sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
95c07a43d6ac9eef9f46a760e66e6c4b507a45b51d25d4fc530cc057661626cc | Go | 20,843 | 484 | package main
import (
"flag"
"fmt"
"log"
"math/rand"
"os"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/interval"
"github.com/vertgenlab/gonomics/sam"
)
func buildU... |
2113389734f5f17cd610b9f457d58838d0b38ff8bfff7bd7f35accfd0c8e9114 | Go | 21,156 | 311 | package align
import (
"log"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/numbers"
)
// ConstGap aligns two sequences (alpha, beta) using a score matrix (scores) and a constant gap penalty of gapPen.
// The return values are the alignment score and the cigar representing the alignment.
// ... |
3c748c78077cf836d567a7c7323c62ff1b9adf8070ed24aeefae12c7b5a97ec8 | Go | 21,546 | 344 | package align
import (
"log"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/numbers"
)
// reminder that unlike constGap, affineGap is an alignment algorithm that favors having a long gap compared to multiple gaps. In the code, affineGap data structures have an additional "k" dimension, which... |
5ba59de6ddf12b7128b67398ac91b2fe211cdba02422b11e577086963a3b187f | Go | 22,698 | 524 | // Package simulate contains functions for simulation of genomic data, including generating random sequences,
// variants, reads, or regions.
package simulate
import (
"log"
"math/rand"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/expandedTree"
"github.com/vertgenlab/gonomics/fasta"
"git... |
68ca1f60306a1089644d5727f3dc6896c9fd0b994b2d888000ca7f6e18b60c0d | Go | 22,947 | 622 | package genomeGraph
import (
"bytes"
"io"
"log"
"math"
"sort"
"sync"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/dna/dnaTwoBit"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fastq"
"github.com/vertgenlab/gonomics/... |
17034ad7cd8e2589bde1495a79bbb17c10529a41a91d9deeda28a4637fcfd4ca | Go | 25,095 | 625 | package reconstruct
import (
"testing"
"github.com/vertgenlab/gonomics/dna/pDna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/expandedTree"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fasta/pFasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/ver... |
32ab0d7230a0544bd82b30cc61d24145defabbb926cba80b185ff1c403470ffc | Go | 29,262 | 487 | // Command Group: "Linear Alignment Tools"
// Operates on 2 species, takes alignment maf, filters for trusted matches (s lines generated from the same chromosome in both species), and aligns the gap sequences between the trusted matches (affineGap, DefaultScoreMatrix)
package main
import (
"flag"
"fmt"
"io"
"log"... |
a7c0e93e7b94ec834857b732561617793efb55d8debf52e335a6f35d127fb997 | Go | 200,000 | 6,094 | package presets
func MakeNcbiMap() map[string]string {
n := map[string]string{
"NR_046018.2": "DDX11L1",
"NR_024540.1": "WASH7P",
"NR_106918.1": "MIR6859-1",
"NR_036051.1": "MIR1302-2",
"NR_026818.1": "FAM138A",
"NM_001005484.2": "OR4F5",
"NR_039983.2": "LOC729737"... |
f9acc8202a40019b9151ebb8f48a3e73a80a283b0ff2d61cc93be9a50fdc2e13 | Java | 113 | 5 | package org.broadinstitute.dropseqrna.utils.readiterators;
public enum StrandStrategy {
SENSE,ANTISENSE,BOTH
}
|
92f7e4e639d5a32fa68a9326516ec9f62e143d4e66d81107e1d0e16dc53be976 | Java | 126 | 4 | package arcade.core.agent.cell;
/** A {@code CellState} enum represents a cell agent state. */
public interface CellState {}
|
b79953ddbcb68eb322eb5fbd45f202980256e267ffaeca86a46491cd95c4b426 | Java | 141 | 6 | package org.broadinstitute.dropseqrna.annotation.functionaldata;
public enum FunctionalDataProcessorStrategy {
DROPSEQ,
STARSOLO;
}
|
5cd17a795222d4710cc35e1d056a0e3b7c2cd36f33d90469269fa13bfab5bdb4 | Java | 142 | 4 | package arcade.core.agent.process;
/** A {@code ProcessDomain} enum represents an agent process domain. */
public interface ProcessDomain {}
|
7fe7ee6e2edea56f572a8c3cdd12ab9219c6e9708ca4d3f5f637132b5293ad64 | Java | 147 | 6 | package org.broadinstitute.dropseqrna.annotation.functionaldata;
public interface PriorityScoreI {
public int getScore(FunctionalData fd);
}
|
4c5bd7c2d2d541ca3fc8a9530317d1b7d25bbc6895b10ded96f698e00c26bd5f | Java | 161 | 4 | package arcade.core.env.operation;
/** An {@code OperationCategory} enum represents an environment operation category. */
public interface OperationCategory {}
|
878bbd0d6b3e3e66214c29a99174ff2ca29b9f4aafd18531b169d7bb2f618f4a | Java | 162 | 5 | package de.uol.neuropsy.recorda.recorder;
public interface StreamQualityListener {
void streamQualityChanged(int streamNumber, QualityMetrics qualityNow);
}
|
3dd71cff3ac19eb409b005c2a362e2566008c258fc661943b30e64dbbe284a99 | Java | 172 | 9 | package edu.msu.cme.rdp.classifier.train;
public class NameRankDupException extends Exception {
public NameRankDupException(String msg){
super(msg);
}
}
|
2d5f84b95e5cbd3785c0adad785ed0d35963ae3eba7e82242e16966612833475 | Java | 191 | 7 | package org.broadinstitute.dropseqrna.barnyard.digitalallelecounts;
