?");
// } finally {
// if (!IndexedFastaSequenceFile.canCreateIndexedFastaReader(p.toFile())) {
// log.error("Could not create FASTA index for file " + p);
// throw new Exception("Could not create FASTA index for file " + p);
// }
// }
// }
// }
| import java.io.IOException;
import java.nio.file.Path;
import net.sf.picard.reference.FastaSequenceIndex;
import net.sf.picard.reference.FastaSequenceIndexEntry;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.samtools.util.StringUtil;
import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.genomeview.dnaproperties.DNAProperty;
import com.beust.jcommander.Parameter;
import edu.ucsc.genome.TrackHeader;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Contig;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.WigFileWriter;
import edu.unc.utils.Samtools; | package edu.unc.genomics.dna;
/**
* This tool calculates DNA properties from a table lookup and creates a Wig
* file with the property for each position
*
* @author timpalpant
*
*/
public class DNAPropertyCalculator extends CommandLineTool {
private static final Logger log = Logger.getLogger(DNAPropertyCalculator.class);
| // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/utils/Samtools.java
// public class Samtools {
//
// private static final Logger log = Logger.getLogger(Samtools.class);
//
// /**
// * Index a FASTA file with 'samtools faidx'
// *
// * @param p
// * the FASTA file to index
// * @throws Exception
// * if the index is not created successfully
// */
// public static void indexFasta(Path p) throws Exception {
// log.debug("Attempting to generate FASTA index by calling 'samtools faidx'");
//
// try {
// Process proc = new ProcessBuilder("samtools", "faidx", p.toString()).start();
// proc.waitFor();
// } catch (Exception e) {
// log.error("Error attempting to call 'samtools faidx'. Is samtools available in the PATH?");
// } finally {
// if (!IndexedFastaSequenceFile.canCreateIndexedFastaReader(p.toFile())) {
// log.error("Could not create FASTA index for file " + p);
// throw new Exception("Could not create FASTA index for file " + p);
// }
// }
// }
// }
// Path: src/edu/unc/genomics/dna/DNAPropertyCalculator.java
import java.io.IOException;
import java.nio.file.Path;
import net.sf.picard.reference.FastaSequenceIndex;
import net.sf.picard.reference.FastaSequenceIndexEntry;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.samtools.util.StringUtil;
import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.genomeview.dnaproperties.DNAProperty;
import com.beust.jcommander.Parameter;
import edu.ucsc.genome.TrackHeader;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Contig;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.WigFileWriter;
import edu.unc.utils.Samtools;
package edu.unc.genomics.dna;
/**
* This tool calculates DNA properties from a table lookup and creates a Wig
* file with the property for each position
*
* @author timpalpant
*
*/
public class DNAPropertyCalculator extends CommandLineTool {
private static final Logger log = Logger.getLogger(DNAPropertyCalculator.class);
| @Parameter(names = { "-i", "--input" }, description = "Input file (FASTA)", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/ngs/FilterRegions.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.IOException;
import java.nio.file.Path;
import java.util.Iterator;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Contig;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.genomics.io.WigFileWriter; | package edu.unc.genomics.ngs;
/**
* Removes regions of a Wig file
*
* @author timpalpant
*
*/
public class FilterRegions extends CommandLineTool {
private static final Logger log = Logger.getLogger(FilterRegions.class);
| // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/ngs/FilterRegions.java
import java.io.IOException;
import java.nio.file.Path;
import java.util.Iterator;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Contig;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.genomics.io.WigFileWriter;
package edu.unc.genomics.ngs;
/**
* Removes regions of a Wig file
*
* @author timpalpant
*
*/
public class FilterRegions extends CommandLineTool {
private static final Logger log = Logger.getLogger(FilterRegions.class);
| @Parameter(names = { "-i", "--input" }, description = "Input (Big)wig", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/ngs/FilterRegions.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.IOException;
import java.nio.file.Path;
import java.util.Iterator;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Contig;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.genomics.io.WigFileWriter; | int stop = reader.getChrStop(chr);
log.debug("Processing chromosome " + chr + " region " + bp + "-" + stop);
// Process the chromosome in chunks
while (bp < stop) {
int chunkStart = bp;
int chunkStop = Math.min(bp + DEFAULT_CHUNK_SIZE - 1, stop);
Interval chunk = new Interval(chr, chunkStart, chunkStop);
log.debug("Processing chunk " + chunk);
try {
Contig contig = reader.query(chunk);
Iterator<? extends Interval> it = loci.query(contig);
int start = contig.getStart();
// Copy the data up to the excluded point, then skip past the
// excluded point
while (it.hasNext()) {
Interval exclude = it.next();
log.debug("Skipping interval " + exclude);
if (exclude.low() - 1 > start) {
writer.write(contig.copy(start, exclude.low() - 1));
}
start = exclude.high() + 1;
}
// Copy the remaining data, if there is any
if (start <= contig.getStop()) {
writer.write(contig.copy(start, contig.getStop()));
}
} catch (WigFileException e) { | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/ngs/FilterRegions.java
import java.io.IOException;
import java.nio.file.Path;
import java.util.Iterator;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Contig;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.genomics.io.WigFileWriter;
int stop = reader.getChrStop(chr);
log.debug("Processing chromosome " + chr + " region " + bp + "-" + stop);
// Process the chromosome in chunks
while (bp < stop) {
int chunkStart = bp;
int chunkStop = Math.min(bp + DEFAULT_CHUNK_SIZE - 1, stop);
Interval chunk = new Interval(chr, chunkStart, chunkStop);
log.debug("Processing chunk " + chunk);
try {
Contig contig = reader.query(chunk);
Iterator<? extends Interval> it = loci.query(contig);
int start = contig.getStart();
// Copy the data up to the excluded point, then skip past the
// excluded point
while (it.hasNext()) {
Interval exclude = it.next();
log.debug("Skipping interval " + exclude);
if (exclude.low() - 1 > start) {
writer.write(contig.copy(start, exclude.low() - 1));
}
start = exclude.high() + 1;
}
// Copy the remaining data, if there is any
if (start <= contig.getStop()) {
writer.write(contig.copy(start, contig.getStop()));
}
} catch (WigFileException e) { | throw new CommandLineToolException("Wig file error while processing chunk " + chr + ":" + chunkStart + "-" |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/ngs/ReadLengthDistributionMatrix.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.BufferedWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Iterator;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader; | package edu.unc.genomics.ngs;
/**
* Creates a heatmap matrix of sequencing read coverage separated by read length
* See Floer M, et al. (2010) A RSC/nucleosome complex determines chromatin
* architecture and facilitates activator binding. Cell 141: 407-418 for
* examples.
*
* @author timpalpant
*
*/
public class ReadLengthDistributionMatrix extends CommandLineTool {
private static final Logger log = Logger.getLogger(ReadLengthDistributionMatrix.class);
| // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/ngs/ReadLengthDistributionMatrix.java
import java.io.BufferedWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Iterator;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
package edu.unc.genomics.ngs;
/**
* Creates a heatmap matrix of sequencing read coverage separated by read length
* See Floer M, et al. (2010) A RSC/nucleosome complex determines chromatin
* architecture and facilitates activator binding. Cell 141: 407-418 for
* examples.
*
* @author timpalpant
*
*/
public class ReadLengthDistributionMatrix extends CommandLineTool {
private static final Logger log = Logger.getLogger(ReadLengthDistributionMatrix.class);
| @Parameter(names = { "-i", "--input" }, description = "Input file (reads)", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/ngs/Subsample.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.IOException;
import java.nio.file.Path;
import java.util.Random;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
import edu.unc.genomics.io.IntervalFileWriter; | package edu.unc.genomics.ngs;
/**
* Randomly select N reads out of a total of M
*
* @author timpalpant
*
*/
public class Subsample extends CommandLineTool {
private static final Logger log = Logger.getLogger(Subsample.class);
| // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/ngs/Subsample.java
import java.io.IOException;
import java.nio.file.Path;
import java.util.Random;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
import edu.unc.genomics.io.IntervalFileWriter;
package edu.unc.genomics.ngs;
/**
* Randomly select N reads out of a total of M
*
* @author timpalpant
*
*/
public class Subsample extends CommandLineTool {
private static final Logger log = Logger.getLogger(Subsample.class);
| @Parameter(names = { "-i", "--input" }, required = true, description = "Input file", validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/ngs/Subsample.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.IOException;
import java.nio.file.Path;
import java.util.Random;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
import edu.unc.genomics.io.IntervalFileWriter; | package edu.unc.genomics.ngs;
/**
* Randomly select N reads out of a total of M
*
* @author timpalpant
*
*/
public class Subsample extends CommandLineTool {
private static final Logger log = Logger.getLogger(Subsample.class);
@Parameter(names = { "-i", "--input" }, required = true, description = "Input file", validateWith = ReadablePathValidator.class)
public Path input;
@Parameter(names = { "-n", "--select" }, required = true, description = "Number of entries to select")
public int n;
@Parameter(names = { "-o", "--output" }, required = true, description = "Output file")
public Path output;
@Override
public void run() throws IOException {
try (IntervalFileReader<? extends Interval> reader = IntervalFileReader.autodetect(input);
IntervalFileWriter<Interval> writer = new IntervalFileWriter<>(output)) {
int nRemaining = reader.count();
log.info("Input file has " + nRemaining + " entries");
if (n >= reader.count()) { | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/ngs/Subsample.java
import java.io.IOException;
import java.nio.file.Path;
import java.util.Random;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
import edu.unc.genomics.io.IntervalFileWriter;
package edu.unc.genomics.ngs;
/**
* Randomly select N reads out of a total of M
*
* @author timpalpant
*
*/
public class Subsample extends CommandLineTool {
private static final Logger log = Logger.getLogger(Subsample.class);
@Parameter(names = { "-i", "--input" }, required = true, description = "Input file", validateWith = ReadablePathValidator.class)
public Path input;
@Parameter(names = { "-n", "--select" }, required = true, description = "Number of entries to select")
public int n;
@Parameter(names = { "-o", "--output" }, required = true, description = "Output file")
public Path output;
@Override
public void run() throws IOException {
try (IntervalFileReader<? extends Interval> reader = IntervalFileReader.autodetect(input);
IntervalFileWriter<Interval> writer = new IntervalFileWriter<>(output)) {
int nRemaining = reader.count();
log.info("Input file has " + nRemaining + " entries");
if (n >= reader.count()) { | throw new CommandLineToolException("Cannot select " + n + " entries from a file with " + nRemaining); |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/ngs/SplitWigIntervals.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.IOException;
import java.nio.file.Path;
import java.nio.file.Paths;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.Contig;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileWriter;
import edu.unc.genomics.io.WigFileException;
import edu.ucsc.genome.TrackHeader; | package edu.unc.genomics.ngs;
/**
* For each interval, output a new Wig file of data
* @author timpalpant
*
*/
public class SplitWigIntervals extends CommandLineTool {
private static final Logger log = Logger.getLogger(IntervalStats.class);
@Parameter(names = {"-i", "--input"}, description = "Input file (Wig)", | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/ngs/SplitWigIntervals.java
import java.io.IOException;
import java.nio.file.Path;
import java.nio.file.Paths;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.Contig;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileWriter;
import edu.unc.genomics.io.WigFileException;
import edu.ucsc.genome.TrackHeader;
package edu.unc.genomics.ngs;
/**
* For each interval, output a new Wig file of data
* @author timpalpant
*
*/
public class SplitWigIntervals extends CommandLineTool {
private static final Logger log = Logger.getLogger(IntervalStats.class);
@Parameter(names = {"-i", "--input"}, description = "Input file (Wig)", | required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/wigmath/GaussianSmooth.java | // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
| import java.io.IOException;
import java.nio.file.Path;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Contig;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException; | package edu.unc.genomics.wigmath;
/**
* Smooth a Wig file with a Gaussian filter
*
* @author timpalpant
*
*/
public class GaussianSmooth extends WigMathTool {
private static final Logger log = Logger.getLogger(GaussianSmooth.class);
| // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
// Path: src/edu/unc/genomics/wigmath/GaussianSmooth.java
import java.io.IOException;
import java.nio.file.Path;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Contig;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
package edu.unc.genomics.wigmath;
/**
* Smooth a Wig file with a Gaussian filter
*
* @author timpalpant
*
*/
public class GaussianSmooth extends WigMathTool {
private static final Logger log = Logger.getLogger(GaussianSmooth.class);
| @Parameter(names = { "-i", "--input" }, description = "Input file", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/wigmath/Shift.java | // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
| import java.io.IOException;
import java.nio.file.Path;
import java.util.HashMap;
import java.util.Map;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException; | package edu.unc.genomics.wigmath;
/**
* Shift a Wig file to have a specified mean
*
* @author timpalpant
*
*/
public class Shift extends WigMathTool {
private static final Logger log = Logger.getLogger(Shift.class);
| // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
// Path: src/edu/unc/genomics/wigmath/Shift.java
import java.io.IOException;
import java.nio.file.Path;
import java.util.HashMap;
import java.util.Map;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
package edu.unc.genomics.wigmath;
/**
* Shift a Wig file to have a specified mean
*
* @author timpalpant
*
*/
public class Shift extends WigMathTool {
private static final Logger log = Logger.getLogger(Shift.class);
| @Parameter(names = { "-i", "--input" }, description = "Input file", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/ngs/ExtractDataFromRegion.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
| import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.io.WigFileException;
import edu.unc.genomics.io.WigFileReader; | package edu.unc.genomics.ngs;
/**
* Extracts the values from a (Big)Wig file for a given interval
*
* @author timpalpant
*
*/
public class ExtractDataFromRegion extends CommandLineTool {
private static final Logger log = Logger.getLogger(ExtractDataFromRegion.class);
@Parameter(description = "Input files (BigWig/Wig)", required = true)
public List<String> inputFiles = new ArrayList<String>();
@Parameter(names = { "-c", "--chr" }, description = "Chromosome", required = true)
public String chr;
@Parameter(names = { "-s", "--start" }, description = "Start base pair", required = true)
public int start;
@Parameter(names = { "-e", "--stop" }, description = "Stop base pair", required = true)
public int stop;
@Parameter(names = { "-o", "--output" }, description = "Output file (tabular)", required = true)
public Path outputFile;
@Override
public void run() throws IOException {
// Query each wig file and get the data for the region
log.debug("Loading data for region from " + inputFiles.size() + " wig files");
Interval region = new Interval(chr, start, stop);
float[][] data = new float[inputFiles.size()][region.length()];
for (int i = 0; i < inputFiles.size(); i++) {
try (WigFileReader reader = WigFileReader.autodetect(Paths.get(inputFiles.get(i)))) {
data[i] = reader.query(region).getValues();
} catch (WigFileException e) { | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
// Path: src/edu/unc/genomics/ngs/ExtractDataFromRegion.java
import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.io.WigFileException;
import edu.unc.genomics.io.WigFileReader;
package edu.unc.genomics.ngs;
/**
* Extracts the values from a (Big)Wig file for a given interval
*
* @author timpalpant
*
*/
public class ExtractDataFromRegion extends CommandLineTool {
private static final Logger log = Logger.getLogger(ExtractDataFromRegion.class);
@Parameter(description = "Input files (BigWig/Wig)", required = true)
public List<String> inputFiles = new ArrayList<String>();
@Parameter(names = { "-c", "--chr" }, description = "Chromosome", required = true)
public String chr;
@Parameter(names = { "-s", "--start" }, description = "Start base pair", required = true)
public int start;
@Parameter(names = { "-e", "--stop" }, description = "Stop base pair", required = true)
public int stop;
@Parameter(names = { "-o", "--output" }, description = "Output file (tabular)", required = true)
public Path outputFile;
@Override
public void run() throws IOException {
// Query each wig file and get the data for the region
log.debug("Loading data for region from " + inputFiles.size() + " wig files");
Interval region = new Interval(chr, start, stop);
float[][] data = new float[inputFiles.size()][region.length()];
for (int i = 0; i < inputFiles.size(); i++) {
try (WigFileReader reader = WigFileReader.autodetect(Paths.get(inputFiles.get(i)))) {
data[i] = reader.query(region).getValues();
} catch (WigFileException e) { | throw new CommandLineToolException(e); |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/ngs/WaveletTransform.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/utils/ArrayScaler.java
// public class ArrayScaler {
//
// private UnivariateFunction interp;
//
// /**
// * Create a new ArrayScaler
// *
// * @param x
// * the seed array to downsample/upsample
// */
// public ArrayScaler(double[] x) {
// double[] indices = new double[x.length];
// for (int i = 0; i < indices.length; i++) {
// indices[i] = ((double) i) / (x.length - 1);
// }
//
// UnivariateInterpolator interpolator = new SplineInterpolator();
// interp = interpolator.interpolate(indices, x);
// }
//
// /**
// * Interpolate to create a new scaled vector of length l
// *
// * @param l
// * the desired vector length
// * @return a new vector of length l created by interpolating x
// */
// public double[] getScaled(int l) {
// double[] stretched = new double[l];
// for (int i = 0; i < l; i++) {
// stretched[i] = interp.value(((double) i) / l);
// }
// return stretched;
// }
// }
| import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.utils.ArrayScaler; | package edu.unc.genomics.ngs;
/**
* This tool performs a Wavelet scaling analysis on data from a genomic interval
*
* @author timpalpant
*
*/
public class WaveletTransform extends CommandLineTool {
private static final Logger log = Logger.getLogger(WaveletTransform.class);
| // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/utils/ArrayScaler.java
// public class ArrayScaler {
//
// private UnivariateFunction interp;
//
// /**
// * Create a new ArrayScaler
// *
// * @param x
// * the seed array to downsample/upsample
// */
// public ArrayScaler(double[] x) {
// double[] indices = new double[x.length];
// for (int i = 0; i < indices.length; i++) {
// indices[i] = ((double) i) / (x.length - 1);
// }
//
// UnivariateInterpolator interpolator = new SplineInterpolator();
// interp = interpolator.interpolate(indices, x);
// }
//
// /**
// * Interpolate to create a new scaled vector of length l
// *
// * @param l
// * the desired vector length
// * @return a new vector of length l created by interpolating x
// */
// public double[] getScaled(int l) {
// double[] stretched = new double[l];
// for (int i = 0; i < l; i++) {
// stretched[i] = interp.value(((double) i) / l);
// }
// return stretched;
// }
// }
// Path: src/edu/unc/genomics/ngs/WaveletTransform.java
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
import edu.unc.utils.ArrayScaler;
package edu.unc.genomics.ngs;
/**
* This tool performs a Wavelet scaling analysis on data from a genomic interval
*
* @author timpalpant
*
*/
public class WaveletTransform extends CommandLineTool {
private static final Logger log = Logger.getLogger(WaveletTransform.class);
| @Parameter(names = { "-i", "--input" }, description = "Input file (Wig)", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/ngs/IntervalLengthDistribution.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
| import java.io.IOException;
import java.io.PrintWriter;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.math3.stat.Frequency;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader; | package edu.unc.genomics.ngs;
/**
* Generate a histogram of interval lengths, such as read lengths or gene
* lengths
*
* @author timpalpant
*
*/
public class IntervalLengthDistribution extends CommandLineTool {
private static final Logger log = Logger.getLogger(IntervalLengthDistribution.class);
| // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
// Path: src/edu/unc/genomics/ngs/IntervalLengthDistribution.java
import java.io.IOException;
import java.io.PrintWriter;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.math3.stat.Frequency;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.Interval;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.genomics.io.IntervalFileReader;
package edu.unc.genomics.ngs;
/**
* Generate a histogram of interval lengths, such as read lengths or gene
* lengths
*
* @author timpalpant
*
*/
public class IntervalLengthDistribution extends CommandLineTool {
private static final Logger log = Logger.getLogger(IntervalLengthDistribution.class);
| @Parameter(names = { "-i", "--input" }, description = "Interval file", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/converters/RomanNumeralize.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/utils/RomanNumeral.java
// public class RomanNumeral {
//
// final static RomanValue[] ROMAN_VALUE_TABLE = { new RomanValue(1000, "M"), new RomanValue(900, "CM"),
// new RomanValue(500, "D"), new RomanValue(400, "CD"), new RomanValue(100, "C"), new RomanValue(90, "XC"),
// new RomanValue(50, "L"), new RomanValue(40, "XL"), new RomanValue(10, "X"), new RomanValue(9, "IX"),
// new RomanValue(5, "V"), new RomanValue(4, "IV"), new RomanValue(1, "I") };
//
// /**
// * Convert an int to Roman numeral
// *
// * @param n
// * an integer between 1-3999
// * @return n as a Roman numeral
// */
// public static String int2roman(int n) {
// if (n >= 4000 || n < 1) {
// throw new NumberFormatException("Numbers must be in range 1-3999");
// }
//
// // ... Start with largest value, and work toward smallest.
// StringBuilder result = new StringBuilder(10);
// for (RomanValue equiv : ROMAN_VALUE_TABLE) {
// // ... Remove as many of this value as possible (maybe none).
// while (n >= equiv.intVal) {
// n -= equiv.intVal; // Subtract value.
// result.append(equiv.romVal); // Add roman equivalent.
// }
// }
//
// return result.toString();
// }
//
// private static class RomanValue {
// // ... No need to make this fields private because they are
// // used only in this private value class.
// int intVal; // Integer value.
// String romVal; // Equivalent roman numeral.
//
// RomanValue(int dec, String rom) {
// this.intVal = dec;
// this.romVal = rom;
// }
// }
// }
| import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.utils.RomanNumeral; | package edu.unc.genomics.converters;
/**
* Convert instances of "chr12" to "chrXII" in a text file, etc.
*
* @author timpalpant
*
*/
public class RomanNumeralize extends CommandLineTool {
private static final Logger log = Logger.getLogger(RomanNumeralize.class);
| // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/utils/RomanNumeral.java
// public class RomanNumeral {
//
// final static RomanValue[] ROMAN_VALUE_TABLE = { new RomanValue(1000, "M"), new RomanValue(900, "CM"),
// new RomanValue(500, "D"), new RomanValue(400, "CD"), new RomanValue(100, "C"), new RomanValue(90, "XC"),
// new RomanValue(50, "L"), new RomanValue(40, "XL"), new RomanValue(10, "X"), new RomanValue(9, "IX"),
// new RomanValue(5, "V"), new RomanValue(4, "IV"), new RomanValue(1, "I") };
//
// /**
// * Convert an int to Roman numeral
// *
// * @param n
// * an integer between 1-3999
// * @return n as a Roman numeral
// */
// public static String int2roman(int n) {
// if (n >= 4000 || n < 1) {
// throw new NumberFormatException("Numbers must be in range 1-3999");
// }
//
// // ... Start with largest value, and work toward smallest.
// StringBuilder result = new StringBuilder(10);
// for (RomanValue equiv : ROMAN_VALUE_TABLE) {
// // ... Remove as many of this value as possible (maybe none).
// while (n >= equiv.intVal) {
// n -= equiv.intVal; // Subtract value.
// result.append(equiv.romVal); // Add roman equivalent.
// }
// }
//
// return result.toString();
// }
//
// private static class RomanValue {
// // ... No need to make this fields private because they are
// // used only in this private value class.
// int intVal; // Integer value.