import java.util.Iterator;
public interface DigitalAlleleCountsGeneIteratorI extends Iterator<DigitalAlleleCounts> {
}
|
accb8577c1478a2fbde056d87aa4a10fad17e247a4ebeece1126365829f149c1 | Java | 212 | 9 | package org.broadinstitute.dropseqrna.barnyard.digitalallelecounts;
import htsjdk.samtools.util.Interval;
public interface SNPIntervalRecordI {
public Interval getSNPInterval ();
public int getNumBases();
}
|
ef82956cbc59f85ff4f18227f54369e639cf9785be9fbbb1dba716df9a2483cc | Java | 260 | 13 | package org.broadinstitute.dropseqrna.utils;
/**
* Interface to tag iterators that track how many reads pass or fail
* @author nemesh
*
*/
public interface PassFailTrackingIteratorI {
public long getRecordsPassed();
public long getRecordsFailed();
}
|
6d5fd0bf89883004a2d8e24454d102d8c476ac13b5c05dab864976424a17c018 | Java | 272 | 13 | package de.uol.neuropsy.recorda.recorder;
public enum QualityState {
OK("good"),
NOT_RESPONDING("not responding"),
LAGGY("lagging");
public final String displayName;
QualityState(String displayName) {
this.displayName = displayName;
}
}
|
ad531f8015064c3722c4ffa079e4fa6f3620de012b7edfc1ac3061759767d6f0 | Java | 278 | 11 | package org.broadinstitute.dropseqrna.barnyard.digitalallelecounts.sampleassignment;
import org.testng.annotations.Test;
public class GenerateSyntheticDoubletsTest {
@Test(enabled=false)
public void doWorkTest() {
throw new RuntimeException("Test not implemented");
}
}
|
6b6cfee5ecc11a79ebb39afa8a251d882534099bc57be43c3ffc83cfb21c452a | Java | 280 | 12 | package org.broadinstitute.dropseqrna.annotation.functionaldata.disambiguate;
public enum FunctionCategory {
SENSE_CODING,
RESOLVED_ANTISENSE_CODING,
ANTISENSE_CODING,
RESOLVED_SENSE_INTRONIC,
SENSE_INTRONIC,
AMBIGUOUS,
UNRESOLVED,
UNAMBIGUOUS;
}
|
929a0b16adf188802844fd370d174c89b75894156c9903eea555f7178b4a40f6 | Java | 373 | 23 | /*
* Taxon.java
*
* Created on November 10, 2003, 4:43 PM
*/
package edu.msu.cme.rdp.classifier.comparison;
/**
*
* @author wangqion
*/
public interface Taxon {
// the methods used by the JSP
String getName();
String getRank();
int getTaxid();
int getS1Count();
int getS2Count();
i... |
a59cee064d5fc404daf534f4cb4e26085fe8417528c7a77ea04b85a365f1a7a0 | Java | 501 | 18 | package org.broadinstitute.dropseqrna.utils.readiterators;
import java.util.Arrays;
import java.util.List;
import org.testng.Assert;
import org.testng.annotations.Test;
public class DEIteratorUtilsTest {
@Test
public void testRoundTrip() {
List<String> tags = Arrays.asList("XC", "XM");
List<Short> shortTags = ... |
01c398083284bfb38d7ee02d8821509fff6b2b3cab4594ca98a520bef9ee69b0 | Java | 504 | 30 | /*
* Window.java
*
* Created on November 15, 2006, 10:57 AM
*/
package edu.msu.cme.rdp.classifier.train.validation.movingwindow;
/**
*
* @author wangqion
*/
public class Window {
private int start;
private int stop;
/** Creates a new instance of Window */
public Window(int start, int stop) {
... |
a275331d634ad096d26759dd03b03e7eed86c580d455a92e56507509fa4571c9 | Java | 505 | 21 | /*
* ComparisonBrowserNode.java
*
* Created on November 17, 2003, 4:11 PM
*/
package edu.msu.cme.rdp.classifier.comparison;
import java.util.Iterator;
/**
*
* @author wangqion
*/
public interface ComparisonBrowserNode {
// the methods used by the ComparisonBrowserBean
void changeConfidence(SigCa... |
0bbc872c925050fddc7777f5b4304c6d37a283004f178d1cbd13356afef39c48 | Java | 515 | 16 | package examples;
import edu.ucsd.sccn.LSL;
public class ReceiveStringMarkers {
public static void main(String[] args) throws Exception {
System.out.println("Resolving a marker stream...");
LSL.StreamInfo[] results = LSL.resolve_stream("type","Markers");
LSL.StreamInlet inlet = new LSL.Str... |
f7ffca23b314ba99124945d7c245f31cafeb9b18f59c509f7f1aa162540722af | Java | 525 | 16 | package arcade.potts.sim.hamiltonian;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
import static arcade.core.ARCADETestUtilities.*;
public class JunctionHamiltonianConfigTest {
private static final double EPSILON = 1E-10;
@Test
public void getLambda_called_returnsV... |
58d050752ef61efaf575fd05696cbbfcb1dcbaa203a76fa75dc7119b2aedcdf4 | Java | 543 | 16 | package arcade.potts.sim.hamiltonian;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
import static arcade.core.ARCADETestUtilities.*;
public class SubstrateHamiltonianConfigTest {
private static final double EPSILON = 1E-10;
@Test
public void getSubstrate_called_retu... |
4c021593af3a10d560e08bae31e3900bdb84e0beb152a89b1901f26e07df17cf | Java | 552 | 22 | package arcade.potts.sim.output;
import com.google.gson.Gson;
import arcade.core.sim.Series;
import arcade.core.sim.output.OutputSaver;
/** Custom saver for potts-specific serialization. */
public final class PottsOutputSaver extends OutputSaver {
/**
* Creates a {@code PottsOutputSaver} for the series.