// String romVal; // Equivalent roman numeral.
//
// RomanValue(int dec, String rom) {
// this.intVal = dec;
// this.romVal = rom;
// }
// }
// }
// Path: src/edu/unc/genomics/converters/RomanNumeralize.java
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.utils.RomanNumeral;
package edu.unc.genomics.converters;
/**
* Convert instances of "chr12" to "chrXII" in a text file, etc.
*
* @author timpalpant
*
*/
public class RomanNumeralize extends CommandLineTool {
private static final Logger log = Logger.getLogger(RomanNumeralize.class);
| @Parameter(names = { "-i", "--input" }, description = "Input file", required = true, validateWith = ReadablePathValidator.class) |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/converters/RomanNumeralize.java | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/utils/RomanNumeral.java
// public class RomanNumeral {
//
// final static RomanValue[] ROMAN_VALUE_TABLE = { new RomanValue(1000, "M"), new RomanValue(900, "CM"),
// new RomanValue(500, "D"), new RomanValue(400, "CD"), new RomanValue(100, "C"), new RomanValue(90, "XC"),
// new RomanValue(50, "L"), new RomanValue(40, "XL"), new RomanValue(10, "X"), new RomanValue(9, "IX"),
// new RomanValue(5, "V"), new RomanValue(4, "IV"), new RomanValue(1, "I") };
//
// /**
// * Convert an int to Roman numeral
// *
// * @param n
// * an integer between 1-3999
// * @return n as a Roman numeral
// */
// public static String int2roman(int n) {
// if (n >= 4000 || n < 1) {
// throw new NumberFormatException("Numbers must be in range 1-3999");
// }
//
// // ... Start with largest value, and work toward smallest.
// StringBuilder result = new StringBuilder(10);
// for (RomanValue equiv : ROMAN_VALUE_TABLE) {
// // ... Remove as many of this value as possible (maybe none).
// while (n >= equiv.intVal) {
// n -= equiv.intVal; // Subtract value.
// result.append(equiv.romVal); // Add roman equivalent.
// }
// }
//
// return result.toString();
// }
//
// private static class RomanValue {
// // ... No need to make this fields private because they are
// // used only in this private value class.
// int intVal; // Integer value.
// String romVal; // Equivalent roman numeral.
//
// RomanValue(int dec, String rom) {
// this.intVal = dec;
// this.romVal = rom;
// }
// }
// }
| import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.utils.RomanNumeral; | package edu.unc.genomics.converters;
/**
* Convert instances of "chr12" to "chrXII" in a text file, etc.
*
* @author timpalpant
*
*/
public class RomanNumeralize extends CommandLineTool {
private static final Logger log = Logger.getLogger(RomanNumeralize.class);
@Parameter(names = { "-i", "--input" }, description = "Input file", required = true, validateWith = ReadablePathValidator.class)
public Path inputFile;
@Parameter(names = { "-o", "--output" }, description = "Output file", required = true)
public Path outputFile;
/**
* Pattern for finding "chr12" tokens (will find "chr1" through "chr99")
*/
Pattern p = Pattern.compile("chr[\\d]{1,2}");
@Override
public void run() throws IOException {
try (BufferedReader reader = Files.newBufferedReader(inputFile, Charset.defaultCharset());
BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
log.debug("Copying input to output and replacing with Roman Numerals");
String line;
while ((line = reader.readLine()) != null) {
Matcher m = p.matcher(line);
StringBuffer converted = new StringBuffer(line.length());
while (m.find()) {
String chrNum = line.substring(m.start() + 3, m.end());
int arabic = Integer.parseInt(chrNum); | // Path: src/edu/unc/genomics/CommandLineTool.java
// public abstract class CommandLineTool {
//
// /**
// * The default bite-size to use for applications that process files in chunks
// * TODO Read from a configuration file
// */
// public static final int DEFAULT_CHUNK_SIZE = 10_000_000;
//
// /**
// * Do the main computation of this tool
// *
// * @throws IOException
// */
// public abstract void run() throws IOException;
//
// /**
// * Parse command-line arguments and run the tool Exit on parameter exceptions
// *
// * @param args
// */
// public void instanceMain(String[] args) throws CommandLineToolException {
// // Initialize the command-line options parser
// JCommander jc = new JCommander(this);
//
// // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
// jc.addConverterFactory(new PathFactory());
// jc.addConverterFactory(new AssemblyFactory());
//
// // Set the program name to be the class name
// String[] nameParts = getClass().getName().split("\\.");
// String shortName = StringUtils.join(Arrays.copyOfRange(nameParts, nameParts.length - 2, nameParts.length), '.');
// jc.setProgramName(shortName);
//
// try {
// jc.parse(args);
// } catch (ParameterException e) {
// System.err.println(e.getMessage());
// jc.usage();
// System.exit(-1);
// }
//
// ValidationStringency stringency = SAMFileReader.getDefaultValidationStringency();
// try {
// SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
// run();
// } catch (IOException e) {
// throw new CommandLineToolException("IO error while running", e);
// } finally {
// SAMFileReader.setDefaultValidationStringency(stringency);
// }
// }
// }
//
// Path: src/edu/unc/genomics/ReadablePathValidator.java
// public class ReadablePathValidator implements IParameterValidator {
//
// /*
// * (non-Javadoc)
// *
// * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String,
// * java.lang.String)
// */
// @Override
// public void validate(String name, String value) throws ParameterException {
// PathConverter converter = new PathConverter();
// Path p = converter.convert(value);
// if (!Files.isReadable(p)) {
// throw new ParameterException("Parameter " + name + " should be a readable file");
// }
// }
//
// }
//
// Path: src/edu/unc/utils/RomanNumeral.java
// public class RomanNumeral {
//
// final static RomanValue[] ROMAN_VALUE_TABLE = { new RomanValue(1000, "M"), new RomanValue(900, "CM"),
// new RomanValue(500, "D"), new RomanValue(400, "CD"), new RomanValue(100, "C"), new RomanValue(90, "XC"),
// new RomanValue(50, "L"), new RomanValue(40, "XL"), new RomanValue(10, "X"), new RomanValue(9, "IX"),
// new RomanValue(5, "V"), new RomanValue(4, "IV"), new RomanValue(1, "I") };
//
// /**
// * Convert an int to Roman numeral
// *
// * @param n
// * an integer between 1-3999
// * @return n as a Roman numeral
// */
// public static String int2roman(int n) {
// if (n >= 4000 || n < 1) {
// throw new NumberFormatException("Numbers must be in range 1-3999");
// }
//
// // ... Start with largest value, and work toward smallest.
// StringBuilder result = new StringBuilder(10);
// for (RomanValue equiv : ROMAN_VALUE_TABLE) {
// // ... Remove as many of this value as possible (maybe none).
// while (n >= equiv.intVal) {
// n -= equiv.intVal; // Subtract value.
// result.append(equiv.romVal); // Add roman equivalent.
// }
// }
//
// return result.toString();
// }
//
// private static class RomanValue {
// // ... No need to make this fields private because they are
// // used only in this private value class.
// int intVal; // Integer value.
// String romVal; // Equivalent roman numeral.
//
// RomanValue(int dec, String rom) {
// this.intVal = dec;
// this.romVal = rom;
// }
// }
// }
// Path: src/edu/unc/genomics/converters/RomanNumeralize.java
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.utils.RomanNumeral;
package edu.unc.genomics.converters;
/**
* Convert instances of "chr12" to "chrXII" in a text file, etc.
*
* @author timpalpant
*
*/
public class RomanNumeralize extends CommandLineTool {
private static final Logger log = Logger.getLogger(RomanNumeralize.class);
@Parameter(names = { "-i", "--input" }, description = "Input file", required = true, validateWith = ReadablePathValidator.class)
public Path inputFile;
@Parameter(names = { "-o", "--output" }, description = "Output file", required = true)
public Path outputFile;
/**
* Pattern for finding "chr12" tokens (will find "chr1" through "chr99")
*/
Pattern p = Pattern.compile("chr[\\d]{1,2}");
@Override
public void run() throws IOException {
try (BufferedReader reader = Files.newBufferedReader(inputFile, Charset.defaultCharset());
BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
log.debug("Copying input to output and replacing with Roman Numerals");
String line;
while ((line = reader.readLine()) != null) {
Matcher m = p.matcher(line);
StringBuffer converted = new StringBuffer(line.length());
while (m.find()) {
String chrNum = line.substring(m.start() + 3, m.end());
int arabic = Integer.parseInt(chrNum); | String roman = RomanNumeral.int2roman(arabic); |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/wigmath/StandardDeviation.java | // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
| import java.io.IOException;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException; | package edu.unc.genomics.wigmath;
/**
* Calculate base pair by base pair variance for a set of Wig files
*
* @author timpalpant
*
*/
public class StandardDeviation extends WigMathTool {
private static final Logger log = Logger.getLogger(StandardDeviation.class);
@Parameter(description = "Input files", required = true)
public List<String> inputFiles = new ArrayList<String>();
@Override
public void setup() {
if (inputFiles.size() < 2) { | // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
// Path: src/edu/unc/genomics/wigmath/StandardDeviation.java
import java.io.IOException;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
package edu.unc.genomics.wigmath;
/**
* Calculate base pair by base pair variance for a set of Wig files
*
* @author timpalpant
*
*/
public class StandardDeviation extends WigMathTool {
private static final Logger log = Logger.getLogger(StandardDeviation.class);
@Parameter(description = "Input files", required = true)
public List<String> inputFiles = new ArrayList<String>();
@Override
public void setup() {
if (inputFiles.size() < 2) { | throw new CommandLineToolException("Cannot compute variance with < 2 files."); |
timpalpant/java-genomics-toolkit | src/edu/unc/genomics/wigmath/Add.java | // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
| import java.io.IOException;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException; | package edu.unc.genomics.wigmath;
/**
* This tool will add all values in the specified Wig files base pair by base
* pair.
*
* @author timpalpant
*
*/
public class Add extends WigMathTool {
private static final Logger log = Logger.getLogger(Add.class);
@Parameter(description = "Input files", required = true)
public List<String> inputFiles = new ArrayList<String>();
@Override
public void setup() {
if (inputFiles.size() < 2) { | // Path: src/edu/unc/genomics/CommandLineToolException.java
// public class CommandLineToolException extends RuntimeException {
//
// /**
// *
// */
// private static final long serialVersionUID = 4740440799806133636L;
//
// /**
// *
// */
// public CommandLineToolException() {
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// */
// public CommandLineToolException(String message) {
// super(message);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param cause
// */
// public CommandLineToolException(Throwable cause) {
// super(cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// */
// public CommandLineToolException(String message, Throwable cause) {
// super(message, cause);
// // TODO Auto-generated constructor stub
// }
//
// /**
// * @param message
// * @param cause
// * @param enableSuppression
// * @param writableStackTrace
// */
// public CommandLineToolException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
// super(message, cause, enableSuppression, writableStackTrace);
// // TODO Auto-generated constructor stub
// }
//
// }
//
// Path: src/edu/unc/genomics/WigMathTool.java
// public abstract class WigMathTool extends WigAnalysisTool {
//
// private static final Logger log = Logger.getLogger(WigMathTool.class);
//
// @Parameter(names = { "-f", "--fixedstep" }, description = "Force fixedStep output")
// public boolean fixedStep = false;
// @Parameter(names = { "-v", "--variablestep" }, description = "Force variableStep output")
// public boolean variableStep = false;
// @Parameter(names = { "--step" }, description = "Step size for output Wig files")
// public int step = 1;
// @Parameter(names = { "-o", "--output" }, required = true, description = "Output Wig file")
// public Path outputFile;
//
// private WigFileWriter writer;
//
// /**
// * Setup the computation, and add all input Wig files
// */
// protected abstract void setup();
//
// /**
// * Do the computation on a chunk and return the results. Must return
// * chunk.length() values (one for every base pair in chunk)
// *
// * @param chunk
// * the interval to process
// * @return the results of the computation for this chunk
// * @throws IOException
// * @throws WigFileException
// */
// protected abstract float[] compute(Interval chunk) throws IOException, WigFileException;
//
// /**
// * Setup the computation. Should add all input Wig files with addInputFile()
// * during setup
// *
// * @throws IOException
// */
// @Override
// protected final void prepare() {
// // Setup the input files
// setup();
//
// // Setup the output file
// try {
// writer = new WigFileWriter(outputFile, TrackHeader.newWiggle());
// } catch (IOException e) {
// throw new CommandLineToolException("Error initializing output file " + outputFile, e);
// }
// }
//
// /**
// * Shutdown the computation and do any cleanup / final processing
// *
// * @throws IOException
// */
// @Override
// protected final void shutdown() throws IOException {
// writer.close();
// super.shutdown();
// }
//
// @Override
// public final void process(Interval chunk) throws IOException, WigFileException {
// float[] result = compute(chunk);
//
// // Verify that the computation returned the correct number of
// // values for the chunk. It must either be 1 value per base pair,
// // or one value per step (if the script already computed the reduction).
// Contig outputContig = null;
// if (result.length != chunk.length()) {
// int nValues = (int) Math.ceil(((float) chunk.length()) / step);
// if (result.length == nValues) { // already reduced
// // assume values have already been condensed to a certain step
// outputContig = new Contig(chunk, result, step);
// } else {
// log.error("Expected result length=" + chunk.length() + ", got=" + result.length);
// throw new CommandLineToolException("Result of Wig computation is not the expected length!");
// }
// } else { // 1 value per base pair
// outputContig = new Contig(chunk, result);
// if (step != 1) {
// outputContig.setSpan(step);
// }
// }
//
// // Write the result of the computation for this chunk to disk
// if (fixedStep) {
// writer.writeFixedStepContig(outputContig);
// } else if (variableStep) {
// writer.writeVariableStepContig(outputContig);
// } else {
// writer.write(outputContig);
// }
// }
// }
// Path: src/edu/unc/genomics/wigmath/Add.java
import java.io.IOException;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import com.beust.jcommander.Parameter;
import edu.unc.genomics.CommandLineToolException;
import edu.unc.genomics.Interval;
import edu.unc.genomics.WigMathTool;
import edu.unc.genomics.io.WigFileReader;
import edu.unc.genomics.io.WigFileException;
package edu.unc.genomics.wigmath;
/**
* This tool will add all values in the specified Wig files base pair by base
* pair.
*
* @author timpalpant
*
*/
public class Add extends WigMathTool {
private static final Logger log = Logger.getLogger(Add.class);
@Parameter(description = "Input files", required = true)
public List<String> inputFiles = new ArrayList<String>();
@Override
public void setup() {
if (inputFiles.size() < 2) { | throw new CommandLineToolException("No reason to add < 2 files."); |
ocpsoft/prettytime | core/src/test/java/org/ocpsoft/prettytime/PrettyTimeI18n_IT_Test.java | // Path: core/src/main/java/org/ocpsoft/prettytime/units/JustNow.java
// public class JustNow extends ResourcesTimeUnit
// {
//
// public JustNow()
// {
// setMaxQuantity(1000L * 60L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "JustNow";
// }
//
// @Override
// public boolean isPrecise()
// {
// return false;
// }
//
// }
| import static org.junit.Assert.assertEquals;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Locale;
import org.junit.Before;
import org.junit.Test;
import org.ocpsoft.prettytime.units.JustNow; | /*
* Copyright 2012 <a href="mailto:lincolnbaxter@gmail.com">Lincoln Baxter, III</a>
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ocpsoft.prettytime;
public class PrettyTimeI18n_IT_Test
{
private Locale locale;
@Before
public void setUp() throws Exception
{
locale = new Locale("it");
}
private PrettyTime newPrettyTimeWOJustNow(Date ref, Locale locale)
{
PrettyTime t = new PrettyTime(ref, locale);
List<TimeUnit> units = t.getUnits();
List<TimeFormat> formats = new ArrayList<TimeFormat>();
for (TimeUnit timeUnit : units) { | // Path: core/src/main/java/org/ocpsoft/prettytime/units/JustNow.java
// public class JustNow extends ResourcesTimeUnit
// {
//
// public JustNow()
// {
// setMaxQuantity(1000L * 60L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "JustNow";
// }
//
// @Override
// public boolean isPrecise()
// {
// return false;
// }
//
// }
// Path: core/src/test/java/org/ocpsoft/prettytime/PrettyTimeI18n_IT_Test.java
import static org.junit.Assert.assertEquals;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Locale;
import org.junit.Before;
import org.junit.Test;
import org.ocpsoft.prettytime.units.JustNow;
/*
* Copyright 2012 <a href="mailto:lincolnbaxter@gmail.com">Lincoln Baxter, III</a>
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ocpsoft.prettytime;
public class PrettyTimeI18n_IT_Test
{
private Locale locale;
@Before
public void setUp() throws Exception
{
locale = new Locale("it");
}
private PrettyTime newPrettyTimeWOJustNow(Date ref, Locale locale)
{
PrettyTime t = new PrettyTime(ref, locale);
List<TimeUnit> units = t.getUnits();
List<TimeFormat> formats = new ArrayList<TimeFormat>();
for (TimeUnit timeUnit : units) { | if (!(timeUnit instanceof JustNow)) { |
ocpsoft/prettytime | core/src/main/java/org/ocpsoft/prettytime/i18n/Resources_uk.java | // Path: core/src/main/java/org/ocpsoft/prettytime/TimeFormat.java
// public interface TimeFormat
// {
// /**
// * Given a populated {@link Duration} object. Apply formatting (with rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public abstract String format(final Duration duration);
//
// /**
// * Given a populated {@link Duration} object. Apply formatting (without rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public String formatUnrounded(Duration duration);
//
// /**
// * Decorate with past or future prefix/suffix (with rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorate(Duration duration, String time);
//
// /**
// * Decorate with past or future prefix/suffix (without rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorateUnrounded(Duration duration, String time);
//
// }
| import org.ocpsoft.prettytime.Duration;
import org.ocpsoft.prettytime.TimeFormat;
import org.ocpsoft.prettytime.TimeUnit;
import org.ocpsoft.prettytime.impl.TimeFormatProvider;
import org.ocpsoft.prettytime.units.*;
import java.util.ListResourceBundle; | /*
* Copyright 2012 <a href="mailto:lincolnbaxter@gmail.com">Lincoln Baxter, III</a>
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ocpsoft.prettytime.i18n;
/**
* Created with IntelliJ IDEA. User: Tumin Alexander Date: 2012-12-13 Time: 03:33
*
* reedit to Ukrainian with Eclipse). User: Ihor Lavrynuk Date: 2013-01-06 Time: 15:04
*
*/
public class Resources_uk extends ListResourceBundle implements TimeFormatProvider
{
private static final Object[][] OBJECTS = new Object[0][0];
private static final int tolerance = 50;
// see http://translate.sourceforge.net/wiki/l10n/pluralforms
private static final int slavicPluralForms = 3;
| // Path: core/src/main/java/org/ocpsoft/prettytime/TimeFormat.java
// public interface TimeFormat
// {
// /**
// * Given a populated {@link Duration} object. Apply formatting (with rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public abstract String format(final Duration duration);
//
// /**
// * Given a populated {@link Duration} object. Apply formatting (without rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public String formatUnrounded(Duration duration);
//
// /**
// * Decorate with past or future prefix/suffix (with rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorate(Duration duration, String time);
//
// /**
// * Decorate with past or future prefix/suffix (without rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorateUnrounded(Duration duration, String time);
//
// }
// Path: core/src/main/java/org/ocpsoft/prettytime/i18n/Resources_uk.java
import org.ocpsoft.prettytime.Duration;
import org.ocpsoft.prettytime.TimeFormat;
import org.ocpsoft.prettytime.TimeUnit;
import org.ocpsoft.prettytime.impl.TimeFormatProvider;
import org.ocpsoft.prettytime.units.*;
import java.util.ListResourceBundle;
/*
* Copyright 2012 <a href="mailto:lincolnbaxter@gmail.com">Lincoln Baxter, III</a>
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ocpsoft.prettytime.i18n;
/**
* Created with IntelliJ IDEA. User: Tumin Alexander Date: 2012-12-13 Time: 03:33
*
* reedit to Ukrainian with Eclipse). User: Ihor Lavrynuk Date: 2013-01-06 Time: 15:04
*
*/
public class Resources_uk extends ListResourceBundle implements TimeFormatProvider
{
private static final Object[][] OBJECTS = new Object[0][0];
private static final int tolerance = 50;
// see http://translate.sourceforge.net/wiki/l10n/pluralforms
private static final int slavicPluralForms = 3;
| private static class TimeFormatAided implements TimeFormat |
ocpsoft/prettytime | core/src/main/java/org/ocpsoft/prettytime/i18n/Resources_pl.java | // Path: core/src/main/java/org/ocpsoft/prettytime/TimeFormat.java
// public interface TimeFormat
// {
// /**
// * Given a populated {@link Duration} object. Apply formatting (with rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public abstract String format(final Duration duration);
//
// /**
// * Given a populated {@link Duration} object. Apply formatting (without rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public String formatUnrounded(Duration duration);
//
// /**
// * Decorate with past or future prefix/suffix (with rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorate(Duration duration, String time);
//
// /**
// * Decorate with past or future prefix/suffix (without rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorateUnrounded(Duration duration, String time);
//
// }
| import org.ocpsoft.prettytime.Duration;
import org.ocpsoft.prettytime.TimeFormat;
import org.ocpsoft.prettytime.TimeUnit;
import org.ocpsoft.prettytime.impl.TimeFormatProvider;
import org.ocpsoft.prettytime.units.*;
import java.util.ListResourceBundle; | /*
* Copyright 2012 <a href="mailto:lincolnbaxter@gmail.com">Lincoln Baxter, III</a>
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ocpsoft.prettytime.i18n;
public class Resources_pl extends ListResourceBundle implements TimeFormatProvider
{
private static final Object[][] OBJECTS = new Object[0][0];
private static final int tolerance = 50;
// see http://translate.sourceforge.net/wiki/l10n/pluralforms
private static final int polishPluralForms = 3;
| // Path: core/src/main/java/org/ocpsoft/prettytime/TimeFormat.java