... |
3b7d9b1acf083002d36bc670772da4509deea9150330c8837cc316b6f5e9e63b | Java | 562 | 22 | package arcade.potts.sim.output;
import com.google.gson.Gson;
import arcade.core.sim.Series;
import arcade.core.sim.output.OutputLoader;
/** Custom loader for potts-specific deserialization. */
public final class PottsOutputLoader extends OutputLoader {
/**
* Creates a {@code PottsOutputLoader} for the serie... |
96b606edfbd7b782525d61f5c0b2a43ee9a6eb0f69d8730b16f621f0632a6802 | Java | 563 | 22 | package arcade.patch.sim.output;
import com.google.gson.Gson;
import arcade.core.sim.Series;
import arcade.core.sim.output.OutputLoader;
/** Custom loader for patch-specific deserialization. */
public final class PatchOutputLoader extends OutputLoader {
/**
* Creates an {@code PatchOutputLoader} for the seri... |
980126fada88ae7d4b450bbff1fe3741a474ed4ed70f545be5d8fd6a37c874f9 | Java | 568 | 15 | package org.broadinstitute.dropseqrna.utils.readiterators;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.util.IntervalList;
import org.broadinstitute.dropseqrna.utils.PredicateFilteredIterator;
import java.util.Iterator;
public class IntervalFilteringIterator extends PredicateFilteredIterator<SAMRecord> {... |
579b4b567106412fbc7234acb94ba9bb1b1b1c3a6b434803c9402fd76d9e247a | Java | 573 | 19 | package de.uol.neuropsy.recorda.util;
import android.os.AsyncTask;
import de.uol.neuropsy.recorda.MainActivity;
import edu.ucsd.sccn.LSL;
public class ResolveStreamsTask extends AsyncTask<MainActivity, Integer, LSL.StreamInfo[]> {
MainActivity parent;
protected LSL.StreamInfo[] do... |
0efc3dea1f437406d91ff4ded94df5efad38f33b46a3af0d09d1ae632f754e0c | Java | 574 | 18 | package arcade.potts.sim.output;
import org.junit.jupiter.api.Test;
import com.google.gson.Gson;
import arcade.core.sim.Series;
import arcade.core.sim.output.OutputSerializerTest;
import static org.mockito.Mockito.*;
public class PottsOutputSaverTest {
@Test
public void makeGSON_called_returnsObjects() {
... |
9581ae5c83b1f8932cad0d00f9e99aa3b8eefc005631b79bae2d5759d58e6e2a | Java | 578 | 20 | package org.broadinstitute.dropseqrna.annotation.functionaldata;
import picard.annotation.LocusFunction;
public class DropSeqPriorityScore implements PriorityScoreI {
public int getScore(FunctionalData fd) {
int result = switch (fd.getLocusFunction()) {
case null -> Integer.MAX_VALUE;
... |
4e26e39ad9975da85e940751f2f08b7ff3a78e67db1113597ed046533efcc827 | Java | 581 | 25 | package arcade.potts.sim.hamiltonian;
/** Configuration for {@link JunctionHamiltonian} parameters. */
class JunctionHamiltonianConfig {
/** Lambda multiplier for cell. */
private final double lambda;
/**
* Creates parameter configuration for {@code JunctionHamiltonian}.
*
* @param lambda t... |
fe3394548aee57f8f13c42c6485552806f2c5eee10b1e928538698ef008765c1 | Java | 583 | 31 | /*
* SeqErrorBean.java
*
* Created on November 17, 2003, 2:56 PM
*/
package edu.msu.cme.rdp.classifier.comparison;
/**
*
* @author siddiq15
*/
public class SeqErrorBean {
private String description;
private String message;
/** Creates a new instance of SeqErrorBean */
public SeqError... |
6057da2c9891d8ad7ae417e3e9bb8efa8a0375a530c452b6796f6636bbd8c1e7 | Java | 584 | 14 | package arcade.core.util.exceptions;
/** Exception thrown when parameter value is not equal to single expected value. */
public class InvalidParameterValueException extends RuntimeException {
/**
* Constructs an {@code InvalidParameterException} with the specified detail message.