// public interface TimeFormat
// {
// /**
// * Given a populated {@link Duration} object. Apply formatting (with rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public abstract String format(final Duration duration);
//
// /**
// * Given a populated {@link Duration} object. Apply formatting (without rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public String formatUnrounded(Duration duration);
//
// /**
// * Decorate with past or future prefix/suffix (with rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorate(Duration duration, String time);
//
// /**
// * Decorate with past or future prefix/suffix (without rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorateUnrounded(Duration duration, String time);
//
// }
// Path: core/src/main/java/org/ocpsoft/prettytime/i18n/Resources_pl.java
import org.ocpsoft.prettytime.Duration;
import org.ocpsoft.prettytime.TimeFormat;
import org.ocpsoft.prettytime.TimeUnit;
import org.ocpsoft.prettytime.impl.TimeFormatProvider;
import org.ocpsoft.prettytime.units.*;
import java.util.ListResourceBundle;
/*
* Copyright 2012 <a href="mailto:lincolnbaxter@gmail.com">Lincoln Baxter, III</a>
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ocpsoft.prettytime.i18n;
public class Resources_pl extends ListResourceBundle implements TimeFormatProvider
{
private static final Object[][] OBJECTS = new Object[0][0];
private static final int tolerance = 50;
// see http://translate.sourceforge.net/wiki/l10n/pluralforms
private static final int polishPluralForms = 3;
| private static class TimeFormatAided implements TimeFormat |
ocpsoft/prettytime | core/src/test/java/org/ocpsoft/prettytime/PrettyTimeI18n_EL_Test.java | // Path: core/src/main/java/org/ocpsoft/prettytime/impl/ResourcesTimeFormat.java
// public class ResourcesTimeFormat extends SimpleTimeFormat
// {
// private final ResourcesTimeUnit unit;
// private TimeFormat override;
// private String overrideResourceBundle; // If used this bundle will override the included bundle
//
// public ResourcesTimeFormat(ResourcesTimeUnit unit)
// {
// this.unit = unit;
// }
//
// public ResourcesTimeFormat(ResourcesTimeUnit unit, String overrideResourceBundle)
// {
// this.unit = unit;
// this.overrideResourceBundle = overrideResourceBundle;
// }
//
// @Override
// public ResourcesTimeFormat setLocale(Locale locale)
// {
// ResourceBundle bundle = null;
// if (overrideResourceBundle != null) {
// try {
// // Attempt to load the bundle that the user passed in, maybe it exists, maybe not
// bundle = ResourceBundle.getBundle(overrideResourceBundle, locale);
// }
// catch (Exception e) {
// // Throw away if the bundle doesn't contain this local
// }
// }
//
// // If the bundle doesn't exist then load the default included one
// if (bundle == null) {
// bundle = ResourceBundle.getBundle(unit.getResourceBundleName(), locale);
// }
//
// if (bundle instanceof TimeFormatProvider) {
// TimeFormat format = ((TimeFormatProvider) bundle).getFormatFor(unit);
// if (format != null) {
// this.override = format;
// }
// }
// else {
// override = null;
// }
//
// if (override == null) {
// setPattern(bundle.getString(unit.getResourceKeyPrefix() + "Pattern"));
// setFuturePrefix(bundle.getString(unit.getResourceKeyPrefix() + "FuturePrefix"));
// setFutureSuffix(bundle.getString(unit.getResourceKeyPrefix() + "FutureSuffix"));
// setPastPrefix(bundle.getString(unit.getResourceKeyPrefix() + "PastPrefix"));
// setPastSuffix(bundle.getString(unit.getResourceKeyPrefix() + "PastSuffix"));
//
// setSingularName(bundle.getString(unit.getResourceKeyPrefix() + "SingularName"));
// setPluralName(bundle.getString(unit.getResourceKeyPrefix() + "PluralName"));
//
// try {
// setFuturePluralName(bundle.getString(unit.getResourceKeyPrefix() + "FuturePluralName"));
// }
// catch (Exception e) {
// }
// try {
// setFutureSingularName((bundle.getString(unit.getResourceKeyPrefix() + "FutureSingularName")));
// }
// catch (Exception e) {
// }
// try {
// setPastPluralName((bundle.getString(unit.getResourceKeyPrefix() + "PastPluralName")));
// }
// catch (Exception e) {
// }
// try {
// setPastSingularName((bundle.getString(unit.getResourceKeyPrefix() + "PastSingularName")));
// }
// catch (Exception e) {
// }
//
// }
//
// return this;
// }
//
// @Override
// public String decorate(Duration duration, String time)
// {
// return override == null ? super.decorate(duration, time) : override.decorate(duration, time);
// }
//
// @Override
// public String decorateUnrounded(Duration duration, String time)
// {
// return override == null ? super.decorateUnrounded(duration, time) : override.decorateUnrounded(duration, time);
// }
//
// @Override
// public String format(Duration duration)
// {
// return override == null ? super.format(duration) : override.format(duration);
// }
//
// @Override
// public String formatUnrounded(Duration duration)
// {
// return override == null ? super.formatUnrounded(duration) : override.formatUnrounded(duration);
// }
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Minute.java
// public class Minute extends ResourcesTimeUnit
// {
//
// public Minute()
// {
// setMillisPerUnit(1000L * 60L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Minute";
// }
//
// }
| import org.junit.After;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.ocpsoft.prettytime.impl.ResourcesTimeFormat;
import org.ocpsoft.prettytime.units.Minute;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.List;
import java.util.Locale; | Assert.assertEquals("1 μήνας Πριν από", t.format(then));
}
@Test
public void testNullDate() throws Exception {
PrettyTime t = new PrettyTime();
final String format = t.format((Date) null);
Assert.assertTrue("πριν από στιγμές".equals(format) || "στιγμές από τώρα".equals(format));
}
@Test
public void testRightNow() throws Exception {
PrettyTime t = new PrettyTime();
Assert.assertEquals("στιγμές από τώρα", t.format(new Date()));
}
@Test
public void testCalculatePreciceDuration() throws Exception {
PrettyTime t = new PrettyTime();
List<Duration> preciseDuration = t.calculatePreciseDuration(
new Date(System.currentTimeMillis() - (2 * 60 * 60 * 1000) - (2 * 60 * 1000)));
Assert.assertEquals("2 ώρες 2 λεπτά Πριν από", t.format(preciseDuration));
Assert.assertEquals("2 ώρες 2 λεπτά", t.formatDuration(preciseDuration));
Assert.assertEquals("στιγμές από τώρα", t.format(t.calculatePreciseDuration(new Date())));
}
@Test
public void testCalculatePreciseDuration2() {
PrettyTime prettyTime = new PrettyTime();
prettyTime.clearUnits(); | // Path: core/src/main/java/org/ocpsoft/prettytime/impl/ResourcesTimeFormat.java
// public class ResourcesTimeFormat extends SimpleTimeFormat
// {
// private final ResourcesTimeUnit unit;
// private TimeFormat override;
// private String overrideResourceBundle; // If used this bundle will override the included bundle
//
// public ResourcesTimeFormat(ResourcesTimeUnit unit)
// {
// this.unit = unit;
// }
//
// public ResourcesTimeFormat(ResourcesTimeUnit unit, String overrideResourceBundle)
// {
// this.unit = unit;
// this.overrideResourceBundle = overrideResourceBundle;
// }
//
// @Override
// public ResourcesTimeFormat setLocale(Locale locale)
// {
// ResourceBundle bundle = null;
// if (overrideResourceBundle != null) {
// try {
// // Attempt to load the bundle that the user passed in, maybe it exists, maybe not
// bundle = ResourceBundle.getBundle(overrideResourceBundle, locale);
// }
// catch (Exception e) {
// // Throw away if the bundle doesn't contain this local
// }
// }
//
// // If the bundle doesn't exist then load the default included one
// if (bundle == null) {
// bundle = ResourceBundle.getBundle(unit.getResourceBundleName(), locale);
// }
//
// if (bundle instanceof TimeFormatProvider) {
// TimeFormat format = ((TimeFormatProvider) bundle).getFormatFor(unit);
// if (format != null) {
// this.override = format;
// }
// }
// else {
// override = null;
// }
//
// if (override == null) {
// setPattern(bundle.getString(unit.getResourceKeyPrefix() + "Pattern"));
// setFuturePrefix(bundle.getString(unit.getResourceKeyPrefix() + "FuturePrefix"));
// setFutureSuffix(bundle.getString(unit.getResourceKeyPrefix() + "FutureSuffix"));
// setPastPrefix(bundle.getString(unit.getResourceKeyPrefix() + "PastPrefix"));
// setPastSuffix(bundle.getString(unit.getResourceKeyPrefix() + "PastSuffix"));
//
// setSingularName(bundle.getString(unit.getResourceKeyPrefix() + "SingularName"));
// setPluralName(bundle.getString(unit.getResourceKeyPrefix() + "PluralName"));
//
// try {
// setFuturePluralName(bundle.getString(unit.getResourceKeyPrefix() + "FuturePluralName"));
// }
// catch (Exception e) {
// }
// try {
// setFutureSingularName((bundle.getString(unit.getResourceKeyPrefix() + "FutureSingularName")));
// }
// catch (Exception e) {
// }
// try {
// setPastPluralName((bundle.getString(unit.getResourceKeyPrefix() + "PastPluralName")));
// }
// catch (Exception e) {
// }
// try {
// setPastSingularName((bundle.getString(unit.getResourceKeyPrefix() + "PastSingularName")));
// }
// catch (Exception e) {
// }
//
// }
//
// return this;
// }
//
// @Override
// public String decorate(Duration duration, String time)
// {
// return override == null ? super.decorate(duration, time) : override.decorate(duration, time);
// }
//
// @Override
// public String decorateUnrounded(Duration duration, String time)
// {
// return override == null ? super.decorateUnrounded(duration, time) : override.decorateUnrounded(duration, time);
// }
//
// @Override
// public String format(Duration duration)
// {
// return override == null ? super.format(duration) : override.format(duration);
// }
//
// @Override
// public String formatUnrounded(Duration duration)
// {
// return override == null ? super.formatUnrounded(duration) : override.formatUnrounded(duration);
// }
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Minute.java
// public class Minute extends ResourcesTimeUnit
// {
//
// public Minute()
// {
// setMillisPerUnit(1000L * 60L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Minute";
// }
//
// }
// Path: core/src/test/java/org/ocpsoft/prettytime/PrettyTimeI18n_EL_Test.java
import org.junit.After;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.ocpsoft.prettytime.impl.ResourcesTimeFormat;
import org.ocpsoft.prettytime.units.Minute;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.List;
import java.util.Locale;
Assert.assertEquals("1 μήνας Πριν από", t.format(then));
}
@Test
public void testNullDate() throws Exception {
PrettyTime t = new PrettyTime();
final String format = t.format((Date) null);
Assert.assertTrue("πριν από στιγμές".equals(format) || "στιγμές από τώρα".equals(format));
}
@Test
public void testRightNow() throws Exception {
PrettyTime t = new PrettyTime();
Assert.assertEquals("στιγμές από τώρα", t.format(new Date()));
}
@Test
public void testCalculatePreciceDuration() throws Exception {
PrettyTime t = new PrettyTime();
List<Duration> preciseDuration = t.calculatePreciseDuration(
new Date(System.currentTimeMillis() - (2 * 60 * 60 * 1000) - (2 * 60 * 1000)));
Assert.assertEquals("2 ώρες 2 λεπτά Πριν από", t.format(preciseDuration));
Assert.assertEquals("2 ώρες 2 λεπτά", t.formatDuration(preciseDuration));
Assert.assertEquals("στιγμές από τώρα", t.format(t.calculatePreciseDuration(new Date())));
}
@Test
public void testCalculatePreciseDuration2() {
PrettyTime prettyTime = new PrettyTime();
prettyTime.clearUnits(); | Minute minutes = new Minute(); |
ocpsoft/prettytime | core/src/test/java/org/ocpsoft/prettytime/PrettyTimeI18n_EL_Test.java | // Path: core/src/main/java/org/ocpsoft/prettytime/impl/ResourcesTimeFormat.java
// public class ResourcesTimeFormat extends SimpleTimeFormat
// {
// private final ResourcesTimeUnit unit;
// private TimeFormat override;
// private String overrideResourceBundle; // If used this bundle will override the included bundle
//
// public ResourcesTimeFormat(ResourcesTimeUnit unit)
// {
// this.unit = unit;
// }
//
// public ResourcesTimeFormat(ResourcesTimeUnit unit, String overrideResourceBundle)
// {
// this.unit = unit;
// this.overrideResourceBundle = overrideResourceBundle;
// }
//
// @Override
// public ResourcesTimeFormat setLocale(Locale locale)
// {
// ResourceBundle bundle = null;
// if (overrideResourceBundle != null) {
// try {
// // Attempt to load the bundle that the user passed in, maybe it exists, maybe not
// bundle = ResourceBundle.getBundle(overrideResourceBundle, locale);
// }
// catch (Exception e) {
// // Throw away if the bundle doesn't contain this local
// }
// }
//
// // If the bundle doesn't exist then load the default included one
// if (bundle == null) {
// bundle = ResourceBundle.getBundle(unit.getResourceBundleName(), locale);
// }
//
// if (bundle instanceof TimeFormatProvider) {
// TimeFormat format = ((TimeFormatProvider) bundle).getFormatFor(unit);
// if (format != null) {
// this.override = format;
// }
// }
// else {
// override = null;
// }
//
// if (override == null) {
// setPattern(bundle.getString(unit.getResourceKeyPrefix() + "Pattern"));
// setFuturePrefix(bundle.getString(unit.getResourceKeyPrefix() + "FuturePrefix"));
// setFutureSuffix(bundle.getString(unit.getResourceKeyPrefix() + "FutureSuffix"));
// setPastPrefix(bundle.getString(unit.getResourceKeyPrefix() + "PastPrefix"));
// setPastSuffix(bundle.getString(unit.getResourceKeyPrefix() + "PastSuffix"));
//
// setSingularName(bundle.getString(unit.getResourceKeyPrefix() + "SingularName"));
// setPluralName(bundle.getString(unit.getResourceKeyPrefix() + "PluralName"));
//
// try {
// setFuturePluralName(bundle.getString(unit.getResourceKeyPrefix() + "FuturePluralName"));
// }
// catch (Exception e) {
// }
// try {
// setFutureSingularName((bundle.getString(unit.getResourceKeyPrefix() + "FutureSingularName")));
// }
// catch (Exception e) {
// }
// try {
// setPastPluralName((bundle.getString(unit.getResourceKeyPrefix() + "PastPluralName")));
// }
// catch (Exception e) {
// }
// try {
// setPastSingularName((bundle.getString(unit.getResourceKeyPrefix() + "PastSingularName")));
// }
// catch (Exception e) {
// }
//
// }
//
// return this;
// }
//
// @Override
// public String decorate(Duration duration, String time)
// {
// return override == null ? super.decorate(duration, time) : override.decorate(duration, time);
// }
//
// @Override
// public String decorateUnrounded(Duration duration, String time)
// {
// return override == null ? super.decorateUnrounded(duration, time) : override.decorateUnrounded(duration, time);
// }
//
// @Override
// public String format(Duration duration)
// {
// return override == null ? super.format(duration) : override.format(duration);
// }
//
// @Override
// public String formatUnrounded(Duration duration)
// {
// return override == null ? super.formatUnrounded(duration) : override.formatUnrounded(duration);
// }
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Minute.java
// public class Minute extends ResourcesTimeUnit
// {
//
// public Minute()
// {
// setMillisPerUnit(1000L * 60L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Minute";
// }
//
// }
| import org.junit.After;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.ocpsoft.prettytime.impl.ResourcesTimeFormat;
import org.ocpsoft.prettytime.units.Minute;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.List;
import java.util.Locale; | }
@Test
public void testNullDate() throws Exception {
PrettyTime t = new PrettyTime();
final String format = t.format((Date) null);
Assert.assertTrue("πριν από στιγμές".equals(format) || "στιγμές από τώρα".equals(format));
}
@Test
public void testRightNow() throws Exception {
PrettyTime t = new PrettyTime();
Assert.assertEquals("στιγμές από τώρα", t.format(new Date()));
}
@Test
public void testCalculatePreciceDuration() throws Exception {
PrettyTime t = new PrettyTime();
List<Duration> preciseDuration = t.calculatePreciseDuration(
new Date(System.currentTimeMillis() - (2 * 60 * 60 * 1000) - (2 * 60 * 1000)));
Assert.assertEquals("2 ώρες 2 λεπτά Πριν από", t.format(preciseDuration));
Assert.assertEquals("2 ώρες 2 λεπτά", t.formatDuration(preciseDuration));
Assert.assertEquals("στιγμές από τώρα", t.format(t.calculatePreciseDuration(new Date())));
}
@Test
public void testCalculatePreciseDuration2() {
PrettyTime prettyTime = new PrettyTime();
prettyTime.clearUnits();
Minute minutes = new Minute(); | // Path: core/src/main/java/org/ocpsoft/prettytime/impl/ResourcesTimeFormat.java
// public class ResourcesTimeFormat extends SimpleTimeFormat
// {
// private final ResourcesTimeUnit unit;
// private TimeFormat override;
// private String overrideResourceBundle; // If used this bundle will override the included bundle
//
// public ResourcesTimeFormat(ResourcesTimeUnit unit)
// {
// this.unit = unit;
// }
//
// public ResourcesTimeFormat(ResourcesTimeUnit unit, String overrideResourceBundle)
// {
// this.unit = unit;
// this.overrideResourceBundle = overrideResourceBundle;
// }
//
// @Override
// public ResourcesTimeFormat setLocale(Locale locale)
// {
// ResourceBundle bundle = null;
// if (overrideResourceBundle != null) {
// try {
// // Attempt to load the bundle that the user passed in, maybe it exists, maybe not
// bundle = ResourceBundle.getBundle(overrideResourceBundle, locale);
// }
// catch (Exception e) {
// // Throw away if the bundle doesn't contain this local
// }
// }
//
// // If the bundle doesn't exist then load the default included one
// if (bundle == null) {
// bundle = ResourceBundle.getBundle(unit.getResourceBundleName(), locale);
// }
//
// if (bundle instanceof TimeFormatProvider) {
// TimeFormat format = ((TimeFormatProvider) bundle).getFormatFor(unit);
// if (format != null) {
// this.override = format;
// }
// }
// else {
// override = null;
// }
//
// if (override == null) {
// setPattern(bundle.getString(unit.getResourceKeyPrefix() + "Pattern"));
// setFuturePrefix(bundle.getString(unit.getResourceKeyPrefix() + "FuturePrefix"));
// setFutureSuffix(bundle.getString(unit.getResourceKeyPrefix() + "FutureSuffix"));
// setPastPrefix(bundle.getString(unit.getResourceKeyPrefix() + "PastPrefix"));
// setPastSuffix(bundle.getString(unit.getResourceKeyPrefix() + "PastSuffix"));
//
// setSingularName(bundle.getString(unit.getResourceKeyPrefix() + "SingularName"));
// setPluralName(bundle.getString(unit.getResourceKeyPrefix() + "PluralName"));
//
// try {
// setFuturePluralName(bundle.getString(unit.getResourceKeyPrefix() + "FuturePluralName"));
// }
// catch (Exception e) {
// }
// try {
// setFutureSingularName((bundle.getString(unit.getResourceKeyPrefix() + "FutureSingularName")));
// }
// catch (Exception e) {
// }
// try {
// setPastPluralName((bundle.getString(unit.getResourceKeyPrefix() + "PastPluralName")));
// }
// catch (Exception e) {
// }
// try {
// setPastSingularName((bundle.getString(unit.getResourceKeyPrefix() + "PastSingularName")));
// }
// catch (Exception e) {
// }
//
// }
//
// return this;
// }
//
// @Override
// public String decorate(Duration duration, String time)
// {
// return override == null ? super.decorate(duration, time) : override.decorate(duration, time);
// }
//
// @Override
// public String decorateUnrounded(Duration duration, String time)
// {
// return override == null ? super.decorateUnrounded(duration, time) : override.decorateUnrounded(duration, time);
// }
//
// @Override
// public String format(Duration duration)
// {
// return override == null ? super.format(duration) : override.format(duration);
// }
//
// @Override
// public String formatUnrounded(Duration duration)
// {
// return override == null ? super.formatUnrounded(duration) : override.formatUnrounded(duration);
// }
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Minute.java
// public class Minute extends ResourcesTimeUnit
// {
//
// public Minute()
// {
// setMillisPerUnit(1000L * 60L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Minute";
// }
//
// }
// Path: core/src/test/java/org/ocpsoft/prettytime/PrettyTimeI18n_EL_Test.java
import org.junit.After;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.ocpsoft.prettytime.impl.ResourcesTimeFormat;
import org.ocpsoft.prettytime.units.Minute;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.List;
import java.util.Locale;
}
@Test
public void testNullDate() throws Exception {
PrettyTime t = new PrettyTime();
final String format = t.format((Date) null);
Assert.assertTrue("πριν από στιγμές".equals(format) || "στιγμές από τώρα".equals(format));
}
@Test
public void testRightNow() throws Exception {
PrettyTime t = new PrettyTime();
Assert.assertEquals("στιγμές από τώρα", t.format(new Date()));
}
@Test
public void testCalculatePreciceDuration() throws Exception {
PrettyTime t = new PrettyTime();
List<Duration> preciseDuration = t.calculatePreciseDuration(
new Date(System.currentTimeMillis() - (2 * 60 * 60 * 1000) - (2 * 60 * 1000)));
Assert.assertEquals("2 ώρες 2 λεπτά Πριν από", t.format(preciseDuration));
Assert.assertEquals("2 ώρες 2 λεπτά", t.formatDuration(preciseDuration));
Assert.assertEquals("στιγμές από τώρα", t.format(t.calculatePreciseDuration(new Date())));
}
@Test
public void testCalculatePreciseDuration2() {
PrettyTime prettyTime = new PrettyTime();
prettyTime.clearUnits();
Minute minutes = new Minute(); | prettyTime.registerUnit(minutes, new ResourcesTimeFormat(minutes)); |
ocpsoft/prettytime | nlp/src/main/java/org/ocpsoft/prettytime/nlp/PrettyTimeParser.java | // Path: nlp/src/main/java/org/ocpsoft/prettytime/nlp/parse/DateGroup.java
// public interface DateGroup
// {
// /**
// * Get the line in which this {@link DateGroup} was found.
// */
// int getLine();
//
// /**
// * Get the text fragment parsed into this {@link DateGroup}.
// */
// String getText();
//
// /**
// * Get the {@link Date} to which this {@link DateGroup} recurs.
// */
// Date getRecursUntil();
//
// /**
// * Get the starting position of this {@link DateGroup} in the language text.
// */
// int getPosition();
//
// /**
// * Get all {@link Date} instances parsed from the language text.
// */
// List<Date> getDates();
//
// /**
// * Return <code>true</code> if this {@link DateGroup} is a recurring event.
// */
// boolean isRecurring();
//
// /**
// * If this {@link DateGroup} is recurring, return the interval in milliseconds with which this {@link DateGroup}
// * recurs, otherwise return -1;
// */
// long getRecurInterval();
// }
| import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.TimeZone;
import org.ocpsoft.prettytime.nlp.parse.DateGroup;
import com.joestelmach.natty.Parser; | else if (number < 100)
{
int unit = number % 10;
key = tensNames[number / 10] + numNames[unit];
}
else
{
int unit = number % 10;
int ten = number % 100 - unit;
int hundred = (number - ten) / 100;
if (hundred < 20)
key = numNames[hundred] + " hundred";
else
key = tensNames[hundred / 10] + numNames[hundred % 10] + " hundred";
if (ten + unit < 20 && ten + unit > 10)
key += numNames[ten + unit];
else
key += tensNames[ten / 10] + numNames[unit];
}
return key.trim();
}
/**
* Parse the given language and return a {@link List} with all discovered {@link Date} instances.
*/
public List<Date> parse(String language)
{
language = words2numbers(language);
List<Date> result = new ArrayList<Date>(); | // Path: nlp/src/main/java/org/ocpsoft/prettytime/nlp/parse/DateGroup.java
// public interface DateGroup
// {
// /**
// * Get the line in which this {@link DateGroup} was found.
// */
// int getLine();
//
// /**
// * Get the text fragment parsed into this {@link DateGroup}.
// */
// String getText();
//
// /**
// * Get the {@link Date} to which this {@link DateGroup} recurs.
// */
// Date getRecursUntil();
//
// /**
// * Get the starting position of this {@link DateGroup} in the language text.
// */
// int getPosition();
//
// /**
// * Get all {@link Date} instances parsed from the language text.
// */
// List<Date> getDates();
//
// /**
// * Return <code>true</code> if this {@link DateGroup} is a recurring event.
// */
// boolean isRecurring();
//
// /**
// * If this {@link DateGroup} is recurring, return the interval in milliseconds with which this {@link DateGroup}
// * recurs, otherwise return -1;
// */
// long getRecurInterval();
// }
// Path: nlp/src/main/java/org/ocpsoft/prettytime/nlp/PrettyTimeParser.java
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.TimeZone;
import org.ocpsoft.prettytime.nlp.parse.DateGroup;
import com.joestelmach.natty.Parser;
else if (number < 100)
{
int unit = number % 10;
key = tensNames[number / 10] + numNames[unit];
}
else
{
int unit = number % 10;
int ten = number % 100 - unit;
int hundred = (number - ten) / 100;
if (hundred < 20)
key = numNames[hundred] + " hundred";
else
key = tensNames[hundred / 10] + numNames[hundred % 10] + " hundred";
if (ten + unit < 20 && ten + unit > 10)
key += numNames[ten + unit];
else
key += tensNames[ten / 10] + numNames[unit];
}
return key.trim();
}
/**
* Parse the given language and return a {@link List} with all discovered {@link Date} instances.
*/
public List<Date> parse(String language)
{
language = words2numbers(language);
List<Date> result = new ArrayList<Date>(); | List<com.joestelmach.natty.DateGroup> groups = parser.parse(language); |
ocpsoft/prettytime | core/src/main/java/org/ocpsoft/prettytime/i18n/Resources_ja.java | // Path: core/src/main/java/org/ocpsoft/prettytime/TimeFormat.java
// public interface TimeFormat
// {
// /**
// * Given a populated {@link Duration} object. Apply formatting (with rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public abstract String format(final Duration duration);
//
// /**
// * Given a populated {@link Duration} object. Apply formatting (without rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public String formatUnrounded(Duration duration);
//
// /**
// * Decorate with past or future prefix/suffix (with rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorate(Duration duration, String time);
//
// /**
// * Decorate with past or future prefix/suffix (without rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorateUnrounded(Duration duration, String time);
//
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Decade.java
// public class Decade extends ResourcesTimeUnit
// {
//
// public Decade()
// {
// setMillisPerUnit(315569259747L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Decade";
// }
//
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Millennium.java
// public class Millennium extends ResourcesTimeUnit
// {
//
// public Millennium()
// {
// setMillisPerUnit(31556926000000L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Millennium";
// }
//
// }
| import java.util.ListResourceBundle;
import java.util.Map;
import java.util.ResourceBundle;
import java.util.concurrent.ConcurrentHashMap;
import org.ocpsoft.prettytime.Duration;
import org.ocpsoft.prettytime.TimeFormat;
import org.ocpsoft.prettytime.TimeUnit;
import org.ocpsoft.prettytime.impl.TimeFormatProvider;
import org.ocpsoft.prettytime.units.Decade;
import org.ocpsoft.prettytime.units.Millennium; | { "SecondSingularName", "秒" },
{ "SecondPluralName", "秒" },
{ "WeekPattern", "%n%u" },
{ "WeekFuturePrefix", "今から" },
{ "WeekFutureSuffix", "後" },
{ "WeekPastPrefix", "" },
{ "WeekPastSuffix", "前" },
{ "WeekSingularName", "週間" },
{ "WeekPluralName", "週間" },
{ "YearPattern", "%n%u" },
{ "YearFuturePrefix", "今から" },
{ "YearFutureSuffix", "後" },
{ "YearPastPrefix", "" },
{ "YearPastSuffix", "前" },
{ "YearSingularName", "年" },
{ "YearPluralName", "年" },
{ "AbstractTimeUnitPattern", "" },
{ "AbstractTimeUnitFuturePrefix", "" },
{ "AbstractTimeUnitFutureSuffix", "" },
{ "AbstractTimeUnitPastPrefix", "" },
{ "AbstractTimeUnitPastSuffix", "" },
{ "AbstractTimeUnitSingularName", "" },
{ "AbstractTimeUnitPluralName", "" } };
@Override
public Object[][] getContents()
{
return OBJECTS;
}
| // Path: core/src/main/java/org/ocpsoft/prettytime/TimeFormat.java
// public interface TimeFormat
// {
// /**
// * Given a populated {@link Duration} object. Apply formatting (with rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public abstract String format(final Duration duration);
//
// /**
// * Given a populated {@link Duration} object. Apply formatting (without rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public String formatUnrounded(Duration duration);
//
// /**
// * Decorate with past or future prefix/suffix (with rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorate(Duration duration, String time);
//
// /**
// * Decorate with past or future prefix/suffix (without rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorateUnrounded(Duration duration, String time);
//
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Decade.java
// public class Decade extends ResourcesTimeUnit
// {
//
// public Decade()
// {
// setMillisPerUnit(315569259747L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Decade";
// }
//
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Millennium.java
// public class Millennium extends ResourcesTimeUnit
// {
//
// public Millennium()
// {
// setMillisPerUnit(31556926000000L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Millennium";
// }
//
// }
// Path: core/src/main/java/org/ocpsoft/prettytime/i18n/Resources_ja.java
import java.util.ListResourceBundle;
import java.util.Map;
import java.util.ResourceBundle;
import java.util.concurrent.ConcurrentHashMap;
import org.ocpsoft.prettytime.Duration;
import org.ocpsoft.prettytime.TimeFormat;
import org.ocpsoft.prettytime.TimeUnit;
import org.ocpsoft.prettytime.impl.TimeFormatProvider;
import org.ocpsoft.prettytime.units.Decade;
import org.ocpsoft.prettytime.units.Millennium;
{ "SecondSingularName", "秒" },
{ "SecondPluralName", "秒" },
{ "WeekPattern", "%n%u" },
{ "WeekFuturePrefix", "今から" },
{ "WeekFutureSuffix", "後" },
{ "WeekPastPrefix", "" },
{ "WeekPastSuffix", "前" },
{ "WeekSingularName", "週間" },
{ "WeekPluralName", "週間" },
{ "YearPattern", "%n%u" },
{ "YearFuturePrefix", "今から" },
{ "YearFutureSuffix", "後" },
{ "YearPastPrefix", "" },
{ "YearPastSuffix", "前" },
{ "YearSingularName", "年" },
{ "YearPluralName", "年" },
{ "AbstractTimeUnitPattern", "" },
{ "AbstractTimeUnitFuturePrefix", "" },
{ "AbstractTimeUnitFutureSuffix", "" },
{ "AbstractTimeUnitPastPrefix", "" },
{ "AbstractTimeUnitPastSuffix", "" },
{ "AbstractTimeUnitSingularName", "" },
{ "AbstractTimeUnitPluralName", "" } };
@Override
public Object[][] getContents()
{
return OBJECTS;
}
| private final Map<TimeUnit, TimeFormat> formatMap = new ConcurrentHashMap<>(); |
ocpsoft/prettytime | core/src/main/java/org/ocpsoft/prettytime/i18n/Resources_ja.java | // Path: core/src/main/java/org/ocpsoft/prettytime/TimeFormat.java
// public interface TimeFormat
// {
// /**
// * Given a populated {@link Duration} object. Apply formatting (with rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public abstract String format(final Duration duration);
//
// /**
// * Given a populated {@link Duration} object. Apply formatting (without rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public String formatUnrounded(Duration duration);
//
// /**
// * Decorate with past or future prefix/suffix (with rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorate(Duration duration, String time);
//
// /**
// * Decorate with past or future prefix/suffix (without rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorateUnrounded(Duration duration, String time);
//
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Decade.java
// public class Decade extends ResourcesTimeUnit
// {
//
// public Decade()
// {
// setMillisPerUnit(315569259747L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Decade";
// }
//
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Millennium.java
// public class Millennium extends ResourcesTimeUnit
// {
//
// public Millennium()
// {
// setMillisPerUnit(31556926000000L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Millennium";
// }
//
// }
| import java.util.ListResourceBundle;
import java.util.Map;
import java.util.ResourceBundle;
import java.util.concurrent.ConcurrentHashMap;
import org.ocpsoft.prettytime.Duration;
import org.ocpsoft.prettytime.TimeFormat;
import org.ocpsoft.prettytime.TimeUnit;
import org.ocpsoft.prettytime.impl.TimeFormatProvider;
import org.ocpsoft.prettytime.units.Decade;
import org.ocpsoft.prettytime.units.Millennium; | }
try {
setPastSingularName((bundle.getString(getUnitName(unit) + "PastSingularName")));
}
catch (Exception e) {
}
}
private String getUnitName(TimeUnit unit)
{
return unit.getClass().getSimpleName();
}
@Override
public String format(final Duration duration)
{
return format(duration, true);
}
@Override
public String formatUnrounded(Duration duration)
{
return format(duration, false);
}
private String format(final Duration duration, final boolean round)
{
String sign = getSign(duration);
String unit = getGramaticallyCorrectName(duration, round);
long quantity = getQuantity(duration, round); | // Path: core/src/main/java/org/ocpsoft/prettytime/TimeFormat.java
// public interface TimeFormat
// {
// /**
// * Given a populated {@link Duration} object. Apply formatting (with rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public abstract String format(final Duration duration);
//
// /**
// * Given a populated {@link Duration} object. Apply formatting (without rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public String formatUnrounded(Duration duration);
//
// /**
// * Decorate with past or future prefix/suffix (with rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorate(Duration duration, String time);
//
// /**
// * Decorate with past or future prefix/suffix (without rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorateUnrounded(Duration duration, String time);
//
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Decade.java
// public class Decade extends ResourcesTimeUnit
// {
//
// public Decade()
// {
// setMillisPerUnit(315569259747L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Decade";
// }
//
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Millennium.java
// public class Millennium extends ResourcesTimeUnit
// {
//
// public Millennium()
// {
// setMillisPerUnit(31556926000000L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Millennium";
// }
//
// }
// Path: core/src/main/java/org/ocpsoft/prettytime/i18n/Resources_ja.java
import java.util.ListResourceBundle;
import java.util.Map;
import java.util.ResourceBundle;
import java.util.concurrent.ConcurrentHashMap;
import org.ocpsoft.prettytime.Duration;
import org.ocpsoft.prettytime.TimeFormat;
import org.ocpsoft.prettytime.TimeUnit;
import org.ocpsoft.prettytime.impl.TimeFormatProvider;
import org.ocpsoft.prettytime.units.Decade;
import org.ocpsoft.prettytime.units.Millennium;
}
try {
setPastSingularName((bundle.getString(getUnitName(unit) + "PastSingularName")));
}
catch (Exception e) {
}
}
private String getUnitName(TimeUnit unit)
{
return unit.getClass().getSimpleName();
}
@Override
public String format(final Duration duration)
{
return format(duration, true);
}
@Override
public String formatUnrounded(Duration duration)
{
return format(duration, false);
}
private String format(final Duration duration, final boolean round)
{
String sign = getSign(duration);
String unit = getGramaticallyCorrectName(duration, round);
long quantity = getQuantity(duration, round); | if (duration.getUnit() instanceof Decade) |
ocpsoft/prettytime | core/src/main/java/org/ocpsoft/prettytime/i18n/Resources_ja.java | // Path: core/src/main/java/org/ocpsoft/prettytime/TimeFormat.java
// public interface TimeFormat
// {
// /**
// * Given a populated {@link Duration} object. Apply formatting (with rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public abstract String format(final Duration duration);
//
// /**
// * Given a populated {@link Duration} object. Apply formatting (without rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public String formatUnrounded(Duration duration);
//
// /**
// * Decorate with past or future prefix/suffix (with rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorate(Duration duration, String time);
//
// /**
// * Decorate with past or future prefix/suffix (without rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorateUnrounded(Duration duration, String time);
//
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Decade.java
// public class Decade extends ResourcesTimeUnit
// {
//
// public Decade()
// {
// setMillisPerUnit(315569259747L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Decade";
// }
//
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Millennium.java
// public class Millennium extends ResourcesTimeUnit
// {
//
// public Millennium()
// {
// setMillisPerUnit(31556926000000L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Millennium";
// }
//
// }
| import java.util.ListResourceBundle;
import java.util.Map;
import java.util.ResourceBundle;
import java.util.concurrent.ConcurrentHashMap;
import org.ocpsoft.prettytime.Duration;
import org.ocpsoft.prettytime.TimeFormat;
import org.ocpsoft.prettytime.TimeUnit;
import org.ocpsoft.prettytime.impl.TimeFormatProvider;
import org.ocpsoft.prettytime.units.Decade;
import org.ocpsoft.prettytime.units.Millennium; | setPastSingularName((bundle.getString(getUnitName(unit) + "PastSingularName")));
}
catch (Exception e) {
}
}
private String getUnitName(TimeUnit unit)
{
return unit.getClass().getSimpleName();
}
@Override
public String format(final Duration duration)
{
return format(duration, true);
}
@Override
public String formatUnrounded(Duration duration)
{
return format(duration, false);
}
private String format(final Duration duration, final boolean round)
{
String sign = getSign(duration);
String unit = getGramaticallyCorrectName(duration, round);
long quantity = getQuantity(duration, round);
if (duration.getUnit() instanceof Decade)
quantity *= 10; | // Path: core/src/main/java/org/ocpsoft/prettytime/TimeFormat.java
// public interface TimeFormat
// {
// /**
// * Given a populated {@link Duration} object. Apply formatting (with rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public abstract String format(final Duration duration);
//
// /**
// * Given a populated {@link Duration} object. Apply formatting (without rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public String formatUnrounded(Duration duration);
//
// /**
// * Decorate with past or future prefix/suffix (with rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorate(Duration duration, String time);
//
// /**
// * Decorate with past or future prefix/suffix (without rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorateUnrounded(Duration duration, String time);
//
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Decade.java
// public class Decade extends ResourcesTimeUnit
// {
//
// public Decade()
// {
// setMillisPerUnit(315569259747L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Decade";
// }
//
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Millennium.java
// public class Millennium extends ResourcesTimeUnit
// {
//
// public Millennium()
// {
// setMillisPerUnit(31556926000000L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Millennium";
// }
//
// }
// Path: core/src/main/java/org/ocpsoft/prettytime/i18n/Resources_ja.java
import java.util.ListResourceBundle;
import java.util.Map;
import java.util.ResourceBundle;
import java.util.concurrent.ConcurrentHashMap;
import org.ocpsoft.prettytime.Duration;
import org.ocpsoft.prettytime.TimeFormat;
import org.ocpsoft.prettytime.TimeUnit;
import org.ocpsoft.prettytime.impl.TimeFormatProvider;
import org.ocpsoft.prettytime.units.Decade;
import org.ocpsoft.prettytime.units.Millennium;
setPastSingularName((bundle.getString(getUnitName(unit) + "PastSingularName")));
}
catch (Exception e) {
}
}
private String getUnitName(TimeUnit unit)
{
return unit.getClass().getSimpleName();
}
@Override
public String format(final Duration duration)
{
return format(duration, true);
}
@Override
public String formatUnrounded(Duration duration)
{
return format(duration, false);
}
private String format(final Duration duration, final boolean round)
{
String sign = getSign(duration);
String unit = getGramaticallyCorrectName(duration, round);
long quantity = getQuantity(duration, round);
if (duration.getUnit() instanceof Decade)
quantity *= 10; | if (duration.getUnit() instanceof Millennium) |
ocpsoft/prettytime | core/src/test/java/org/ocpsoft/prettytime/PrettyTimeAPIManipulationTest.java | // Path: core/src/main/java/org/ocpsoft/prettytime/units/JustNow.java
// public class JustNow extends ResourcesTimeUnit
// {
//
// public JustNow()
// {
// setMaxQuantity(1000L * 60L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "JustNow";
// }
//
// @Override
// public boolean isPrecise()
// {
// return false;
// }
//
// }
| import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import java.time.Instant;
import java.time.LocalDate;
import java.time.LocalDateTime;
import java.time.OffsetDateTime;
import java.time.ZonedDateTime;
import java.util.Calendar;
import java.util.Date;
import java.util.List;
import org.junit.Assert;
import org.junit.Test;
import org.ocpsoft.prettytime.units.JustNow; | t.toString();
}
@Test
public void testApiMisuse16() throws Exception
{
Assert.assertNull(t.removeUnit((Class<TimeUnit>) null));
}
@Test
public void testApiMisuse17() throws Exception
{
Assert.assertNull(t.removeUnit((TimeUnit) null));
}
@Test
public void testApiMisuse18() throws Exception
{
Assert.assertNull(t.getUnit(null));
}
@Test
public void testApiMisuse19() throws Exception
{
Assert.assertNull(t.getUnit((Class<TimeUnit>) null));
}
@Test
public void testGetUnit()
{ | // Path: core/src/main/java/org/ocpsoft/prettytime/units/JustNow.java
// public class JustNow extends ResourcesTimeUnit
// {
//
// public JustNow()
// {
// setMaxQuantity(1000L * 60L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "JustNow";
// }
//
// @Override
// public boolean isPrecise()
// {
// return false;
// }
//
// }
// Path: core/src/test/java/org/ocpsoft/prettytime/PrettyTimeAPIManipulationTest.java
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import java.time.Instant;
import java.time.LocalDate;
import java.time.LocalDateTime;
import java.time.OffsetDateTime;
import java.time.ZonedDateTime;
import java.util.Calendar;
import java.util.Date;
import java.util.List;
import org.junit.Assert;
import org.junit.Test;
import org.ocpsoft.prettytime.units.JustNow;
t.toString();
}
@Test
public void testApiMisuse16() throws Exception
{
Assert.assertNull(t.removeUnit((Class<TimeUnit>) null));
}
@Test
public void testApiMisuse17() throws Exception
{
Assert.assertNull(t.removeUnit((TimeUnit) null));
}
@Test
public void testApiMisuse18() throws Exception
{
Assert.assertNull(t.getUnit(null));
}
@Test
public void testApiMisuse19() throws Exception
{
Assert.assertNull(t.getUnit((Class<TimeUnit>) null));
}
@Test
public void testGetUnit()
{ | JustNow unit = t.getUnit(JustNow.class); |
ocpsoft/prettytime | core/src/test/java/org/ocpsoft/prettytime/PrettyTimeI18n_SK_Test.java | // Path: core/src/main/java/org/ocpsoft/prettytime/units/JustNow.java
// public class JustNow extends ResourcesTimeUnit
// {
//
// public JustNow()
// {
// setMaxQuantity(1000L * 60L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "JustNow";
// }
//
// @Override
// public boolean isPrecise()
// {
// return false;
// }
//
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Month.java
// public class Month extends ResourcesTimeUnit
// {
//
// public Month()
// {
// setMillisPerUnit(2629743830L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Month";
// }
//
// }
| import static org.junit.Assert.assertEquals;
import java.text.SimpleDateFormat;
import java.util.Calendar;
import java.util.Date;
import java.util.List;
import java.util.Locale;
import org.junit.AfterClass;
import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
import org.ocpsoft.prettytime.units.JustNow;
import org.ocpsoft.prettytime.units.Month; |
@Test
public void testCeilingInterval() throws Exception
{
Date then = format.parse("5/20/2009");
Date ref = format.parse("6/17/2009");
PrettyTime t = new PrettyTime(ref);
assertEquals("pred 1 mesiacom", t.format(then));
}
@Test
public void testRightNow() throws Exception
{
PrettyTime t = new PrettyTime();
assertEquals("o chvíľu", t.format(new Date()));
}
@Test
public void testRightNowVariance() throws Exception
{
PrettyTime t = new PrettyTime(new Date(0));
assertEquals("o chvíľu", t.format(new Date(600)));
}
@Test
public void testMinutesFromNow() throws Exception
{
PrettyTime t = new PrettyTime(new Date(0));
for (TimeUnit u : t.getUnits())
{ | // Path: core/src/main/java/org/ocpsoft/prettytime/units/JustNow.java
// public class JustNow extends ResourcesTimeUnit
// {
//
// public JustNow()
// {
// setMaxQuantity(1000L * 60L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "JustNow";
// }
//
// @Override
// public boolean isPrecise()
// {
// return false;
// }
//
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Month.java
// public class Month extends ResourcesTimeUnit
// {
//
// public Month()
// {
// setMillisPerUnit(2629743830L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Month";
// }
//
// }
// Path: core/src/test/java/org/ocpsoft/prettytime/PrettyTimeI18n_SK_Test.java
import static org.junit.Assert.assertEquals;
import java.text.SimpleDateFormat;
import java.util.Calendar;
import java.util.Date;
import java.util.List;
import java.util.Locale;
import org.junit.AfterClass;
import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
import org.ocpsoft.prettytime.units.JustNow;
import org.ocpsoft.prettytime.units.Month;
@Test
public void testCeilingInterval() throws Exception
{
Date then = format.parse("5/20/2009");
Date ref = format.parse("6/17/2009");
PrettyTime t = new PrettyTime(ref);
assertEquals("pred 1 mesiacom", t.format(then));
}
@Test
public void testRightNow() throws Exception
{
PrettyTime t = new PrettyTime();
assertEquals("o chvíľu", t.format(new Date()));
}
@Test
public void testRightNowVariance() throws Exception
{
PrettyTime t = new PrettyTime(new Date(0));
assertEquals("o chvíľu", t.format(new Date(600)));
}
@Test
public void testMinutesFromNow() throws Exception
{
PrettyTime t = new PrettyTime(new Date(0));
for (TimeUnit u : t.getUnits())
{ | if (u instanceof JustNow) |
ocpsoft/prettytime | core/src/test/java/org/ocpsoft/prettytime/PrettyTimeI18n_SK_Test.java | // Path: core/src/main/java/org/ocpsoft/prettytime/units/JustNow.java
// public class JustNow extends ResourcesTimeUnit
// {
//
// public JustNow()
// {
// setMaxQuantity(1000L * 60L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "JustNow";
// }
//
// @Override
// public boolean isPrecise()
// {
// return false;
// }
//
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Month.java
// public class Month extends ResourcesTimeUnit
// {
//
// public Month()
// {
// setMillisPerUnit(2629743830L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Month";
// }
//
// }
| import static org.junit.Assert.assertEquals;
import java.text.SimpleDateFormat;
import java.util.Calendar;
import java.util.Date;
import java.util.List;
import java.util.Locale;
import org.junit.AfterClass;
import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
import org.ocpsoft.prettytime.units.JustNow;
import org.ocpsoft.prettytime.units.Month; | assertEquals("o 1 minútu", t.format(new Date(1000 * 60 * 1)));
assertEquals("o 3 minúty", t.format(new Date(1000 * 60 * 3)));
assertEquals("o 12 minút", t.format(new Date(1000 * 60 * 12)));
}
@Test
public void testHoursFromNow() throws Exception
{
PrettyTime t = new PrettyTime(new Date(0));
assertEquals("o 1 hodinu", t.format(new Date(1000 * 60 * 60 * 1)));