*
* @param given th... |
7508aa253ea97f6d89de6fadd1c9a216716930835c7321b03a5c06641e86400f | Java | 585 | 18 | package arcade.potts.sim.output;
import org.junit.jupiter.api.Test;
import com.google.gson.Gson;
import arcade.core.sim.Series;
import arcade.core.sim.output.OutputDeserializerTest;
import static org.mockito.Mockito.*;
public class PottsOutputLoaderTest {
@Test
public void makeGSON_called_returnsObjects() {
... |
fabd488878084c5e9392ad1a56df7fa44e7168c4e3aeeaa8015879a2ec26ea02 | Java | 585 | 20 | package arcade.potts.agent.module;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Simulation;
import arcade.potts.agent.cell.PottsCell;
/** Extension of {@link PottsModule} for autosis. */
public class PottsModuleAutosis extends PottsModule {
/**
* Creates an autosis {@code Module} for the given ... |
26024f4b54591f269f3c7e8b06a2672f7386d38f0a51ae2e64d74acb9292c583 | Java | 588 | 20 | package arcade.potts.agent.module;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Simulation;
import arcade.potts.agent.cell.PottsCell;
/** Extension of {@link PottsModule} for necrosis. */
public class PottsModuleNecrosis extends PottsModule {
/**
* Creates a necrosis {@code Module} for the give... |
c5af0beac46c06643c4db9eccb4a738494c03b771a28ba4b95493d6b5db02071 | Java | 601 | 17 | package arcade.patch.env.lattice;
import arcade.core.util.MiniBox;
/** Concrete implementation of {@link PatchLatticeFactory} for triangular geometry. */
public final class PatchLatticeFactoryTri extends PatchLatticeFactory {
/** Creates a factory for making triangular {@link PatchLattice} instances. */
publi... |
12874812ca7105e3b022a86df3b7510192493ed189bb4dfa5edd48a905c3774e | Java | 604 | 18 | package arcade.potts.agent.module;
import org.junit.jupiter.api.Test;
import arcade.potts.agent.cell.PottsCellFlyNeuron;
import arcade.potts.util.PottsEnums.Phase;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.mockito.Mockito.*;
public class PottsModuleQuiescenceTest {
@Test
... |
8f19db19f0a55e04a49ef373b618fbfb603d239e5bc36121787a730e6941b5d8 | Java | 606 | 17 | package arcade.patch.env.lattice;
import arcade.core.util.MiniBox;
/** Concrete implementation of {@link PatchLatticeFactory} for rectangular geometry. */
public final class PatchLatticeFactoryRect extends PatchLatticeFactory {
/** Creates a factory for making rectangular {@link PatchLattice} instances. */
pu... |
8a8bad71f868f2caa55da6652734da73edbb8638cf77bc1256ff53d996c80c39 | Java | 611 | 23 | package org.broadinstitute.dropseqrna.annotation.functionaldata;
import org.apache.commons.collections4.map.HashedMap;
import picard.annotation.LocusFunction;
import java.util.*;
public class StarSoloPriorityScore implements PriorityScoreI {
public int getScore(FunctionalData fd) {
int result = switch (... |
2f89f376b26adbd7861eb43cf44ffce76089cbe4621cc64a69b01c90ee8453b0 | Java | 614 | 25 | package arcade.potts.sim.hamiltonian;
/** Configuration for {@link SubstrateHamiltonian} parameters. */
class SubstrateHamiltonianConfig {
/** Substrate adhesion for cell. */
private final double substrate;
/**
* Creates parameter configuration for {@code SubstrateHamiltonian}.
*
* @param s... |
3222495af6da0dfd9e04fb820426e46174b8aec74059cd43a51e6616648c0b80 | Java | 618 | 20 | package org.broadinstitute.dropseqrna.annotation.functionaldata.disambiguate;
import org.broadinstitute.dropseqrna.annotation.functionaldata.FunctionalData;
import org.broadinstitute.dropseqrna.utils.readiterators.GeneFunctionProcessor;
import java.util.List;
public class ClassifyStarSoloFunctionalData extends Class... |
764d7bb265915bce97f33ed2177c525428ebb515e9a0eff4cd3d0352f8336c60 | Java | 623 | 20 | package de.uol.neuropsy.recorda.recorder;
/**
* One measurement sample of the offset of a stream's time compared to a reference clock.
*/
public class TimingOffsetMeasurement {
/**
* The {@link LSL#local_clock()} time.