assertEquals("o 3 hodiny", t.format(new Date(1000 * 60 * 60 * 3)));
assertEquals("o 10 hodín", t.format(new Date(1000 * 60 * 60 * 10)));
}
@Test
public void testDaysFromNow() throws Exception
{
PrettyTime t = new PrettyTime(new Date(0));
assertEquals("o 1 deň", t.format(new Date(1000 * 60 * 60 * 24 * 1)));
assertEquals("o 3 dni", t.format(new Date(1000 * 60 * 60 * 24 * 3)));
assertEquals("o 5 dní", t.format(new Date(1000 * 60 * 60 * 24 * 5)));
}
@Test
public void testWeeksFromNow() throws Exception
{
PrettyTime t = new PrettyTime(new Date(0));
for (TimeUnit u : t.getUnits())
{ | // Path: core/src/main/java/org/ocpsoft/prettytime/units/JustNow.java
// public class JustNow extends ResourcesTimeUnit
// {
//
// public JustNow()
// {
// setMaxQuantity(1000L * 60L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "JustNow";
// }
//
// @Override
// public boolean isPrecise()
// {
// return false;
// }
//
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Month.java
// public class Month extends ResourcesTimeUnit
// {
//
// public Month()
// {
// setMillisPerUnit(2629743830L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Month";
// }
//
// }
// Path: core/src/test/java/org/ocpsoft/prettytime/PrettyTimeI18n_SK_Test.java
import static org.junit.Assert.assertEquals;
import java.text.SimpleDateFormat;
import java.util.Calendar;
import java.util.Date;
import java.util.List;
import java.util.Locale;
import org.junit.AfterClass;
import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
import org.ocpsoft.prettytime.units.JustNow;
import org.ocpsoft.prettytime.units.Month;
assertEquals("o 1 minútu", t.format(new Date(1000 * 60 * 1)));
assertEquals("o 3 minúty", t.format(new Date(1000 * 60 * 3)));
assertEquals("o 12 minút", t.format(new Date(1000 * 60 * 12)));
}
@Test
public void testHoursFromNow() throws Exception
{
PrettyTime t = new PrettyTime(new Date(0));
assertEquals("o 1 hodinu", t.format(new Date(1000 * 60 * 60 * 1)));
assertEquals("o 3 hodiny", t.format(new Date(1000 * 60 * 60 * 3)));
assertEquals("o 10 hodín", t.format(new Date(1000 * 60 * 60 * 10)));
}
@Test
public void testDaysFromNow() throws Exception
{
PrettyTime t = new PrettyTime(new Date(0));
assertEquals("o 1 deň", t.format(new Date(1000 * 60 * 60 * 24 * 1)));
assertEquals("o 3 dni", t.format(new Date(1000 * 60 * 60 * 24 * 3)));
assertEquals("o 5 dní", t.format(new Date(1000 * 60 * 60 * 24 * 5)));
}
@Test
public void testWeeksFromNow() throws Exception
{
PrettyTime t = new PrettyTime(new Date(0));
for (TimeUnit u : t.getUnits())
{ | if (u instanceof Month) |
ocpsoft/prettytime | core/src/main/java/org/ocpsoft/prettytime/i18n/Resources_ru.java | // Path: core/src/main/java/org/ocpsoft/prettytime/TimeFormat.java
// public interface TimeFormat
// {
// /**
// * Given a populated {@link Duration} object. Apply formatting (with rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public abstract String format(final Duration duration);
//
// /**
// * Given a populated {@link Duration} object. Apply formatting (without rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public String formatUnrounded(Duration duration);
//
// /**
// * Decorate with past or future prefix/suffix (with rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorate(Duration duration, String time);
//
// /**
// * Decorate with past or future prefix/suffix (without rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorateUnrounded(Duration duration, String time);
//
// }
| import org.ocpsoft.prettytime.Duration;
import org.ocpsoft.prettytime.TimeFormat;
import org.ocpsoft.prettytime.TimeUnit;
import org.ocpsoft.prettytime.impl.TimeFormatProvider;
import org.ocpsoft.prettytime.units.*;
import java.util.ListResourceBundle; | package org.ocpsoft.prettytime.i18n;
/**
* Created with IntelliJ IDEA. User: Tumin Alexander Date: 2012-12-13 Time: 03:33
*/
public class Resources_ru extends ListResourceBundle implements TimeFormatProvider
{
private static final Object[][] OBJECTS = new Object[0][0];
private static final int tolerance = 50;
// see http://translate.sourceforge.net/wiki/l10n/pluralforms
private static final int russianPluralForms = 3;
| // Path: core/src/main/java/org/ocpsoft/prettytime/TimeFormat.java
// public interface TimeFormat
// {
// /**
// * Given a populated {@link Duration} object. Apply formatting (with rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public abstract String format(final Duration duration);
//
// /**
// * Given a populated {@link Duration} object. Apply formatting (without rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public String formatUnrounded(Duration duration);
//
// /**
// * Decorate with past or future prefix/suffix (with rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorate(Duration duration, String time);
//
// /**
// * Decorate with past or future prefix/suffix (without rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorateUnrounded(Duration duration, String time);
//
// }
// Path: core/src/main/java/org/ocpsoft/prettytime/i18n/Resources_ru.java
import org.ocpsoft.prettytime.Duration;
import org.ocpsoft.prettytime.TimeFormat;
import org.ocpsoft.prettytime.TimeUnit;
import org.ocpsoft.prettytime.impl.TimeFormatProvider;
import org.ocpsoft.prettytime.units.*;
import java.util.ListResourceBundle;
package org.ocpsoft.prettytime.i18n;
/**
* Created with IntelliJ IDEA. User: Tumin Alexander Date: 2012-12-13 Time: 03:33
*/
public class Resources_ru extends ListResourceBundle implements TimeFormatProvider
{
private static final Object[][] OBJECTS = new Object[0][0];
private static final int tolerance = 50;
// see http://translate.sourceforge.net/wiki/l10n/pluralforms
private static final int russianPluralForms = 3;
| private static class TimeFormatAided implements TimeFormat |
ocpsoft/prettytime | core/src/test/java/org/ocpsoft/prettytime/i18n/Resources_xx.java | // Path: core/src/main/java/org/ocpsoft/prettytime/TimeFormat.java
// public interface TimeFormat
// {
// /**
// * Given a populated {@link Duration} object. Apply formatting (with rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public abstract String format(final Duration duration);
//
// /**
// * Given a populated {@link Duration} object. Apply formatting (without rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public String formatUnrounded(Duration duration);
//
// /**
// * Decorate with past or future prefix/suffix (with rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorate(Duration duration, String time);
//
// /**
// * Decorate with past or future prefix/suffix (without rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorateUnrounded(Duration duration, String time);
//
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Minute.java
// public class Minute extends ResourcesTimeUnit
// {
//
// public Minute()
// {
// setMillisPerUnit(1000L * 60L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Minute";
// }
//
// }
| import java.util.ListResourceBundle;
import org.ocpsoft.prettytime.Duration;
import org.ocpsoft.prettytime.TimeFormat;
import org.ocpsoft.prettytime.TimeUnit;
import org.ocpsoft.prettytime.impl.TimeFormatProvider;
import org.ocpsoft.prettytime.units.Minute; | package org.ocpsoft.prettytime.i18n;
/*
* Copyright 2012 <a href="mailto:lincolnbaxter@gmail.com">Lincoln Baxter, III</a>
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
public class Resources_xx extends ListResourceBundle implements TimeFormatProvider
{
private static final Object[][] OBJECTS = new Object[][] {};
@Override
public Object[][] getContents()
{
return OBJECTS;
}
@Override | // Path: core/src/main/java/org/ocpsoft/prettytime/TimeFormat.java
// public interface TimeFormat
// {
// /**
// * Given a populated {@link Duration} object. Apply formatting (with rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public abstract String format(final Duration duration);
//
// /**
// * Given a populated {@link Duration} object. Apply formatting (without rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public String formatUnrounded(Duration duration);
//
// /**
// * Decorate with past or future prefix/suffix (with rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorate(Duration duration, String time);
//
// /**
// * Decorate with past or future prefix/suffix (without rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorateUnrounded(Duration duration, String time);
//
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Minute.java
// public class Minute extends ResourcesTimeUnit
// {
//
// public Minute()
// {
// setMillisPerUnit(1000L * 60L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Minute";
// }
//
// }
// Path: core/src/test/java/org/ocpsoft/prettytime/i18n/Resources_xx.java
import java.util.ListResourceBundle;
import org.ocpsoft.prettytime.Duration;
import org.ocpsoft.prettytime.TimeFormat;
import org.ocpsoft.prettytime.TimeUnit;
import org.ocpsoft.prettytime.impl.TimeFormatProvider;
import org.ocpsoft.prettytime.units.Minute;
package org.ocpsoft.prettytime.i18n;
/*
* Copyright 2012 <a href="mailto:lincolnbaxter@gmail.com">Lincoln Baxter, III</a>
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
public class Resources_xx extends ListResourceBundle implements TimeFormatProvider
{
private static final Object[][] OBJECTS = new Object[][] {};
@Override
public Object[][] getContents()
{
return OBJECTS;
}
@Override | public TimeFormat getFormatFor(TimeUnit t) |
ocpsoft/prettytime | core/src/test/java/org/ocpsoft/prettytime/i18n/Resources_xx.java | // Path: core/src/main/java/org/ocpsoft/prettytime/TimeFormat.java
// public interface TimeFormat
// {
// /**
// * Given a populated {@link Duration} object. Apply formatting (with rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public abstract String format(final Duration duration);
//
// /**
// * Given a populated {@link Duration} object. Apply formatting (without rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public String formatUnrounded(Duration duration);
//
// /**
// * Decorate with past or future prefix/suffix (with rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorate(Duration duration, String time);
//
// /**
// * Decorate with past or future prefix/suffix (without rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorateUnrounded(Duration duration, String time);
//
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Minute.java
// public class Minute extends ResourcesTimeUnit
// {
//
// public Minute()
// {
// setMillisPerUnit(1000L * 60L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Minute";
// }
//
// }
| import java.util.ListResourceBundle;
import org.ocpsoft.prettytime.Duration;
import org.ocpsoft.prettytime.TimeFormat;
import org.ocpsoft.prettytime.TimeUnit;
import org.ocpsoft.prettytime.impl.TimeFormatProvider;
import org.ocpsoft.prettytime.units.Minute; | package org.ocpsoft.prettytime.i18n;
/*
* Copyright 2012 <a href="mailto:lincolnbaxter@gmail.com">Lincoln Baxter, III</a>
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
public class Resources_xx extends ListResourceBundle implements TimeFormatProvider
{
private static final Object[][] OBJECTS = new Object[][] {};
@Override
public Object[][] getContents()
{
return OBJECTS;
}
@Override
public TimeFormat getFormatFor(TimeUnit t)
{ | // Path: core/src/main/java/org/ocpsoft/prettytime/TimeFormat.java
// public interface TimeFormat
// {
// /**
// * Given a populated {@link Duration} object. Apply formatting (with rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public abstract String format(final Duration duration);
//
// /**
// * Given a populated {@link Duration} object. Apply formatting (without rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public String formatUnrounded(Duration duration);
//
// /**
// * Decorate with past or future prefix/suffix (with rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorate(Duration duration, String time);
//
// /**
// * Decorate with past or future prefix/suffix (without rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorateUnrounded(Duration duration, String time);
//
// }
//
// Path: core/src/main/java/org/ocpsoft/prettytime/units/Minute.java
// public class Minute extends ResourcesTimeUnit
// {
//
// public Minute()
// {
// setMillisPerUnit(1000L * 60L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "Minute";
// }
//
// }
// Path: core/src/test/java/org/ocpsoft/prettytime/i18n/Resources_xx.java
import java.util.ListResourceBundle;
import org.ocpsoft.prettytime.Duration;
import org.ocpsoft.prettytime.TimeFormat;
import org.ocpsoft.prettytime.TimeUnit;
import org.ocpsoft.prettytime.impl.TimeFormatProvider;
import org.ocpsoft.prettytime.units.Minute;
package org.ocpsoft.prettytime.i18n;
/*
* Copyright 2012 <a href="mailto:lincolnbaxter@gmail.com">Lincoln Baxter, III</a>
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
public class Resources_xx extends ListResourceBundle implements TimeFormatProvider
{
private static final Object[][] OBJECTS = new Object[][] {};
@Override
public Object[][] getContents()
{
return OBJECTS;
}
@Override
public TimeFormat getFormatFor(TimeUnit t)
{ | if (t instanceof Minute) |
ocpsoft/prettytime | core/src/main/java/org/ocpsoft/prettytime/i18n/Resources_kk.java | // Path: core/src/main/java/org/ocpsoft/prettytime/TimeFormat.java
// public interface TimeFormat
// {
// /**
// * Given a populated {@link Duration} object. Apply formatting (with rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public abstract String format(final Duration duration);
//
// /**
// * Given a populated {@link Duration} object. Apply formatting (without rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public String formatUnrounded(Duration duration);
//
// /**
// * Decorate with past or future prefix/suffix (with rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorate(Duration duration, String time);
//
// /**
// * Decorate with past or future prefix/suffix (without rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorateUnrounded(Duration duration, String time);
//
// }
| import org.ocpsoft.prettytime.Duration;
import org.ocpsoft.prettytime.TimeFormat;
import org.ocpsoft.prettytime.TimeUnit;
import org.ocpsoft.prettytime.impl.TimeFormatProvider;
import org.ocpsoft.prettytime.units.*;
import java.util.ListResourceBundle; | package org.ocpsoft.prettytime.i18n;
/**
* Created by Azimkhan Yerzhan on 5/8/2017
*/
public class Resources_kk extends ListResourceBundle implements TimeFormatProvider {
private static final Object[][] OBJECTS = new Object[0][0];
@Override
protected Object[][] getContents() {
return OBJECTS;
}
| // Path: core/src/main/java/org/ocpsoft/prettytime/TimeFormat.java
// public interface TimeFormat
// {
// /**
// * Given a populated {@link Duration} object. Apply formatting (with rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public abstract String format(final Duration duration);
//
// /**
// * Given a populated {@link Duration} object. Apply formatting (without rounding) and output the result.
// *
// * @param The original {@link Duration} instance from which the time string should be decorated.
// */
// public String formatUnrounded(Duration duration);
//
// /**
// * Decorate with past or future prefix/suffix (with rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorate(Duration duration, String time);
//
// /**
// * Decorate with past or future prefix/suffix (without rounding)
// *
// * @param duration The original {@link Duration} instance from which the time string should be decorated.
// * @param time The formatted time string.
// */
// public String decorateUnrounded(Duration duration, String time);
//
// }
// Path: core/src/main/java/org/ocpsoft/prettytime/i18n/Resources_kk.java
import org.ocpsoft.prettytime.Duration;
import org.ocpsoft.prettytime.TimeFormat;
import org.ocpsoft.prettytime.TimeUnit;
import org.ocpsoft.prettytime.impl.TimeFormatProvider;
import org.ocpsoft.prettytime.units.*;
import java.util.ListResourceBundle;
package org.ocpsoft.prettytime.i18n;
/**
* Created by Azimkhan Yerzhan on 5/8/2017
*/
public class Resources_kk extends ListResourceBundle implements TimeFormatProvider {
private static final Object[][] OBJECTS = new Object[0][0];
@Override
protected Object[][] getContents() {
return OBJECTS;
}
| private static class KkTimeFormat implements TimeFormat |
ocpsoft/prettytime | core/src/test/java/org/ocpsoft/prettytime/PrettyTimeI18n_ET_Test.java | // Path: core/src/main/java/org/ocpsoft/prettytime/units/JustNow.java
// public class JustNow extends ResourcesTimeUnit
// {
//
// public JustNow()
// {
// setMaxQuantity(1000L * 60L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "JustNow";
// }
//
// @Override
// public boolean isPrecise()
// {
// return false;
// }
//
// }
| import static org.junit.Assert.assertEquals;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Locale;
import org.junit.Before;
import org.junit.Test;
import org.ocpsoft.prettytime.units.JustNow; | package org.ocpsoft.prettytime;
public class PrettyTimeI18n_ET_Test
{
private Locale locale;
@Before
public void setUp() throws Exception
{
locale = new Locale("et");
}
private PrettyTime newPrettyTimeWOJustNow(Date ref, Locale locale)
{
PrettyTime t = new PrettyTime(ref, locale);
List<TimeUnit> units = t.getUnits();
List<TimeFormat> formats = new ArrayList<TimeFormat>();
for (TimeUnit timeUnit : units) { | // Path: core/src/main/java/org/ocpsoft/prettytime/units/JustNow.java
// public class JustNow extends ResourcesTimeUnit
// {
//
// public JustNow()
// {
// setMaxQuantity(1000L * 60L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "JustNow";
// }
//
// @Override
// public boolean isPrecise()
// {
// return false;
// }
//
// }
// Path: core/src/test/java/org/ocpsoft/prettytime/PrettyTimeI18n_ET_Test.java
import static org.junit.Assert.assertEquals;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Locale;
import org.junit.Before;
import org.junit.Test;
import org.ocpsoft.prettytime.units.JustNow;
package org.ocpsoft.prettytime;
public class PrettyTimeI18n_ET_Test
{
private Locale locale;
@Before
public void setUp() throws Exception
{
locale = new Locale("et");
}
private PrettyTime newPrettyTimeWOJustNow(Date ref, Locale locale)
{
PrettyTime t = new PrettyTime(ref, locale);
List<TimeUnit> units = t.getUnits();
List<TimeFormat> formats = new ArrayList<TimeFormat>();
for (TimeUnit timeUnit : units) { | if (!(timeUnit instanceof JustNow)) { |
ocpsoft/prettytime | core/src/test/java/org/ocpsoft/prettytime/PrettyTimeI18n_FI_Test.java | // Path: core/src/main/java/org/ocpsoft/prettytime/units/JustNow.java
// public class JustNow extends ResourcesTimeUnit
// {
//
// public JustNow()
// {
// setMaxQuantity(1000L * 60L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "JustNow";
// }
//
// @Override
// public boolean isPrecise()
// {
// return false;
// }
//
// }
| import static org.junit.Assert.assertEquals;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Locale;
import org.junit.Before;
import org.junit.Test;
import org.ocpsoft.prettytime.units.JustNow; | /*
* Copyright 2012 <a href="mailto:lincolnbaxter@gmail.com">Lincoln Baxter, III</a>
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ocpsoft.prettytime;
public class PrettyTimeI18n_FI_Test
{
private Locale locale;
@Before
public void setUp() throws Exception
{
locale = new Locale("fi");
}
private PrettyTime newPrettyTimeWOJustNow(Date ref, Locale locale)
{
PrettyTime t = new PrettyTime(ref, locale);
List<TimeUnit> units = t.getUnits();
List<TimeFormat> formats = new ArrayList<TimeFormat>();
for (TimeUnit timeUnit : units) { | // Path: core/src/main/java/org/ocpsoft/prettytime/units/JustNow.java
// public class JustNow extends ResourcesTimeUnit
// {
//
// public JustNow()
// {
// setMaxQuantity(1000L * 60L);
// }
//
// @Override
// protected String getResourceKeyPrefix()
// {
// return "JustNow";
// }
//
// @Override
// public boolean isPrecise()
// {
// return false;
// }
//
// }
// Path: core/src/test/java/org/ocpsoft/prettytime/PrettyTimeI18n_FI_Test.java
import static org.junit.Assert.assertEquals;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Locale;
import org.junit.Before;
import org.junit.Test;
import org.ocpsoft.prettytime.units.JustNow;
/*
* Copyright 2012 <a href="mailto:lincolnbaxter@gmail.com">Lincoln Baxter, III</a>
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ocpsoft.prettytime;
public class PrettyTimeI18n_FI_Test
{
private Locale locale;
@Before
public void setUp() throws Exception
{
locale = new Locale("fi");
}
private PrettyTime newPrettyTimeWOJustNow(Date ref, Locale locale)
{
PrettyTime t = new PrettyTime(ref, locale);
List<TimeUnit> units = t.getUnits();
List<TimeFormat> formats = new ArrayList<TimeFormat>();
for (TimeUnit timeUnit : units) { | if (!(timeUnit instanceof JustNow)) { |
davidmoten/rtree | src/test/java/com/github/davidmoten/rtree/ContextTest.java | // Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometry.java
// public interface Geometry {
//
// /**
// * <p>
// * Returns the distance to the given {@link Rectangle}. For a {@link Rectangle}
// * this might be Euclidean distance but for an EPSG4326 lat-long Rectangle might
// * be great-circle distance. The distance function should satisfy the following
// * properties:
// * </p>
// *
// * <p>
// * <code>distance(r) >= 0</code>
// * </p>
// *
// * <p>
// * <code>if r1 contains r2 then distance(r1)<=distance(r2)</code>
// * </p>
// *
// *
// * @param r
// * rectangle to measure distance to
// * @return distance to the rectangle r from the geometry
// */
// double distance(Rectangle r);
//
// /**
// * Returns the minimum bounding rectangle of this geometry.
// *
// * @return minimum bounding rectangle
// */
// Rectangle mbr();
//
// boolean intersects(Rectangle r);
//
// boolean isDoublePrecision();
// }
| import org.junit.Test;
import com.github.davidmoten.rtree.geometry.Geometry;
| package com.github.davidmoten.rtree;
public class ContextTest {
@Test(expected = RuntimeException.class)
public void testContextIllegalMinChildren() {
| // Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometry.java
// public interface Geometry {
//
// /**
// * <p>
// * Returns the distance to the given {@link Rectangle}. For a {@link Rectangle}
// * this might be Euclidean distance but for an EPSG4326 lat-long Rectangle might
// * be great-circle distance. The distance function should satisfy the following
// * properties:
// * </p>
// *
// * <p>
// * <code>distance(r) >= 0</code>
// * </p>
// *
// * <p>
// * <code>if r1 contains r2 then distance(r1)<=distance(r2)</code>
// * </p>
// *
// *
// * @param r
// * rectangle to measure distance to
// * @return distance to the rectangle r from the geometry
// */
// double distance(Rectangle r);
//
// /**
// * Returns the minimum bounding rectangle of this geometry.
// *
// * @return minimum bounding rectangle
// */
// Rectangle mbr();
//
// boolean intersects(Rectangle r);
//
// boolean isDoublePrecision();
// }
// Path: src/test/java/com/github/davidmoten/rtree/ContextTest.java
import org.junit.Test;
import com.github.davidmoten.rtree.geometry.Geometry;
package com.github.davidmoten.rtree;
public class ContextTest {
@Test(expected = RuntimeException.class)
public void testContextIllegalMinChildren() {
| new Context<Object, Geometry>(0, 4, new SelectorMinimalAreaIncrease(),
|
davidmoten/rtree | src/main/java/com/github/davidmoten/rtree/Node.java | // Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometry.java
// public interface Geometry {
//
// /**
// * <p>
// * Returns the distance to the given {@link Rectangle}. For a {@link Rectangle}
// * this might be Euclidean distance but for an EPSG4326 lat-long Rectangle might
// * be great-circle distance. The distance function should satisfy the following
// * properties:
// * </p>
// *
// * <p>
// * <code>distance(r) >= 0</code>
// * </p>
// *
// * <p>
// * <code>if r1 contains r2 then distance(r1)<=distance(r2)</code>
// * </p>
// *
// *
// * @param r
// * rectangle to measure distance to
// * @return distance to the rectangle r from the geometry
// */
// double distance(Rectangle r);
//
// /**
// * Returns the minimum bounding rectangle of this geometry.