*/
public final double collectionTime;
/**
* The current mea... |
759a908aca607cfc18c96469d264c45a16a0d8627a70e0127415bef561b17a77 | Java | 628 | 18 | package org.broadinstitute.dropseqrna.barnyard.digitalallelecounts.sampleassignment.multisample;
import org.testng.Assert;
import org.testng.annotations.Test;
public class SamplePairAssignmentForCellTest {
@Test
public void testEqualsHash() {
SamplePairAssignmentForCell s1 = new SamplePairAssignmentForCell("cel... |
fbc9d6f458c5280097a57b3389bacdbe476837974ef3b13bcaaaea42b81a9a46 | Java | 631 | 20 | package org.broadinstitute.dropseqrna.annotation.functionaldata.disambiguate;
import org.broadinstitute.dropseqrna.utils.readiterators.GeneFunctionProcessor;
public class ClassifyFunctionalDataBase {
final String missingGeneLabel;
final GeneFunctionProcessor gfp;
public static final String DEFAULT_MISSIN... |
7e97c7534768f39d0bb199eb1da551a8ef5351726c8929693bb23492049fb8dd | Java | 661 | 25 | package examples;
import edu.ucsd.sccn.LSL;
public class ReceiveData {
public static void main(String[] args) throws Exception {
try {
System.out.println("Resolving an EEG stream...");
LSL.StreamInfo[] results = LSL.resolve_stream("type","EEG");
// open an inlet
LSL.StreamInlet inlet = new LSL.Stre... |
ae736ab21db063f7b4881b866fc084c710d75866a0ab1e0607f97df69eb1fd67 | Java | 662 | 18 | package org.broadinstitute.dropseqrna.eqtl;
public enum DonorMergeStrategy {
Sum("For each gene, sum the UMIs of each cell into a single MetaCell"),
Mean("For each gene, calculate the mean number of UMIs across cells into a single MetaCell"),
Median("For each gene, calculate the median number ... |
4824af32a16e6935b86d72d35af91bc0820908430e54617cf97131afe4929908 | Java | 674 | 22 | package arcade.potts.agent.module;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Simulation;
import arcade.potts.agent.cell.PottsCell;
import arcade.potts.util.PottsEnums.Phase;
/** Extension of {@link PottsModule} for quiescence. */
public class PottsModuleQuiescence extends PottsModule {
/**
*... |
9d80468aecf8959663588dde4f0c4ce8d8e69beb58fa722e702158d264d84eae | Java | 697 | 26 | package arcade.patch.agent.module;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Simulation;
import arcade.patch.agent.cell.PatchCell;
/**
* Extension of {@link PatchModule} for necrosis.
*
* <p>During necrosis, the cell is stopped but is not removed from the simulation.
*/
public class PatchModuleNe... |
851720b957b86fc19c2226f9694e5b4012290157d165e5d55baab34fd6e437c6 | Java | 703 | 27 | package arcade.core.util;
import java.util.Map;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.*;
public class EventLogTest {
static class EventLogMock extends EventLog {
EventLogMock(int timestamp, String eventType) {
su... |
10105e26da903d3a25e2c6bc043dfb76538ac9517e7367ade457a88343f7d55c | Java | 705 | 18 | package arcade.core.util.exceptions;
/** Exception thrown when a parameter is out of bounds. */
public class OutOfBoundsException extends RuntimeException {
/**
* Constructs an {@code OutOfBoundsException} with the specified detail message.
*
* @param given the given valid parameter value
* @pa... |
972ca3590d71a18ec181bb611e515dcde51a0aee2d5452f361bac0426c7c1b08 | Java | 720 | 25 | // ROI Manager Move Selections
//
// This macro moves all the ROI Manager
// selections a specified distance.
macro "Move Selections" {
requires("1.38e");
dx = 20;
dy = 20;
Dialog.create("Move Selections");
Dialog.addNumber("X Displacement:", dx);
Dialog.addNumber("Y D... |
3bcf79b1e3540d705ee80d7140af2c8740dcf4b29e41abb1d9627dd64a02f267 | Java | 726 | 26 | package arcade.potts.agent.module;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Simulation;
import arcade.potts.agent.cell.PottsCell;
/** Abstract extention of {@link PottsModule} for proliferation modules. */
public abstract class PottsModuleProliferation extends PottsModule {
/**
* Creates a... |
636faf5facb7737ee5218608c8ed7bda224584645e8bdf9f811bc5bb3fd9766a | Java | 727 | 30 | package arcade.core.env.lattice;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Series;
/**
* Factory class for {@link Lattice} objects.
*
* <p>The factory manages the creation of {@link Lattice} objects by:
*
* <ul>
* <li>Generating new instances based on layer settings
* </ul>
*/
public interf... |
7d8840c4609a5ba10ebbef60308cbc73dfcc0dca45a115e0ebc7ed6e4085bdb3 | Java | 747 | 31 | package org.broadinstitute.dropseqrna.utils;
import java.io.File;
import java.io.IOException;
import org.testng.annotations.Test;
import org.testng.Assert;
public class TagBamTest {
File INPUT = new File ("testdata/org/broadinstitute/dropseq/utils/unpaired_reads_tagged.bam");
File EXPECTED = new File ("testda... |
fd78a74e103b2084aa2afec9e68a067b565acd2f01606c91243bb970e6d1e951 | Java | 762 | 23 | /*
* CorrectAssignment.java
*
* Created on August 25, 2003, 3:04 PM
*/
package edu.msu.cme.rdp.classifier.train.validation;
/**
*
* @author wangqion
*/
public class CorrectAssignment {
public final int bins = 11; // bin range: 100-95, 94-90, 89-80, 79-70.....9-0
public int[] numCorrect = new int[bins... |
f5e7e09cc34dfa9dc51f33253547799a346c1543020b04c98a63dd953fffcc33 | Java | 779 | 28 | package org.broadinstitute.dropseqrna.utils.readiterators;
import java.util.function.Predicate;
import htsjdk.samtools.SAMRecord;
public class ReadEditDistancePredicate implements Predicate<SAMRecord> {
private Integer maxEditDistance;
public static final String EDIT_DISTANCE_TAG="NM";
public ReadEditDistancePr... |
79166d6821dd5d2e5c3044a68d7e0b38c758b6aece24bd1c00bf0c5d1780d282 | Java | 787 | 25 | package arcade.patch.agent.module;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Simulation;
import arcade.patch.agent.cell.PatchCell;
/**
* Extension of {@link PatchModule} for quiescence.