// *
// * @return minimum bounding rectangle
// */
// Rectangle mbr();
//
// boolean intersects(Rectangle r);
//
// boolean isDoublePrecision();
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/internal/NodeAndEntries.java
// public final class NodeAndEntries<T, S extends Geometry> {
//
// private final Optional<? extends Node<T, S>> node;
// private final List<Entry<T, S>> entries;
// private final int count;
//
// /**
// * Constructor.
// *
// * @param node
// * absent = whole node was deleted present = either an unchanged
// * node because of no removal or the newly created node without
// * the deleted entry
// * @param entries
// * from nodes that dropped below minChildren in size and thus
// * their entries are to be redistributed (readded to the tree)
// * @param countDeleted
// * count of the number of entries removed
// */
// public NodeAndEntries(Optional<? extends Node<T, S>> node, List<Entry<T, S>> entries,
// int countDeleted) {
// this.node = node;
// this.entries = entries;
// this.count = countDeleted;
// }
//
// public Optional<? extends Node<T, S>> node() {
// return node;
// }
//
// public List<Entry<T, S>> entriesToAdd() {
// return entries;
// }
//
// public int countDeleted() {
// return count;
// }
//
// }
| import java.util.List;
import com.github.davidmoten.rtree.geometry.Geometry;
import com.github.davidmoten.rtree.geometry.HasGeometry;
import com.github.davidmoten.rtree.internal.NodeAndEntries;
import rx.Subscriber;
import rx.functions.Func1; | package com.github.davidmoten.rtree;
public interface Node<T, S extends Geometry> extends HasGeometry {
List<Node<T, S>> add(Entry<? extends T, ? extends S> entry);
| // Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometry.java
// public interface Geometry {
//
// /**
// * <p>
// * Returns the distance to the given {@link Rectangle}. For a {@link Rectangle}
// * this might be Euclidean distance but for an EPSG4326 lat-long Rectangle might
// * be great-circle distance. The distance function should satisfy the following
// * properties:
// * </p>
// *
// * <p>
// * <code>distance(r) >= 0</code>
// * </p>
// *
// * <p>
// * <code>if r1 contains r2 then distance(r1)<=distance(r2)</code>
// * </p>
// *
// *
// * @param r
// * rectangle to measure distance to
// * @return distance to the rectangle r from the geometry
// */
// double distance(Rectangle r);
//
// /**
// * Returns the minimum bounding rectangle of this geometry.
// *
// * @return minimum bounding rectangle
// */
// Rectangle mbr();
//
// boolean intersects(Rectangle r);
//
// boolean isDoublePrecision();
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/internal/NodeAndEntries.java
// public final class NodeAndEntries<T, S extends Geometry> {
//
// private final Optional<? extends Node<T, S>> node;
// private final List<Entry<T, S>> entries;
// private final int count;
//
// /**
// * Constructor.
// *
// * @param node
// * absent = whole node was deleted present = either an unchanged
// * node because of no removal or the newly created node without
// * the deleted entry
// * @param entries
// * from nodes that dropped below minChildren in size and thus
// * their entries are to be redistributed (readded to the tree)
// * @param countDeleted
// * count of the number of entries removed
// */
// public NodeAndEntries(Optional<? extends Node<T, S>> node, List<Entry<T, S>> entries,
// int countDeleted) {
// this.node = node;
// this.entries = entries;
// this.count = countDeleted;
// }
//
// public Optional<? extends Node<T, S>> node() {
// return node;
// }
//
// public List<Entry<T, S>> entriesToAdd() {
// return entries;
// }
//
// public int countDeleted() {
// return count;
// }
//
// }
// Path: src/main/java/com/github/davidmoten/rtree/Node.java
import java.util.List;
import com.github.davidmoten.rtree.geometry.Geometry;
import com.github.davidmoten.rtree.geometry.HasGeometry;
import com.github.davidmoten.rtree.internal.NodeAndEntries;
import rx.Subscriber;
import rx.functions.Func1;
package com.github.davidmoten.rtree;
public interface Node<T, S extends Geometry> extends HasGeometry {
List<Node<T, S>> add(Entry<? extends T, ? extends S> entry);
| NodeAndEntries<T, S> delete(Entry<? extends T, ? extends S> entry, boolean all); |
davidmoten/rtree | src/test/java/com/github/davidmoten/rtree/EntriesTest.java | // Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometries.java
// public final class Geometries {
//
// private Geometries() {
// // prevent instantiation
// }
//
// public static Point point(double x, double y) {
// return PointDouble.create(x, y);
// }
//
// public static Point point(float x, float y) {
// return PointFloat.create(x, y);
// }
//
// public static Point pointGeographic(double lon, double lat) {
// return point(normalizeLongitudeDouble(lon), lat);
// }
//
// public static Point pointGeographic(float lon, float lat) {
// return point(normalizeLongitude(lon), lat);
// }
//
// public static Rectangle rectangle(double x1, double y1, double x2, double y2) {
// return rectangleDouble(x1, y1, x2, y2);
// }
//
// public static Rectangle rectangle(float x1, float y1, float x2, float y2) {
// return RectangleFloat.create(x1, y1, x2, y2);
// }
//
// public static Rectangle rectangleGeographic(double lon1, double lat1, double lon2,
// double lat2) {
// return rectangleGeographic((float) lon1, (float) lat1, (float) lon2, (float) lat2);
// }
//
// public static Rectangle rectangleGeographic(float lon1, float lat1, float lon2, float lat2) {
// float x1 = normalizeLongitude(lon1);
// float x2 = normalizeLongitude(lon2);
// if (x2 < x1) {
// x2 += 360;
// }
// return rectangle(x1, lat1, x2, lat2);
// }
//
// private static Rectangle rectangleDouble(double x1, double y1, double x2, double y2) {
// return RectangleDouble.create(x1, y1, x2, y2);
// }
//
// public static Circle circle(double x, double y, double radius) {
// return CircleDouble.create(x, y, radius);
// }
//
// public static Circle circle(float x, float y, float radius) {
// return CircleFloat.create(x, y, radius);
// }
//
// public static Line line(double x1, double y1, double x2, double y2) {
// return LineDouble.create(x1, y1, x2, y2);
// }
//
// public static Line line(float x1, float y1, float x2, float y2) {
// return LineFloat.create(x1, y1, x2, y2);
// }
//
// @VisibleForTesting
// static double normalizeLongitude(double d) {
// return normalizeLongitude((float) d);
// }
//
// private static float normalizeLongitude(float d) {
// if (d == -180.0f)
// return -180.0f;
// else {
// float sign = Math.signum(d);
// float x = Math.abs(d) / 360;
// float x2 = (x - (float) Math.floor(x)) * 360;
// if (x2 >= 180)
// x2 -= 360;
// return x2 * sign;
// }
// }
//
// private static double normalizeLongitudeDouble(double d) {
// if (d == -180.0f)
// return -180.0d;
// else {
// double sign = Math.signum(d);
// double x = Math.abs(d) / 360;
// double x2 = (x - (float) Math.floor(x)) * 360;
// if (x2 >= 180)
// x2 -= 360;
// return x2 * sign;
// }
// }
//
// }
| import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotEquals;
import org.junit.Test;
import com.github.davidmoten.junit.Asserts;
import com.github.davidmoten.rtree.geometry.Geometries; | package com.github.davidmoten.rtree;
public class EntriesTest {
@Test
public void testValue() { | // Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometries.java
// public final class Geometries {
//
// private Geometries() {
// // prevent instantiation
// }
//
// public static Point point(double x, double y) {
// return PointDouble.create(x, y);
// }
//
// public static Point point(float x, float y) {
// return PointFloat.create(x, y);
// }
//
// public static Point pointGeographic(double lon, double lat) {
// return point(normalizeLongitudeDouble(lon), lat);
// }
//
// public static Point pointGeographic(float lon, float lat) {
// return point(normalizeLongitude(lon), lat);
// }
//
// public static Rectangle rectangle(double x1, double y1, double x2, double y2) {
// return rectangleDouble(x1, y1, x2, y2);
// }
//
// public static Rectangle rectangle(float x1, float y1, float x2, float y2) {
// return RectangleFloat.create(x1, y1, x2, y2);
// }
//
// public static Rectangle rectangleGeographic(double lon1, double lat1, double lon2,
// double lat2) {
// return rectangleGeographic((float) lon1, (float) lat1, (float) lon2, (float) lat2);
// }
//
// public static Rectangle rectangleGeographic(float lon1, float lat1, float lon2, float lat2) {
// float x1 = normalizeLongitude(lon1);
// float x2 = normalizeLongitude(lon2);
// if (x2 < x1) {
// x2 += 360;
// }
// return rectangle(x1, lat1, x2, lat2);
// }
//
// private static Rectangle rectangleDouble(double x1, double y1, double x2, double y2) {
// return RectangleDouble.create(x1, y1, x2, y2);
// }
//
// public static Circle circle(double x, double y, double radius) {
// return CircleDouble.create(x, y, radius);
// }
//
// public static Circle circle(float x, float y, float radius) {
// return CircleFloat.create(x, y, radius);
// }
//
// public static Line line(double x1, double y1, double x2, double y2) {
// return LineDouble.create(x1, y1, x2, y2);
// }
//
// public static Line line(float x1, float y1, float x2, float y2) {
// return LineFloat.create(x1, y1, x2, y2);
// }
//
// @VisibleForTesting
// static double normalizeLongitude(double d) {
// return normalizeLongitude((float) d);
// }
//
// private static float normalizeLongitude(float d) {
// if (d == -180.0f)
// return -180.0f;
// else {
// float sign = Math.signum(d);
// float x = Math.abs(d) / 360;
// float x2 = (x - (float) Math.floor(x)) * 360;
// if (x2 >= 180)
// x2 -= 360;
// return x2 * sign;
// }
// }
//
// private static double normalizeLongitudeDouble(double d) {
// if (d == -180.0f)
// return -180.0d;
// else {
// double sign = Math.signum(d);
// double x = Math.abs(d) / 360;
// double x2 = (x - (float) Math.floor(x)) * 360;
// if (x2 >= 180)
// x2 -= 360;
// return x2 * sign;
// }
// }
//
// }
// Path: src/test/java/com/github/davidmoten/rtree/EntriesTest.java
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotEquals;
import org.junit.Test;
import com.github.davidmoten.junit.Asserts;
import com.github.davidmoten.rtree.geometry.Geometries;
package com.github.davidmoten.rtree;
public class EntriesTest {
@Test
public void testValue() { | assertEquals(1, (int) Entries.entry(1, Geometries.point(0, 0)).value()); |
davidmoten/rtree | src/test/java/com/github/davidmoten/rtree/SplitterRStarTest.java | // Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometries.java
// public final class Geometries {
//
// private Geometries() {
// // prevent instantiation
// }
//
// public static Point point(double x, double y) {
// return PointDouble.create(x, y);
// }
//
// public static Point point(float x, float y) {
// return PointFloat.create(x, y);
// }
//
// public static Point pointGeographic(double lon, double lat) {
// return point(normalizeLongitudeDouble(lon), lat);
// }
//
// public static Point pointGeographic(float lon, float lat) {
// return point(normalizeLongitude(lon), lat);
// }
//
// public static Rectangle rectangle(double x1, double y1, double x2, double y2) {
// return rectangleDouble(x1, y1, x2, y2);
// }
//
// public static Rectangle rectangle(float x1, float y1, float x2, float y2) {
// return RectangleFloat.create(x1, y1, x2, y2);
// }
//
// public static Rectangle rectangleGeographic(double lon1, double lat1, double lon2,
// double lat2) {
// return rectangleGeographic((float) lon1, (float) lat1, (float) lon2, (float) lat2);
// }
//
// public static Rectangle rectangleGeographic(float lon1, float lat1, float lon2, float lat2) {
// float x1 = normalizeLongitude(lon1);
// float x2 = normalizeLongitude(lon2);
// if (x2 < x1) {
// x2 += 360;
// }
// return rectangle(x1, lat1, x2, lat2);
// }
//
// private static Rectangle rectangleDouble(double x1, double y1, double x2, double y2) {
// return RectangleDouble.create(x1, y1, x2, y2);
// }
//
// public static Circle circle(double x, double y, double radius) {
// return CircleDouble.create(x, y, radius);
// }
//
// public static Circle circle(float x, float y, float radius) {
// return CircleFloat.create(x, y, radius);
// }
//
// public static Line line(double x1, double y1, double x2, double y2) {
// return LineDouble.create(x1, y1, x2, y2);
// }
//
// public static Line line(float x1, float y1, float x2, float y2) {
// return LineFloat.create(x1, y1, x2, y2);
// }
//
// @VisibleForTesting
// static double normalizeLongitude(double d) {
// return normalizeLongitude((float) d);
// }
//
// private static float normalizeLongitude(float d) {
// if (d == -180.0f)
// return -180.0f;
// else {
// float sign = Math.signum(d);
// float x = Math.abs(d) / 360;
// float x2 = (x - (float) Math.floor(x)) * 360;
// if (x2 >= 180)
// x2 -= 360;
// return x2 * sign;
// }
// }
//
// private static double normalizeLongitudeDouble(double d) {
// if (d == -180.0f)
// return -180.0d;
// else {
// double sign = Math.signum(d);
// double x = Math.abs(d) / 360;
// double x2 = (x - (float) Math.floor(x)) * 360;
// if (x2 >= 180)
// x2 -= 360;
// return x2 * sign;
// }
// }
//
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/geometry/ListPair.java
// public final class ListPair<T extends HasGeometry> {
// private final Group<T> group1;
// private final Group<T> group2;
// // these non-final variable mean that this class is not thread-safe
// // because access to them is not synchronized
// private double areaSum = -1;
// private final double marginSum;
//
// public ListPair(List<T> list1, List<T> list2) {
// this.group1 = new Group<T>(list1);
// this.group2 = new Group<T>(list2);
// this.marginSum = group1.geometry().mbr().perimeter() + group2.geometry().mbr().perimeter();
// }
//
// public Group<T> group1() {
// return group1;
// }
//
// public Group<T> group2() {
// return group2;
// }
//
// public double areaSum() {
// if (areaSum == -1)
// areaSum = group1.geometry().mbr().area() + group2.geometry().mbr().area();
// return areaSum;
// }
//
// public double marginSum() {
// return marginSum;
// }
//
// }
| import static org.junit.Assert.assertEquals;
import java.util.List;
import org.junit.Test;
import com.github.davidmoten.guavamini.Lists;
import com.github.davidmoten.rtree.geometry.Geometries;
import com.github.davidmoten.rtree.geometry.HasGeometry;
import com.github.davidmoten.rtree.geometry.ListPair; | package com.github.davidmoten.rtree;
public class SplitterRStarTest {
@Test
public void testGetPairs() {
int minSize = 2;
List<HasGeometry> list = Lists.newArrayList(); | // Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometries.java
// public final class Geometries {
//
// private Geometries() {
// // prevent instantiation
// }
//
// public static Point point(double x, double y) {
// return PointDouble.create(x, y);
// }
//
// public static Point point(float x, float y) {
// return PointFloat.create(x, y);
// }
//
// public static Point pointGeographic(double lon, double lat) {
// return point(normalizeLongitudeDouble(lon), lat);
// }
//
// public static Point pointGeographic(float lon, float lat) {
// return point(normalizeLongitude(lon), lat);
// }
//
// public static Rectangle rectangle(double x1, double y1, double x2, double y2) {
// return rectangleDouble(x1, y1, x2, y2);
// }
//
// public static Rectangle rectangle(float x1, float y1, float x2, float y2) {
// return RectangleFloat.create(x1, y1, x2, y2);
// }
//
// public static Rectangle rectangleGeographic(double lon1, double lat1, double lon2,
// double lat2) {
// return rectangleGeographic((float) lon1, (float) lat1, (float) lon2, (float) lat2);
// }
//
// public static Rectangle rectangleGeographic(float lon1, float lat1, float lon2, float lat2) {
// float x1 = normalizeLongitude(lon1);
// float x2 = normalizeLongitude(lon2);
// if (x2 < x1) {
// x2 += 360;
// }
// return rectangle(x1, lat1, x2, lat2);
// }
//
// private static Rectangle rectangleDouble(double x1, double y1, double x2, double y2) {
// return RectangleDouble.create(x1, y1, x2, y2);
// }
//
// public static Circle circle(double x, double y, double radius) {
// return CircleDouble.create(x, y, radius);
// }
//
// public static Circle circle(float x, float y, float radius) {
// return CircleFloat.create(x, y, radius);
// }
//
// public static Line line(double x1, double y1, double x2, double y2) {
// return LineDouble.create(x1, y1, x2, y2);
// }
//
// public static Line line(float x1, float y1, float x2, float y2) {
// return LineFloat.create(x1, y1, x2, y2);
// }
//
// @VisibleForTesting
// static double normalizeLongitude(double d) {
// return normalizeLongitude((float) d);
// }
//
// private static float normalizeLongitude(float d) {
// if (d == -180.0f)
// return -180.0f;
// else {
// float sign = Math.signum(d);
// float x = Math.abs(d) / 360;
// float x2 = (x - (float) Math.floor(x)) * 360;
// if (x2 >= 180)
// x2 -= 360;
// return x2 * sign;
// }
// }
//
// private static double normalizeLongitudeDouble(double d) {
// if (d == -180.0f)
// return -180.0d;
// else {
// double sign = Math.signum(d);
// double x = Math.abs(d) / 360;
// double x2 = (x - (float) Math.floor(x)) * 360;
// if (x2 >= 180)
// x2 -= 360;
// return x2 * sign;
// }
// }
//
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/geometry/ListPair.java
// public final class ListPair<T extends HasGeometry> {
// private final Group<T> group1;
// private final Group<T> group2;
// // these non-final variable mean that this class is not thread-safe
// // because access to them is not synchronized
// private double areaSum = -1;
// private final double marginSum;
//
// public ListPair(List<T> list1, List<T> list2) {
// this.group1 = new Group<T>(list1);
// this.group2 = new Group<T>(list2);
// this.marginSum = group1.geometry().mbr().perimeter() + group2.geometry().mbr().perimeter();
// }
//
// public Group<T> group1() {
// return group1;
// }
//
// public Group<T> group2() {
// return group2;
// }
//
// public double areaSum() {
// if (areaSum == -1)
// areaSum = group1.geometry().mbr().area() + group2.geometry().mbr().area();
// return areaSum;
// }
//
// public double marginSum() {
// return marginSum;
// }
//
// }
// Path: src/test/java/com/github/davidmoten/rtree/SplitterRStarTest.java
import static org.junit.Assert.assertEquals;
import java.util.List;
import org.junit.Test;
import com.github.davidmoten.guavamini.Lists;
import com.github.davidmoten.rtree.geometry.Geometries;
import com.github.davidmoten.rtree.geometry.HasGeometry;
import com.github.davidmoten.rtree.geometry.ListPair;
package com.github.davidmoten.rtree;
public class SplitterRStarTest {
@Test
public void testGetPairs() {
int minSize = 2;
List<HasGeometry> list = Lists.newArrayList(); | list.add(Geometries.point(1, 1).mbr()); |
davidmoten/rtree | src/test/java/com/github/davidmoten/rtree/SplitterRStarTest.java | // Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometries.java
// public final class Geometries {
//
// private Geometries() {
// // prevent instantiation
// }
//
// public static Point point(double x, double y) {
// return PointDouble.create(x, y);
// }
//
// public static Point point(float x, float y) {
// return PointFloat.create(x, y);
// }
//
// public static Point pointGeographic(double lon, double lat) {
// return point(normalizeLongitudeDouble(lon), lat);
// }
//
// public static Point pointGeographic(float lon, float lat) {
// return point(normalizeLongitude(lon), lat);
// }
//
// public static Rectangle rectangle(double x1, double y1, double x2, double y2) {
// return rectangleDouble(x1, y1, x2, y2);
// }
//
// public static Rectangle rectangle(float x1, float y1, float x2, float y2) {
// return RectangleFloat.create(x1, y1, x2, y2);
// }
//
// public static Rectangle rectangleGeographic(double lon1, double lat1, double lon2,
// double lat2) {
// return rectangleGeographic((float) lon1, (float) lat1, (float) lon2, (float) lat2);
// }
//
// public static Rectangle rectangleGeographic(float lon1, float lat1, float lon2, float lat2) {
// float x1 = normalizeLongitude(lon1);
// float x2 = normalizeLongitude(lon2);
// if (x2 < x1) {
// x2 += 360;
// }
// return rectangle(x1, lat1, x2, lat2);
// }
//
// private static Rectangle rectangleDouble(double x1, double y1, double x2, double y2) {
// return RectangleDouble.create(x1, y1, x2, y2);
// }
//
// public static Circle circle(double x, double y, double radius) {
// return CircleDouble.create(x, y, radius);
// }
//
// public static Circle circle(float x, float y, float radius) {
// return CircleFloat.create(x, y, radius);
// }
//
// public static Line line(double x1, double y1, double x2, double y2) {
// return LineDouble.create(x1, y1, x2, y2);
// }
//
// public static Line line(float x1, float y1, float x2, float y2) {
// return LineFloat.create(x1, y1, x2, y2);
// }
//
// @VisibleForTesting
// static double normalizeLongitude(double d) {
// return normalizeLongitude((float) d);
// }
//
// private static float normalizeLongitude(float d) {
// if (d == -180.0f)
// return -180.0f;
// else {
// float sign = Math.signum(d);
// float x = Math.abs(d) / 360;
// float x2 = (x - (float) Math.floor(x)) * 360;
// if (x2 >= 180)
// x2 -= 360;
// return x2 * sign;
// }
// }
//
// private static double normalizeLongitudeDouble(double d) {
// if (d == -180.0f)
// return -180.0d;
// else {
// double sign = Math.signum(d);
// double x = Math.abs(d) / 360;
// double x2 = (x - (float) Math.floor(x)) * 360;
// if (x2 >= 180)
// x2 -= 360;
// return x2 * sign;
// }
// }
//
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/geometry/ListPair.java
// public final class ListPair<T extends HasGeometry> {
// private final Group<T> group1;
// private final Group<T> group2;
// // these non-final variable mean that this class is not thread-safe
// // because access to them is not synchronized
// private double areaSum = -1;
// private final double marginSum;
//
// public ListPair(List<T> list1, List<T> list2) {
// this.group1 = new Group<T>(list1);
// this.group2 = new Group<T>(list2);
// this.marginSum = group1.geometry().mbr().perimeter() + group2.geometry().mbr().perimeter();
// }
//
// public Group<T> group1() {
// return group1;
// }
//
// public Group<T> group2() {
// return group2;
// }
//
// public double areaSum() {
// if (areaSum == -1)
// areaSum = group1.geometry().mbr().area() + group2.geometry().mbr().area();
// return areaSum;
// }
//
// public double marginSum() {
// return marginSum;
// }
//
// }
| import static org.junit.Assert.assertEquals;
import java.util.List;
import org.junit.Test;
import com.github.davidmoten.guavamini.Lists;
import com.github.davidmoten.rtree.geometry.Geometries;
import com.github.davidmoten.rtree.geometry.HasGeometry;
import com.github.davidmoten.rtree.geometry.ListPair; | package com.github.davidmoten.rtree;
public class SplitterRStarTest {
@Test
public void testGetPairs() {
int minSize = 2;
List<HasGeometry> list = Lists.newArrayList();
list.add(Geometries.point(1, 1).mbr());
list.add(Geometries.point(2, 2).mbr());
list.add(Geometries.point(3, 3).mbr());
list.add(Geometries.point(4, 4).mbr());
list.add(Geometries.point(5, 5).mbr()); | // Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometries.java
// public final class Geometries {
//
// private Geometries() {
// // prevent instantiation
// }
//
// public static Point point(double x, double y) {
// return PointDouble.create(x, y);
// }
//
// public static Point point(float x, float y) {
// return PointFloat.create(x, y);
// }
//
// public static Point pointGeographic(double lon, double lat) {
// return point(normalizeLongitudeDouble(lon), lat);
// }
//
// public static Point pointGeographic(float lon, float lat) {
// return point(normalizeLongitude(lon), lat);
// }
//
// public static Rectangle rectangle(double x1, double y1, double x2, double y2) {
// return rectangleDouble(x1, y1, x2, y2);
// }
//
// public static Rectangle rectangle(float x1, float y1, float x2, float y2) {
// return RectangleFloat.create(x1, y1, x2, y2);
// }
//
// public static Rectangle rectangleGeographic(double lon1, double lat1, double lon2,
// double lat2) {
// return rectangleGeographic((float) lon1, (float) lat1, (float) lon2, (float) lat2);
// }
//
// public static Rectangle rectangleGeographic(float lon1, float lat1, float lon2, float lat2) {
// float x1 = normalizeLongitude(lon1);
// float x2 = normalizeLongitude(lon2);
// if (x2 < x1) {
// x2 += 360;
// }
// return rectangle(x1, lat1, x2, lat2);
// }
//
// private static Rectangle rectangleDouble(double x1, double y1, double x2, double y2) {
// return RectangleDouble.create(x1, y1, x2, y2);
// }
//
// public static Circle circle(double x, double y, double radius) {
// return CircleDouble.create(x, y, radius);
// }
//
// public static Circle circle(float x, float y, float radius) {
// return CircleFloat.create(x, y, radius);
// }
//
// public static Line line(double x1, double y1, double x2, double y2) {
// return LineDouble.create(x1, y1, x2, y2);
// }
//
// public static Line line(float x1, float y1, float x2, float y2) {
// return LineFloat.create(x1, y1, x2, y2);
// }
//
// @VisibleForTesting
// static double normalizeLongitude(double d) {
// return normalizeLongitude((float) d);
// }
//
// private static float normalizeLongitude(float d) {
// if (d == -180.0f)
// return -180.0f;
// else {
// float sign = Math.signum(d);
// float x = Math.abs(d) / 360;
// float x2 = (x - (float) Math.floor(x)) * 360;
// if (x2 >= 180)
// x2 -= 360;
// return x2 * sign;
// }
// }
//
// private static double normalizeLongitudeDouble(double d) {
// if (d == -180.0f)
// return -180.0d;
// else {
// double sign = Math.signum(d);
// double x = Math.abs(d) / 360;
// double x2 = (x - (float) Math.floor(x)) * 360;
// if (x2 >= 180)
// x2 -= 360;
// return x2 * sign;
// }
// }
//
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/geometry/ListPair.java
// public final class ListPair<T extends HasGeometry> {
// private final Group<T> group1;
// private final Group<T> group2;
// // these non-final variable mean that this class is not thread-safe
// // because access to them is not synchronized
// private double areaSum = -1;
// private final double marginSum;
//
// public ListPair(List<T> list1, List<T> list2) {
// this.group1 = new Group<T>(list1);
// this.group2 = new Group<T>(list2);
// this.marginSum = group1.geometry().mbr().perimeter() + group2.geometry().mbr().perimeter();
// }
//
// public Group<T> group1() {
// return group1;
// }
//
// public Group<T> group2() {
// return group2;
// }
//
// public double areaSum() {
// if (areaSum == -1)
// areaSum = group1.geometry().mbr().area() + group2.geometry().mbr().area();
// return areaSum;
// }
//
// public double marginSum() {
// return marginSum;
// }
//
// }
// Path: src/test/java/com/github/davidmoten/rtree/SplitterRStarTest.java
import static org.junit.Assert.assertEquals;
import java.util.List;
import org.junit.Test;
import com.github.davidmoten.guavamini.Lists;
import com.github.davidmoten.rtree.geometry.Geometries;
import com.github.davidmoten.rtree.geometry.HasGeometry;
import com.github.davidmoten.rtree.geometry.ListPair;
package com.github.davidmoten.rtree;
public class SplitterRStarTest {
@Test
public void testGetPairs() {
int minSize = 2;
List<HasGeometry> list = Lists.newArrayList();
list.add(Geometries.point(1, 1).mbr());
list.add(Geometries.point(2, 2).mbr());
list.add(Geometries.point(3, 3).mbr());
list.add(Geometries.point(4, 4).mbr());
list.add(Geometries.point(5, 5).mbr()); | List<ListPair<HasGeometry>> pairs = SplitterRStar.getPairs(minSize, list); |
davidmoten/rtree | src/main/java/com/github/davidmoten/rtree/internal/Comparators.java | // Path: src/main/java/com/github/davidmoten/rtree/Entry.java
// public interface Entry<T, S extends Geometry> extends HasGeometry {
//
// T value();
//
// @Override
// S geometry();
//
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/Splitter.java
// public interface Splitter {
//
// /**
// * Splits a list of items into two lists of at least minSize.
// *
// * @param <T>
// * geometry type
// * @param items
// * list of items to split
// * @param minSize
// * min size of each list
// * @return two lists
// */
// <T extends HasGeometry> ListPair<T> split(List<T> items, int minSize);
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometry.java
// public interface Geometry {
//
// /**
// * <p>
// * Returns the distance to the given {@link Rectangle}. For a {@link Rectangle}
// * this might be Euclidean distance but for an EPSG4326 lat-long Rectangle might
// * be great-circle distance. The distance function should satisfy the following
// * properties:
// * </p>
// *
// * <p>
// * <code>distance(r) >= 0</code>
// * </p>
// *
// * <p>
// * <code>if r1 contains r2 then distance(r1)<=distance(r2)</code>
// * </p>
// *
// *
// * @param r
// * rectangle to measure distance to
// * @return distance to the rectangle r from the geometry
// */
// double distance(Rectangle r);
//
// /**
// * Returns the minimum bounding rectangle of this geometry.
// *
// * @return minimum bounding rectangle
// */
// Rectangle mbr();
//
// boolean intersects(Rectangle r);
//
// boolean isDoublePrecision();
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/geometry/Rectangle.java
// public interface Rectangle extends Geometry, HasGeometry {
//
// double x1();
//
// double y1();
//
// double x2();
//
// double y2();
//
// double area();
//
// double intersectionArea(Rectangle r);
//
// double perimeter();
//
// Rectangle add(Rectangle r);
//
// boolean contains(double x, double y);
//
// boolean isDoublePrecision();
//
// }
| import java.util.Comparator;
import java.util.List;
import com.github.davidmoten.rtree.Entry;
import com.github.davidmoten.rtree.Selector;
import com.github.davidmoten.rtree.Splitter;
import com.github.davidmoten.rtree.geometry.Geometry;
import com.github.davidmoten.rtree.geometry.HasGeometry;
import com.github.davidmoten.rtree.geometry.Rectangle; | package com.github.davidmoten.rtree.internal;
/**
* Utility functions asociated with {@link Comparator}s, especially for use with
* {@link Selector}s and {@link Splitter}s.
*
*/
public final class Comparators {
private Comparators() {
// prevent instantiation
}
public static <T extends HasGeometry> Comparator<HasGeometry> overlapAreaThenAreaIncreaseThenAreaComparator( | // Path: src/main/java/com/github/davidmoten/rtree/Entry.java
// public interface Entry<T, S extends Geometry> extends HasGeometry {
//
// T value();
//
// @Override
// S geometry();
//
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/Splitter.java
// public interface Splitter {
//
// /**
// * Splits a list of items into two lists of at least minSize.
// *
// * @param <T>
// * geometry type
// * @param items
// * list of items to split
// * @param minSize
// * min size of each list
// * @return two lists
// */
// <T extends HasGeometry> ListPair<T> split(List<T> items, int minSize);
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometry.java
// public interface Geometry {
//
// /**
// * <p>
// * Returns the distance to the given {@link Rectangle}. For a {@link Rectangle}
// * this might be Euclidean distance but for an EPSG4326 lat-long Rectangle might
// * be great-circle distance. The distance function should satisfy the following
// * properties:
// * </p>
// *
// * <p>
// * <code>distance(r) >= 0</code>
// * </p>
// *
// * <p>
// * <code>if r1 contains r2 then distance(r1)<=distance(r2)</code>
// * </p>
// *
// *
// * @param r
// * rectangle to measure distance to
// * @return distance to the rectangle r from the geometry
// */
// double distance(Rectangle r);
//
// /**
// * Returns the minimum bounding rectangle of this geometry.
// *
// * @return minimum bounding rectangle
// */
// Rectangle mbr();
//
// boolean intersects(Rectangle r);
//
// boolean isDoublePrecision();
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/geometry/Rectangle.java
// public interface Rectangle extends Geometry, HasGeometry {
//
// double x1();
//
// double y1();
//
// double x2();
//
// double y2();
//
// double area();
//
// double intersectionArea(Rectangle r);
//
// double perimeter();
//
// Rectangle add(Rectangle r);
//
// boolean contains(double x, double y);
//
// boolean isDoublePrecision();
//
// }
// Path: src/main/java/com/github/davidmoten/rtree/internal/Comparators.java
import java.util.Comparator;
import java.util.List;
import com.github.davidmoten.rtree.Entry;
import com.github.davidmoten.rtree.Selector;
import com.github.davidmoten.rtree.Splitter;
import com.github.davidmoten.rtree.geometry.Geometry;
import com.github.davidmoten.rtree.geometry.HasGeometry;
import com.github.davidmoten.rtree.geometry.Rectangle;
package com.github.davidmoten.rtree.internal;
/**
* Utility functions asociated with {@link Comparator}s, especially for use with
* {@link Selector}s and {@link Splitter}s.
*
*/
public final class Comparators {
private Comparators() {
// prevent instantiation
}
public static <T extends HasGeometry> Comparator<HasGeometry> overlapAreaThenAreaIncreaseThenAreaComparator( | final Rectangle r, final List<T> list) { |
davidmoten/rtree | src/main/java/com/github/davidmoten/rtree/internal/Comparators.java | // Path: src/main/java/com/github/davidmoten/rtree/Entry.java
// public interface Entry<T, S extends Geometry> extends HasGeometry {
//
// T value();
//
// @Override
// S geometry();
//
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/Splitter.java
// public interface Splitter {
//
// /**
// * Splits a list of items into two lists of at least minSize.
// *
// * @param <T>
// * geometry type
// * @param items
// * list of items to split
// * @param minSize
// * min size of each list
// * @return two lists
// */
// <T extends HasGeometry> ListPair<T> split(List<T> items, int minSize);
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometry.java
// public interface Geometry {
//
// /**
// * <p>
// * Returns the distance to the given {@link Rectangle}. For a {@link Rectangle}
// * this might be Euclidean distance but for an EPSG4326 lat-long Rectangle might
// * be great-circle distance. The distance function should satisfy the following
// * properties:
// * </p>
// *
// * <p>
// * <code>distance(r) >= 0</code>
// * </p>
// *
// * <p>
// * <code>if r1 contains r2 then distance(r1)<=distance(r2)</code>
// * </p>
// *
// *
// * @param r
// * rectangle to measure distance to
// * @return distance to the rectangle r from the geometry
// */
// double distance(Rectangle r);
//
// /**
// * Returns the minimum bounding rectangle of this geometry.
// *
// * @return minimum bounding rectangle
// */
// Rectangle mbr();
//
// boolean intersects(Rectangle r);
//
// boolean isDoublePrecision();
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/geometry/Rectangle.java
// public interface Rectangle extends Geometry, HasGeometry {
//
// double x1();
//
// double y1();
//
// double x2();
//
// double y2();
//
// double area();
//
// double intersectionArea(Rectangle r);
//
// double perimeter();
//
// Rectangle add(Rectangle r);
//
// boolean contains(double x, double y);
//
// boolean isDoublePrecision();
//
// }
| import java.util.Comparator;
import java.util.List;
import com.github.davidmoten.rtree.Entry;
import com.github.davidmoten.rtree.Selector;
import com.github.davidmoten.rtree.Splitter;
import com.github.davidmoten.rtree.geometry.Geometry;
import com.github.davidmoten.rtree.geometry.HasGeometry;
import com.github.davidmoten.rtree.geometry.Rectangle; | for (HasGeometry other : list) {
if (other != g) {
m += gPlusR.intersectionArea(other.geometry().mbr());
}
}
return m;
}
private static double areaIncrease(Rectangle r, HasGeometry g) {
Rectangle gPlusR = g.geometry().mbr().add(r);
return gPlusR.area() - g.geometry().mbr().area();
}
/**
* <p>
* Returns a comparator that can be used to sort entries returned by search
* methods. For example:
* </p>
* <p>
* <code>search(100).toSortedList(ascendingDistance(r))</code>
* </p>
*
* @param <T>
* the value type
* @param <S>
* the entry type
* @param r
* rectangle to measure distance to
* @return a comparator to sort by ascending distance from the rectangle
*/ | // Path: src/main/java/com/github/davidmoten/rtree/Entry.java
// public interface Entry<T, S extends Geometry> extends HasGeometry {
//
// T value();
//
// @Override
// S geometry();
//
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/Splitter.java
// public interface Splitter {
//
// /**
// * Splits a list of items into two lists of at least minSize.
// *
// * @param <T>
// * geometry type
// * @param items
// * list of items to split
// * @param minSize
// * min size of each list
// * @return two lists
// */
// <T extends HasGeometry> ListPair<T> split(List<T> items, int minSize);
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometry.java
// public interface Geometry {
//
// /**
// * <p>
// * Returns the distance to the given {@link Rectangle}. For a {@link Rectangle}
// * this might be Euclidean distance but for an EPSG4326 lat-long Rectangle might
// * be great-circle distance. The distance function should satisfy the following
// * properties:
// * </p>
// *
// * <p>
// * <code>distance(r) >= 0</code>
// * </p>
// *
// * <p>
// * <code>if r1 contains r2 then distance(r1)<=distance(r2)</code>
// * </p>
// *
// *
// * @param r
// * rectangle to measure distance to
// * @return distance to the rectangle r from the geometry
// */
// double distance(Rectangle r);
//
// /**
// * Returns the minimum bounding rectangle of this geometry.
// *
// * @return minimum bounding rectangle
// */
// Rectangle mbr();
//
// boolean intersects(Rectangle r);
//
// boolean isDoublePrecision();
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/geometry/Rectangle.java
// public interface Rectangle extends Geometry, HasGeometry {
//
// double x1();
//
// double y1();
//
// double x2();
//
// double y2();
//
// double area();
//
// double intersectionArea(Rectangle r);
//
// double perimeter();
//
// Rectangle add(Rectangle r);
//
// boolean contains(double x, double y);
//
// boolean isDoublePrecision();
//
// }
// Path: src/main/java/com/github/davidmoten/rtree/internal/Comparators.java
import java.util.Comparator;
import java.util.List;
import com.github.davidmoten.rtree.Entry;
import com.github.davidmoten.rtree.Selector;
import com.github.davidmoten.rtree.Splitter;
import com.github.davidmoten.rtree.geometry.Geometry;
import com.github.davidmoten.rtree.geometry.HasGeometry;
import com.github.davidmoten.rtree.geometry.Rectangle;
for (HasGeometry other : list) {
if (other != g) {
m += gPlusR.intersectionArea(other.geometry().mbr());
}
}
return m;
}
private static double areaIncrease(Rectangle r, HasGeometry g) {
Rectangle gPlusR = g.geometry().mbr().add(r);
return gPlusR.area() - g.geometry().mbr().area();
}
/**
* <p>
* Returns a comparator that can be used to sort entries returned by search
* methods. For example:
* </p>
* <p>
* <code>search(100).toSortedList(ascendingDistance(r))</code>
* </p>
*
* @param <T>
* the value type
* @param <S>
* the entry type
* @param r
* rectangle to measure distance to
* @return a comparator to sort by ascending distance from the rectangle
*/ | public static <T, S extends Geometry> Comparator<Entry<T, S>> ascendingDistance( |
davidmoten/rtree | src/main/java/com/github/davidmoten/rtree/internal/Comparators.java | // Path: src/main/java/com/github/davidmoten/rtree/Entry.java
// public interface Entry<T, S extends Geometry> extends HasGeometry {
//
// T value();
//
// @Override
// S geometry();
//
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/Splitter.java
// public interface Splitter {
//
// /**
// * Splits a list of items into two lists of at least minSize.
// *
// * @param <T>
// * geometry type
// * @param items
// * list of items to split
// * @param minSize
// * min size of each list
// * @return two lists
// */
// <T extends HasGeometry> ListPair<T> split(List<T> items, int minSize);
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometry.java
// public interface Geometry {
//
// /**
// * <p>
// * Returns the distance to the given {@link Rectangle}. For a {@link Rectangle}
// * this might be Euclidean distance but for an EPSG4326 lat-long Rectangle might
// * be great-circle distance. The distance function should satisfy the following
// * properties:
// * </p>
// *
// * <p>
// * <code>distance(r) >= 0</code>
// * </p>
// *
// * <p>
// * <code>if r1 contains r2 then distance(r1)<=distance(r2)</code>
// * </p>
// *
// *
// * @param r
// * rectangle to measure distance to
// * @return distance to the rectangle r from the geometry
// */
// double distance(Rectangle r);
//
// /**
// * Returns the minimum bounding rectangle of this geometry.
// *
// * @return minimum bounding rectangle
// */
// Rectangle mbr();
//
// boolean intersects(Rectangle r);
//
// boolean isDoublePrecision();
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/geometry/Rectangle.java
// public interface Rectangle extends Geometry, HasGeometry {
//
// double x1();
//
// double y1();
//
// double x2();
//
// double y2();
//
// double area();
//
// double intersectionArea(Rectangle r);
//
// double perimeter();
//
// Rectangle add(Rectangle r);
//
// boolean contains(double x, double y);
//
// boolean isDoublePrecision();
//
// }
| import java.util.Comparator;
import java.util.List;
import com.github.davidmoten.rtree.Entry;
import com.github.davidmoten.rtree.Selector;
import com.github.davidmoten.rtree.Splitter;
import com.github.davidmoten.rtree.geometry.Geometry;
import com.github.davidmoten.rtree.geometry.HasGeometry;
import com.github.davidmoten.rtree.geometry.Rectangle; | for (HasGeometry other : list) {
if (other != g) {
m += gPlusR.intersectionArea(other.geometry().mbr());
}
}
return m;
}
private static double areaIncrease(Rectangle r, HasGeometry g) {
Rectangle gPlusR = g.geometry().mbr().add(r);
return gPlusR.area() - g.geometry().mbr().area();
}
/**
* <p>
* Returns a comparator that can be used to sort entries returned by search
* methods. For example:
* </p>
* <p>
* <code>search(100).toSortedList(ascendingDistance(r))</code>
* </p>
*
* @param <T>
* the value type
* @param <S>
* the entry type
* @param r
* rectangle to measure distance to
* @return a comparator to sort by ascending distance from the rectangle
*/ | // Path: src/main/java/com/github/davidmoten/rtree/Entry.java
// public interface Entry<T, S extends Geometry> extends HasGeometry {
//
// T value();
//
// @Override
// S geometry();
//
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/Splitter.java
// public interface Splitter {
//
// /**
// * Splits a list of items into two lists of at least minSize.
// *
// * @param <T>
// * geometry type
// * @param items
// * list of items to split
// * @param minSize
// * min size of each list
// * @return two lists
// */
// <T extends HasGeometry> ListPair<T> split(List<T> items, int minSize);
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometry.java
// public interface Geometry {
//
// /**
// * <p>
// * Returns the distance to the given {@link Rectangle}. For a {@link Rectangle}
// * this might be Euclidean distance but for an EPSG4326 lat-long Rectangle might
// * be great-circle distance. The distance function should satisfy the following
// * properties:
// * </p>
// *
// * <p>
// * <code>distance(r) >= 0</code>
// * </p>
// *
// * <p>
// * <code>if r1 contains r2 then distance(r1)<=distance(r2)</code>
// * </p>
// *
// *
// * @param r
// * rectangle to measure distance to
// * @return distance to the rectangle r from the geometry
// */
// double distance(Rectangle r);
//
// /**
// * Returns the minimum bounding rectangle of this geometry.