*
* <p>During senescence, cells cannot enter proliferative or migratory states but can still become
* apoptotic... |
a6faf7af5c1e530e4c9dc8735ffc109da2f5c479c20ef276d56c4c4013c89550 | Java | 807 | 42 | /*
* ShortSequenceException.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on November 24, 2003, 5:05 PM
*/
package edu.msu.cme.rdp.classifier;
/**
* Handles exception for a short sequence.
* @author wangqion
* @version
*/
public class ShortSequenceException extends Illega... |
6a1b23c3bc5b68dd113649e9e9ccd383563cd1617b1d7865886c641313e86434 | Java | 816 | 24 | package org.broadinstitute.dropseqrna.sbarro;
import org.testng.annotations.Test;
import org.testng.Assert;
public class BipartiteRabiesVirusCollapseResultTest {
/**
* These are purely for code coverage.
*/
@Test
public void equalsTest() {
BipartiteRabiesVirusCollapseResult r1 = new BipartiteRabiesVirusColl... |
6b43b54a6ba682e605a4f1693007d364ee8dd2139f34bd1412e0f3a7f2f2e644 | Java | 826 | 24 | package examples;
import edu.ucsd.sccn.LSL;
public class ReceiveDataInChunks {
public static void main(String[] args) throws Exception {
System.out.println("Resolving an EEG stream...");
LSL.StreamInfo[] results = LSL.resolve_stream("type","EEG");
// open an inlet
LSL.StreamInlet ... |
a55fde8ee4981db3be612c1b84e8b8139542a0b8837ae1a53073de0ef796272e | Java | 832 | 38 | /*
* TrainingDataException.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on November 13, 2003, 3:35 PM
*/
package edu.msu.cme.rdp.classifier;
/**
* Handles the exception occurred when parsing training information.
* @author wangqion
*/
public class TrainingDataException ext... |
64418d9d4e2b3e254deb8f8f41c233d7dfb247a29b7f8adbab8c6fc5893082e1 | Java | 833 | 34 | package org.broadinstitute.dropseqrna.utils;
import java.util.Arrays;
public class ByteArrayWrapper implements Comparable<ByteArrayWrapper> {
private final byte[] data;
public ByteArrayWrapper(byte[] data) {
this.data = data;
}
@Override
public boolean equals(Object obj) {
if (th... |
71fc83f5bbf4512b8b03f65399da5cadb94cda8fa8871b8fa2be1023d2d8d56a | Java | 835 | 28 | package arcade.core.env.location;
import arcade.core.agent.cell.CellContainer;
/**
* Container class for {@link Location} objects.
*
* <p>The container implementation should contain the minimal set of information needed to
* initialize a {@link Location} object. The container is used by the serializers/deserializ... |
f153ff11bd8291e1e99e30f6fc115d5f9216b85cb12a48b8bb3e9fd375c1613f | Java | 838 | 39 | /*
* ClassifierTest.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on September 19, 2003, 10:23 AM
*/
package edu.msu.cme.rdp.classifier.rrnaclassifier;
import junit.framework.*;
/**
* A test class for Classifier.
* @author wangqion
*/
public class ClassifierTest extends Te... |
2dbd1b3646f0f370c81556a1e313df5cc93eb5a82fe5b87f759c83bec2c75d53 | Java | 839 | 25 | package examples;
import edu.ucsd.sccn.LSL;
import java.io.IOException;
public class SendData {
public static void main(String[] args) throws IOException, InterruptedException {
System.out.println("Creating a new StreamInfo...");
LSL.StreamInfo info = new LSL.StreamInfo("BioSemi","EEG",8,100,LSL.C... |
c31b940f66dae05f5718e7b3098214e8b0619d6435772418a63998fb87be2be3 | Java | 843 | 26 | /*
* Copyright (C) 2012 Michigan State University <rdpstaff at msu.edu>
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 2 of the License, or
* (at your option) any later v... |
fcb6a53a1f0bbab829132d61cc7492efacd1c300c26f7e24da46de3a4a02d069 | Java | 846 | 26 | package arcade.patch.agent.module;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Simulation;
import arcade.patch.agent.cell.PatchCell;
/**
* Extension of {@link PatchModule} for quiescence.
*
* <p>During quiescence, cells cannot independently enter proliferative or migratory states unless
* they are ... |
bd2471ea6bde3b660799704f75ccbc66593f7b95b2f402b5764bbfbd92e7bbbe | Java | 856 | 28 | package arcade.patch.agent.module;
import arcade.core.agent.module.Module;
import arcade.patch.agent.cell.PatchCell;
import arcade.patch.env.location.PatchLocation;
/**
* Abstract implementation of {@link Module} for {@link PatchCell} agents.
*
* <p>Each module represents the behaviors of a cell in a given state.
... |
fbfcfda7a37945aa54dc44d4b6184f8be5bdafd6337a11211e486b2b2e3e0013 | Java | 877 | 34 | package org.broadinstitute.dropseqrna.utils.readiterators;
import java.util.Iterator;
import org.broadinstitute.dropseqrna.utils.TransformingIterator;
import htsjdk.samtools.SAMRecord;
/**
* All reads receive the default value for the outTag, which is the collapse tag's current value
* @author nemesh
*
*/
publi... |
1f2c5e91134c27d9028811a853b16ab6f7e3c6c65770267781d27ae6babe85ae | Java | 885 | 41 |
/*
* HierarchyTreeTest.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on June 25, 2002, 3:59 PM
*/
package edu.msu.cme.rdp.classifier.rrnaclassifier;
import junit.framework.*;
import java.io.*;
/**
* A test class for HierarchyTree.
* @author wangqi... |
95c0372e70c7d8eae1700615233e49a4b54c1a22ea444d63b4206d52f652ed58 | Java | 888 | 38 | package arcade.patch.env.location;
/** Representation of a coordinate. */
public abstract class Coordinate {
/** Coordinate z value. */
public final int z;
/**
* Creates a {@code Coordinate}.
*
* @param z the z coordinate value
*/
public Coordinate(int z) {
this.z = z;
... |
2508985860c88fec8fee41e3216f7d667f1995c5aa199becf1246b481cdbe072 | Java | 896 | 25 | package examples;
import edu.ucsd.sccn.LSL;
import java.io.IOException;
public class SendStringMarkers {
public static void main(String[] args) throws IOException, InterruptedException {
System.out.println("Creating a new StreamInfo...");
LSL.StreamInfo info = new LSL.StreamInfo("MyMarkers","Marke... |
353d62183d04735df6866d24e342f10af2e7314c00603a01cf0a43b414c47a68 | Java | 900 | 35 | package org.broadinstitute.dropseqrna.vcftools.filters;
import java.util.Iterator;
import org.broadinstitute.dropseqrna.utils.FilteredIterator;
import htsjdk.samtools.util.Log;
import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.VariantContext;
public class HetSNPFilter extends Filte... |
8ac46c46288a8d719c1fd5eca7532911188a62e2acc042108a6a58373cd9d42a | Java | 900 | 37 | /*
* RawGenusWordConditionalProb.java
* Copyright 2006 Michigan State University Board of Trustees
* Created on September 8, 2003, 1:47 PM
*/
package edu.msu.cme.rdp.classifier.train;
/**
* A RawGenusWordConditionalProb contains the index of the genus node and
* the conditional probability of the node contains ... |
9a09013d9c4b005e68c1eab199c8ba32e215da53979874e365ea4579a4bf367b | Java | 908 | 28 | package arcade.patch.util;
import java.util.Map;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
public class ProliferationEventLogTest {
private static final ProliferationEventLog LOG = new ProliferationEventLog(10, 1, 100);
@Test
public void constructor_called_sets... |
0a7f991d6ebf6ade5da0b254e9641c90716cb12498d0f9faf00a01d9e43208af | Java | 920 | 18 | package org.broadinstitute.dropseqrna.annotation.functionaldata;
import org.apache.commons.lang3.NotImplementedException;
import org.broadinstitute.dropseqrna.utils.readiterators.StrandStrategy;
import picard.annotation.LocusFunction;
import java.util.Collection;
public class FunctionalDataProcessorFactory {
pub... |
0c9d9d30b6f6aa963c756ce5a28be9e75d2b186fcbf3e27284f7fc79a3e323ac | Java | 943 | 34 | package arcade.potts.sim;
import arcade.core.sim.Series;
import arcade.potts.agent.cell.PottsCellFactory;
import arcade.potts.env.location.PottsLocationFactory;
import arcade.potts.env.location.PottsLocationFactory3D;
/** Extension of {@link PottsSimulation} for 3D. */
public final class PottsSimulation3D extends Pot... |
14d606edc9ecbd216ae706264aeaa49cd00d686bf2cb78ef3e37a7f5bc1cc0f5 | Java | 943 | 34 | package arcade.potts.sim;
import arcade.core.sim.Series;
import arcade.potts.agent.cell.PottsCellFactory;
import arcade.potts.env.location.PottsLocationFactory;
import arcade.potts.env.location.PottsLocationFactory2D;
/** Extension of {@link PottsSimulation} for 2D. */
public final class PottsSimulation2D extends Pot... |
75800c01dd731ba17f92a343f756b18ef83b03d093d766a1161b19e14cacc9ed | Java | 961 | 37 | package arcade.agent.module;
import arcade.agent.cell.Cell;
import arcade.sim.Series;
import arcade.sim.Simulation;
/**
* Extension of {@link arcade.agent.module.Signaling} for random signaling.
* <p>
* {@code SignalingRandom} simply randomly sets the migratory flag.
*
* @version 2.2.1
* @since 2.2
*/
publ... |
459f08949f012956d67cc9d3870db9e8a2869f76eeed113c15fe5ca5d601d29a | Java | 965 | 28 | package org.broadinstitute.dropseqrna.utils.editdistance;
import java.util.List;
import java.util.Set;
import org.broadinstitute.dropseqrna.utils.ObjectCounter;
public class FindSimilarEntitiesByEditDistance implements FindSimilarEntities<String, String> {
private final MapBarcodesByEditDistance mbed;
private fin... |
4d3ca7beb9b50689ff700ea8eb6dc2091581831fdf53b1ef34f586bc26ec72af | Java | 969 | 35 | /*
* ComparisonResultTreeSet.java
*
* Created on February 11, 2005, 1:22 PM
*/
package edu.msu.cme.rdp.classifier.comparison;
import java.util.TreeSet;
import java.util.Comparator;
/**
*
* @author wangqion
*/
public class ComparisonResultTreeSet extends TreeSet{
public ComparisonResultTreeSet(){
... |
477692c9a53a1912bf202c4b9476c79f7331372a598961314ed891957e8649b2 | Java | 977 | 39 | package arcade.core.env.location;
/**
* A {@code Location} object defines the cell location within the environment.