// *
// * @return minimum bounding rectangle
// */
// Rectangle mbr();
//
// boolean intersects(Rectangle r);
//
// boolean isDoublePrecision();
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/geometry/Rectangle.java
// public interface Rectangle extends Geometry, HasGeometry {
//
// double x1();
//
// double y1();
//
// double x2();
//
// double y2();
//
// double area();
//
// double intersectionArea(Rectangle r);
//
// double perimeter();
//
// Rectangle add(Rectangle r);
//
// boolean contains(double x, double y);
//
// boolean isDoublePrecision();
//
// }
// Path: src/main/java/com/github/davidmoten/rtree/internal/Comparators.java
import java.util.Comparator;
import java.util.List;
import com.github.davidmoten.rtree.Entry;
import com.github.davidmoten.rtree.Selector;
import com.github.davidmoten.rtree.Splitter;
import com.github.davidmoten.rtree.geometry.Geometry;
import com.github.davidmoten.rtree.geometry.HasGeometry;
import com.github.davidmoten.rtree.geometry.Rectangle;
for (HasGeometry other : list) {
if (other != g) {
m += gPlusR.intersectionArea(other.geometry().mbr());
}
}
return m;
}
private static double areaIncrease(Rectangle r, HasGeometry g) {
Rectangle gPlusR = g.geometry().mbr().add(r);
return gPlusR.area() - g.geometry().mbr().area();
}
/**
* <p>
* Returns a comparator that can be used to sort entries returned by search
* methods. For example:
* </p>
* <p>
* <code>search(100).toSortedList(ascendingDistance(r))</code>
* </p>
*
* @param <T>
* the value type
* @param <S>
* the entry type
* @param r
* rectangle to measure distance to
* @return a comparator to sort by ascending distance from the rectangle
*/ | public static <T, S extends Geometry> Comparator<Entry<T, S>> ascendingDistance( |
davidmoten/rtree | src/test/java/com/github/davidmoten/rtree/Utilities.java | // Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometries.java
// public final class Geometries {
//
// private Geometries() {
// // prevent instantiation
// }
//
// public static Point point(double x, double y) {
// return PointDouble.create(x, y);
// }
//
// public static Point point(float x, float y) {
// return PointFloat.create(x, y);
// }
//
// public static Point pointGeographic(double lon, double lat) {
// return point(normalizeLongitudeDouble(lon), lat);
// }
//
// public static Point pointGeographic(float lon, float lat) {
// return point(normalizeLongitude(lon), lat);
// }
//
// public static Rectangle rectangle(double x1, double y1, double x2, double y2) {
// return rectangleDouble(x1, y1, x2, y2);
// }
//
// public static Rectangle rectangle(float x1, float y1, float x2, float y2) {
// return RectangleFloat.create(x1, y1, x2, y2);
// }
//
// public static Rectangle rectangleGeographic(double lon1, double lat1, double lon2,
// double lat2) {
// return rectangleGeographic((float) lon1, (float) lat1, (float) lon2, (float) lat2);
// }
//
// public static Rectangle rectangleGeographic(float lon1, float lat1, float lon2, float lat2) {
// float x1 = normalizeLongitude(lon1);
// float x2 = normalizeLongitude(lon2);
// if (x2 < x1) {
// x2 += 360;
// }
// return rectangle(x1, lat1, x2, lat2);
// }
//
// private static Rectangle rectangleDouble(double x1, double y1, double x2, double y2) {
// return RectangleDouble.create(x1, y1, x2, y2);
// }
//
// public static Circle circle(double x, double y, double radius) {
// return CircleDouble.create(x, y, radius);
// }
//
// public static Circle circle(float x, float y, float radius) {
// return CircleFloat.create(x, y, radius);
// }
//
// public static Line line(double x1, double y1, double x2, double y2) {
// return LineDouble.create(x1, y1, x2, y2);
// }
//
// public static Line line(float x1, float y1, float x2, float y2) {
// return LineFloat.create(x1, y1, x2, y2);
// }
//
// @VisibleForTesting
// static double normalizeLongitude(double d) {
// return normalizeLongitude((float) d);
// }
//
// private static float normalizeLongitude(float d) {
// if (d == -180.0f)
// return -180.0f;
// else {
// float sign = Math.signum(d);
// float x = Math.abs(d) / 360;
// float x2 = (x - (float) Math.floor(x)) * 360;
// if (x2 >= 180)
// x2 -= 360;
// return x2 * sign;
// }
// }
//
// private static double normalizeLongitudeDouble(double d) {
// if (d == -180.0f)
// return -180.0d;
// else {
// double sign = Math.signum(d);
// double x = Math.abs(d) / 360;
// double x2 = (x - (float) Math.floor(x)) * 360;
// if (x2 >= 180)
// x2 -= 360;
// return x2 * sign;
// }
// }
//
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/geometry/Rectangle.java
// public interface Rectangle extends Geometry, HasGeometry {
//
// double x1();
//
// double y1();
//
// double x2();
//
// double y2();
//
// double area();
//
// double intersectionArea(Rectangle r);
//
// double perimeter();
//
// Rectangle add(Rectangle r);
//
// boolean contains(double x, double y);
//
// boolean isDoublePrecision();
//
// }
| import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.List;
import com.github.davidmoten.rtree.geometry.Geometries;
import com.github.davidmoten.rtree.geometry.Rectangle; | package com.github.davidmoten.rtree;
public class Utilities {
static List<Entry<Object, Rectangle>> entries1000(Precision precision) {
List<Entry<Object, Rectangle>> list = new ArrayList<Entry<Object, Rectangle>>();
BufferedReader br = new BufferedReader(
new InputStreamReader(BenchmarksRTree.class.getResourceAsStream("/1000.txt")));
String line;
try {
while ((line = br.readLine()) != null) {
String[] items = line.split(" ");
double x = Double.parseDouble(items[0]);
double y = Double.parseDouble(items[1]);
Entry<Object, Rectangle> entry;
if (precision == Precision.DOUBLE) | // Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometries.java
// public final class Geometries {
//
// private Geometries() {
// // prevent instantiation
// }
//
// public static Point point(double x, double y) {
// return PointDouble.create(x, y);
// }
//
// public static Point point(float x, float y) {
// return PointFloat.create(x, y);
// }
//
// public static Point pointGeographic(double lon, double lat) {
// return point(normalizeLongitudeDouble(lon), lat);
// }
//
// public static Point pointGeographic(float lon, float lat) {
// return point(normalizeLongitude(lon), lat);
// }
//
// public static Rectangle rectangle(double x1, double y1, double x2, double y2) {
// return rectangleDouble(x1, y1, x2, y2);
// }
//
// public static Rectangle rectangle(float x1, float y1, float x2, float y2) {
// return RectangleFloat.create(x1, y1, x2, y2);
// }
//
// public static Rectangle rectangleGeographic(double lon1, double lat1, double lon2,
// double lat2) {
// return rectangleGeographic((float) lon1, (float) lat1, (float) lon2, (float) lat2);
// }
//
// public static Rectangle rectangleGeographic(float lon1, float lat1, float lon2, float lat2) {
// float x1 = normalizeLongitude(lon1);
// float x2 = normalizeLongitude(lon2);
// if (x2 < x1) {
// x2 += 360;
// }
// return rectangle(x1, lat1, x2, lat2);
// }
//
// private static Rectangle rectangleDouble(double x1, double y1, double x2, double y2) {
// return RectangleDouble.create(x1, y1, x2, y2);
// }
//
// public static Circle circle(double x, double y, double radius) {
// return CircleDouble.create(x, y, radius);
// }
//
// public static Circle circle(float x, float y, float radius) {
// return CircleFloat.create(x, y, radius);
// }
//
// public static Line line(double x1, double y1, double x2, double y2) {
// return LineDouble.create(x1, y1, x2, y2);
// }
//
// public static Line line(float x1, float y1, float x2, float y2) {
// return LineFloat.create(x1, y1, x2, y2);
// }
//
// @VisibleForTesting
// static double normalizeLongitude(double d) {
// return normalizeLongitude((float) d);
// }
//
// private static float normalizeLongitude(float d) {
// if (d == -180.0f)
// return -180.0f;
// else {
// float sign = Math.signum(d);
// float x = Math.abs(d) / 360;
// float x2 = (x - (float) Math.floor(x)) * 360;
// if (x2 >= 180)
// x2 -= 360;
// return x2 * sign;
// }
// }
//
// private static double normalizeLongitudeDouble(double d) {
// if (d == -180.0f)
// return -180.0d;
// else {
// double sign = Math.signum(d);
// double x = Math.abs(d) / 360;
// double x2 = (x - (float) Math.floor(x)) * 360;
// if (x2 >= 180)
// x2 -= 360;
// return x2 * sign;
// }
// }
//
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/geometry/Rectangle.java
// public interface Rectangle extends Geometry, HasGeometry {
//
// double x1();
//
// double y1();
//
// double x2();
//
// double y2();
//
// double area();
//
// double intersectionArea(Rectangle r);
//
// double perimeter();
//
// Rectangle add(Rectangle r);
//
// boolean contains(double x, double y);
//
// boolean isDoublePrecision();
//
// }
// Path: src/test/java/com/github/davidmoten/rtree/Utilities.java
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.List;
import com.github.davidmoten.rtree.geometry.Geometries;
import com.github.davidmoten.rtree.geometry.Rectangle;
package com.github.davidmoten.rtree;
public class Utilities {
static List<Entry<Object, Rectangle>> entries1000(Precision precision) {
List<Entry<Object, Rectangle>> list = new ArrayList<Entry<Object, Rectangle>>();
BufferedReader br = new BufferedReader(
new InputStreamReader(BenchmarksRTree.class.getResourceAsStream("/1000.txt")));
String line;
try {
while ((line = br.readLine()) != null) {
String[] items = line.split(" ");
double x = Double.parseDouble(items[0]);
double y = Double.parseDouble(items[1]);
Entry<Object, Rectangle> entry;
if (precision == Precision.DOUBLE) | entry = Entries.entry(new Object(), Geometries.rectangle(x, y, x + 1, y + 1)); |
davidmoten/rtree | src/test/java/com/github/davidmoten/rtree/GalleryMain.java | // Path: src/main/java/com/github/davidmoten/rtree/geometry/Point.java
// public interface Point extends Rectangle {
//
// double x();
//
// double y();
//
// }
| import java.util.Arrays;
import java.util.List;
import com.github.davidmoten.rtree.geometry.Point;
import rx.Observable; | package com.github.davidmoten.rtree;
public class GalleryMain {
public static void main(String[] args) { | // Path: src/main/java/com/github/davidmoten/rtree/geometry/Point.java
// public interface Point extends Rectangle {
//
// double x();
//
// double y();
//
// }
// Path: src/test/java/com/github/davidmoten/rtree/GalleryMain.java
import java.util.Arrays;
import java.util.List;
import com.github.davidmoten.rtree.geometry.Point;
import rx.Observable;
package com.github.davidmoten.rtree;
public class GalleryMain {
public static void main(String[] args) { | Observable<Entry<Object, Point>> entries = GreekEarthquakes.entries(Precision.DOUBLE) |
davidmoten/rtree | src/main/java/com/github/davidmoten/rtree/SerializerHelper.java | // Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometry.java
// public interface Geometry {
//
// /**
// * <p>
// * Returns the distance to the given {@link Rectangle}. For a {@link Rectangle}
// * this might be Euclidean distance but for an EPSG4326 lat-long Rectangle might
// * be great-circle distance. The distance function should satisfy the following
// * properties:
// * </p>
// *
// * <p>
// * <code>distance(r) >= 0</code>
// * </p>
// *
// * <p>
// * <code>if r1 contains r2 then distance(r1)<=distance(r2)</code>
// * </p>
// *
// *
// * @param r
// * rectangle to measure distance to
// * @return distance to the rectangle r from the geometry
// */
// double distance(Rectangle r);
//
// /**
// * Returns the minimum bounding rectangle of this geometry.
// *
// * @return minimum bounding rectangle
// */
// Rectangle mbr();
//
// boolean intersects(Rectangle r);
//
// boolean isDoublePrecision();
// }
| import com.github.davidmoten.rtree.geometry.Geometry;
import java.util.Optional; | package com.github.davidmoten.rtree;
public final class SerializerHelper {
private SerializerHelper() {
// prevent instantiation
}
| // Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometry.java
// public interface Geometry {
//
// /**
// * <p>
// * Returns the distance to the given {@link Rectangle}. For a {@link Rectangle}
// * this might be Euclidean distance but for an EPSG4326 lat-long Rectangle might
// * be great-circle distance. The distance function should satisfy the following
// * properties:
// * </p>
// *
// * <p>
// * <code>distance(r) >= 0</code>
// * </p>
// *
// * <p>
// * <code>if r1 contains r2 then distance(r1)<=distance(r2)</code>
// * </p>
// *
// *
// * @param r
// * rectangle to measure distance to
// * @return distance to the rectangle r from the geometry
// */
// double distance(Rectangle r);
//
// /**
// * Returns the minimum bounding rectangle of this geometry.
// *
// * @return minimum bounding rectangle
// */
// Rectangle mbr();
//
// boolean intersects(Rectangle r);
//
// boolean isDoublePrecision();
// }
// Path: src/main/java/com/github/davidmoten/rtree/SerializerHelper.java
import com.github.davidmoten.rtree.geometry.Geometry;
import java.util.Optional;
package com.github.davidmoten.rtree;
public final class SerializerHelper {
private SerializerHelper() {
// prevent instantiation
}
| public static <T, S extends Geometry> RTree<T, S> create(Optional<Node<T, S>> root, int size, |
davidmoten/rtree | src/main/java/com/github/davidmoten/rtree/Entries.java | // Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometry.java
// public interface Geometry {
//
// /**
// * <p>
// * Returns the distance to the given {@link Rectangle}. For a {@link Rectangle}
// * this might be Euclidean distance but for an EPSG4326 lat-long Rectangle might
// * be great-circle distance. The distance function should satisfy the following
// * properties:
// * </p>
// *
// * <p>
// * <code>distance(r) >= 0</code>
// * </p>
// *
// * <p>
// * <code>if r1 contains r2 then distance(r1)<=distance(r2)</code>
// * </p>
// *
// *
// * @param r
// * rectangle to measure distance to
// * @return distance to the rectangle r from the geometry
// */
// double distance(Rectangle r);
//
// /**
// * Returns the minimum bounding rectangle of this geometry.
// *
// * @return minimum bounding rectangle
// */
// Rectangle mbr();
//
// boolean intersects(Rectangle r);
//
// boolean isDoublePrecision();
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/internal/EntryDefault.java
// public final class EntryDefault<T, S extends Geometry> implements Entry<T, S> {
// private final T value;
// private final S geometry;
//
// /**
// * Constructor.
// *
// * @param value
// * the value of the entry
// * @param geometry
// * the geometry of the value
// */
// public EntryDefault(T value, S geometry) {
// Preconditions.checkNotNull(geometry);
// this.value = value;
// this.geometry = geometry;
// }
//
// /**
// * Factory method.
// *
// * @param <T>
// * type of value
// * @param <S>
// * type of geometry
// * @param value
// * object being given a spatial context
// * @param geometry
// * geometry associated with the value
// * @return entry wrapping value and associated geometry
// */
// public static <T, S extends Geometry> Entry<T, S> entry(T value, S geometry) {
// return new EntryDefault<T, S>(value, geometry);
// }
//
// /**
// * Returns the value wrapped by this {@link EntryDefault}.
// *
// * @return the entry value
// */
// @Override
// public T value() {
// return value;
// }
//
// @Override
// public S geometry() {
// return geometry;
// }
//
// @Override
// public String toString() {
// String builder = "Entry [value=" + value + ", geometry=" + geometry + "]";
// return builder;
// }
//
// @Override
// public int hashCode() {
// return Objects.hash(value, geometry);
// }
//
// @Override
// public boolean equals(Object obj) {
// @SuppressWarnings("rawtypes")
// Optional<EntryDefault> other = ObjectsHelper.asClass(obj, EntryDefault.class);
// if (other.isPresent()) {
// return Objects.equals(value, other.get().value)
// && Objects.equals(geometry, other.get().geometry);
// } else
// return false;
// }
//
// }
| import com.github.davidmoten.rtree.geometry.Geometry;
import com.github.davidmoten.rtree.internal.EntryDefault; | package com.github.davidmoten.rtree;
public final class Entries {
private Entries() {
// prevent instantiation
}
| // Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometry.java
// public interface Geometry {
//
// /**
// * <p>
// * Returns the distance to the given {@link Rectangle}. For a {@link Rectangle}
// * this might be Euclidean distance but for an EPSG4326 lat-long Rectangle might
// * be great-circle distance. The distance function should satisfy the following
// * properties:
// * </p>
// *
// * <p>
// * <code>distance(r) >= 0</code>
// * </p>
// *
// * <p>
// * <code>if r1 contains r2 then distance(r1)<=distance(r2)</code>
// * </p>
// *
// *
// * @param r
// * rectangle to measure distance to
// * @return distance to the rectangle r from the geometry
// */
// double distance(Rectangle r);
//
// /**
// * Returns the minimum bounding rectangle of this geometry.
// *
// * @return minimum bounding rectangle
// */
// Rectangle mbr();
//
// boolean intersects(Rectangle r);
//
// boolean isDoublePrecision();
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/internal/EntryDefault.java
// public final class EntryDefault<T, S extends Geometry> implements Entry<T, S> {
// private final T value;
// private final S geometry;
//
// /**
// * Constructor.
// *
// * @param value
// * the value of the entry
// * @param geometry
// * the geometry of the value
// */
// public EntryDefault(T value, S geometry) {
// Preconditions.checkNotNull(geometry);
// this.value = value;
// this.geometry = geometry;
// }
//
// /**
// * Factory method.
// *
// * @param <T>
// * type of value
// * @param <S>
// * type of geometry
// * @param value
// * object being given a spatial context
// * @param geometry
// * geometry associated with the value
// * @return entry wrapping value and associated geometry
// */
// public static <T, S extends Geometry> Entry<T, S> entry(T value, S geometry) {
// return new EntryDefault<T, S>(value, geometry);
// }
//
// /**
// * Returns the value wrapped by this {@link EntryDefault}.
// *
// * @return the entry value
// */
// @Override
// public T value() {
// return value;
// }
//
// @Override
// public S geometry() {
// return geometry;
// }
//
// @Override
// public String toString() {
// String builder = "Entry [value=" + value + ", geometry=" + geometry + "]";
// return builder;
// }
//
// @Override
// public int hashCode() {
// return Objects.hash(value, geometry);
// }
//
// @Override
// public boolean equals(Object obj) {
// @SuppressWarnings("rawtypes")
// Optional<EntryDefault> other = ObjectsHelper.asClass(obj, EntryDefault.class);
// if (other.isPresent()) {
// return Objects.equals(value, other.get().value)
// && Objects.equals(geometry, other.get().geometry);
// } else
// return false;
// }
//
// }
// Path: src/main/java/com/github/davidmoten/rtree/Entries.java
import com.github.davidmoten.rtree.geometry.Geometry;
import com.github.davidmoten.rtree.internal.EntryDefault;
package com.github.davidmoten.rtree;
public final class Entries {
private Entries() {
// prevent instantiation
}
| public static <T, S extends Geometry> Entry<T,S> entry(T object, S geometry) { |
davidmoten/rtree | src/main/java/com/github/davidmoten/rtree/Entries.java | // Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometry.java
// public interface Geometry {
//
// /**
// * <p>
// * Returns the distance to the given {@link Rectangle}. For a {@link Rectangle}
// * this might be Euclidean distance but for an EPSG4326 lat-long Rectangle might
// * be great-circle distance. The distance function should satisfy the following
// * properties:
// * </p>
// *
// * <p>
// * <code>distance(r) >= 0</code>
// * </p>
// *
// * <p>
// * <code>if r1 contains r2 then distance(r1)<=distance(r2)</code>
// * </p>
// *
// *
// * @param r
// * rectangle to measure distance to
// * @return distance to the rectangle r from the geometry
// */
// double distance(Rectangle r);
//
// /**
// * Returns the minimum bounding rectangle of this geometry.
// *
// * @return minimum bounding rectangle
// */
// Rectangle mbr();
//
// boolean intersects(Rectangle r);
//
// boolean isDoublePrecision();
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/internal/EntryDefault.java
// public final class EntryDefault<T, S extends Geometry> implements Entry<T, S> {
// private final T value;
// private final S geometry;
//
// /**
// * Constructor.
// *
// * @param value
// * the value of the entry
// * @param geometry
// * the geometry of the value
// */
// public EntryDefault(T value, S geometry) {
// Preconditions.checkNotNull(geometry);
// this.value = value;
// this.geometry = geometry;
// }
//
// /**
// * Factory method.
// *
// * @param <T>
// * type of value
// * @param <S>
// * type of geometry
// * @param value
// * object being given a spatial context
// * @param geometry
// * geometry associated with the value
// * @return entry wrapping value and associated geometry
// */
// public static <T, S extends Geometry> Entry<T, S> entry(T value, S geometry) {
// return new EntryDefault<T, S>(value, geometry);
// }
//
// /**
// * Returns the value wrapped by this {@link EntryDefault}.
// *
// * @return the entry value
// */
// @Override
// public T value() {
// return value;
// }
//
// @Override
// public S geometry() {
// return geometry;
// }
//
// @Override
// public String toString() {
// String builder = "Entry [value=" + value + ", geometry=" + geometry + "]";
// return builder;
// }
//
// @Override
// public int hashCode() {
// return Objects.hash(value, geometry);
// }
//
// @Override
// public boolean equals(Object obj) {
// @SuppressWarnings("rawtypes")
// Optional<EntryDefault> other = ObjectsHelper.asClass(obj, EntryDefault.class);
// if (other.isPresent()) {
// return Objects.equals(value, other.get().value)
// && Objects.equals(geometry, other.get().geometry);
// } else
// return false;
// }
//
// }
| import com.github.davidmoten.rtree.geometry.Geometry;
import com.github.davidmoten.rtree.internal.EntryDefault; | package com.github.davidmoten.rtree;
public final class Entries {
private Entries() {
// prevent instantiation
}
public static <T, S extends Geometry> Entry<T,S> entry(T object, S geometry) { | // Path: src/main/java/com/github/davidmoten/rtree/geometry/Geometry.java
// public interface Geometry {
//
// /**
// * <p>
// * Returns the distance to the given {@link Rectangle}. For a {@link Rectangle}
// * this might be Euclidean distance but for an EPSG4326 lat-long Rectangle might
// * be great-circle distance. The distance function should satisfy the following
// * properties:
// * </p>
// *
// * <p>
// * <code>distance(r) >= 0</code>
// * </p>
// *
// * <p>
// * <code>if r1 contains r2 then distance(r1)<=distance(r2)</code>
// * </p>
// *
// *
// * @param r
// * rectangle to measure distance to
// * @return distance to the rectangle r from the geometry
// */
// double distance(Rectangle r);
//
// /**
// * Returns the minimum bounding rectangle of this geometry.
// *
// * @return minimum bounding rectangle
// */
// Rectangle mbr();
//
// boolean intersects(Rectangle r);
//
// boolean isDoublePrecision();
// }
//
// Path: src/main/java/com/github/davidmoten/rtree/internal/EntryDefault.java
// public final class EntryDefault<T, S extends Geometry> implements Entry<T, S> {
// private final T value;
// private final S geometry;
//
// /**
// * Constructor.
// *
// * @param value
// * the value of the entry
// * @param geometry
// * the geometry of the value
// */
// public EntryDefault(T value, S geometry) {
// Preconditions.checkNotNull(geometry);
// this.value = value;
// this.geometry = geometry;
// }
//
// /**
// * Factory method.
// *
// * @param <T>
// * type of value
// * @param <S>
// * type of geometry
// * @param value
// * object being given a spatial context
// * @param geometry
// * geometry associated with the value
// * @return entry wrapping value and associated geometry
// */
// public static <T, S extends Geometry> Entry<T, S> entry(T value, S geometry) {
// return new EntryDefault<T, S>(value, geometry);
// }
//
// /**
// * Returns the value wrapped by this {@link EntryDefault}.
// *
// * @return the entry value
// */
// @Override
// public T value() {
// return value;
// }
//
// @Override
// public S geometry() {
// return geometry;
// }
//
// @Override
// public String toString() {
// String builder = "Entry [value=" + value + ", geometry=" + geometry + "]";
// return builder;
// }
//
// @Override
// public int hashCode() {
// return Objects.hash(value, geometry);
// }
//
// @Override
// public boolean equals(Object obj) {
// @SuppressWarnings("rawtypes")
// Optional<EntryDefault> other = ObjectsHelper.asClass(obj, EntryDefault.class);
// if (other.isPresent()) {
// return Objects.equals(value, other.get().value)
// && Objects.equals(geometry, other.get().geometry);
// } else
// return false;
// }
//
// }
// Path: src/main/java/com/github/davidmoten/rtree/Entries.java
import com.github.davidmoten.rtree.geometry.Geometry;
import com.github.davidmoten.rtree.internal.EntryDefault;
package com.github.davidmoten.rtree;
public final class Entries {
private Entries() {
// prevent instantiation
}
public static <T, S extends Geometry> Entry<T,S> entry(T object, S geometry) { | return EntryDefault.entry(object, geometry); |
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