*
* <p>Each agent has a {@code Location} that identifies where they are within the {@link
* arcade.core.env.grid.Grid} (relative to other agents) and the {@link
* arcade.core.env.lattice.Lattice} (l... |
83560fa1fa4ae42d8415126474694cc117109b26192b44bb7c408a32571234f8 | Java | 978 | 34 | package org.broadinstitute.dropseqrna.utils.readiterators;
import htsjdk.samtools.SAMRecord;
import org.broadinstitute.dropseqrna.utils.FilteredIterator;
import org.broadinstitute.dropseqrna.utils.PredicateFilteredIterator;
import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator;
import java.... |
3f373f8ea92641f776e11899cc06ffb05b12500587c0c2b7c27c799d655d1416 | Java | 980 | 36 | package arcade.potts;
import arcade.core.ARCADE;
import arcade.core.sim.Series;
import arcade.core.sim.input.InputBuilder;
import arcade.core.sim.output.OutputLoader;
import arcade.core.sim.output.OutputSaver;
import arcade.potts.sim.input.PottsInputBuilder;
import arcade.potts.sim.output.PottsOutputLoader;
import arc... |
e6ae8e314b85e02322c6a6a108efba56a266b1dc128cbaea7118afe42936dd39 | Java | 1,003 | 43 |
/*
* ClassificationSuite.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on June 25, 2002, 3:59 PM
*/
package edu.msu.cme.rdp.classifier.train;
import junit.framework.*;
/**
* A test suite for package edu.msu.cme.rdp.classifier.train.
* @author wang... |
ba9b25d2892a4e603dd521d7e6f3e7ba4dec59f317c8d87d06fe4f5a7cd07a83 | Java | 1,017 | 26 | package examples;
import edu.ucsd.sccn.LSL;
import java.io.IOException;
public class SendDataInChunks {
public static void main(String[] args) throws IOException, InterruptedException {
System.out.println("Creating a new StreamInfo...");
LSL.StreamInfo info = new LSL.StreamInfo("BioSemi","EEG",8,1... |
52197fc235fa97e124b43d3e79ce432deabe5f851798218e4fa362afd78f718b | Java | 1,032 | 35 | package arcade.patch.agent.process;
import arcade.core.agent.process.Process;
import arcade.patch.agent.cell.PatchCell;
import arcade.patch.env.location.PatchLocation;
/**
* Abstract implementation of {@link Process} for {@link PatchCell} agents.
*
* <p>Each process represents internal cell mechanisms.
*/
public ... |
83188099472d0bc9097f225ca0a5bd51003eb3ae73eff692e0a1a2fe4f8a0016 | Java | 1,033 | 38 | package arcade.core.env.location;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Series;
/**
* Factory class for {@link Location} objects.
*
* <p>The factory manages the creation of {@link Location} objects by either:
*
* <ul>
* <li>Loading existing {@link LocationContainer} instances from a given... |
f22d92ac3dfc5906f65d5fddbad403d2d5128ad7e7942587f5edb3e739b2288e | Java | 1,048 | 34 | package arcade.patch.env.operation;
import arcade.core.env.operation.Operation;
import arcade.patch.env.lattice.PatchLattice;
/** Abstract implementation of {@link Operation} for {@link PatchLattice} environments. */
public abstract class PatchOperation implements Operation {
/** The {@link PatchLattice} the oper... |
334ad8a7e812619076b2d17ac3bd29dac21958cb487c473ff07b0a8485e85147 | Java | 1,058 | 39 | package org.broadinstitute.dropseqrna.utils.editdistance;
import org.testng.annotations.Test;
import org.testng.Assert;
public class BarcodeWithCountTest {
@SuppressWarnings("unlikely-arg-type")
@Test
public void testBarcodeWithCountTest() {
BarcodeWithCount b1 = new BarcodeWithCount("AAAA", 5);
BarcodeWithC... |
ea537a43e79da1d6fea58d2a2931aa3fe16c9147b5428a6a8d628e3bb06c967d | Java | 1,061 | 43 | package arcade.env.grid;
import arcade.env.loc.*;
import sim.util.Bag;
/**
* Extension of {@link arcade.env.grid.AgentGrid} for hexagonal grid.
* <p>
* Each hexagon location has six positions.
* Uses {@link arcade.env.loc.HexLocation} as {@link arcade.env.loc.Location} object.
*
* @version 2.3.0
* @since 2.0... |
1042a6ae73acd1fff841898ef797b96116abe6fcaed779a52c8822f602accdf6 | Java | 1,063 | 30 | package org.broadinstitute.dropseqrna.utils.readiterators;
import java.util.Collections;
import java.util.Iterator;
import org.testng.Assert;
import org.testng.annotations.Test;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordSetBuilder;
public class EditDistanceFilteringIteratorTest {
@Test
pub... |
11326db7fa1b4aa60bd07c9cbd87bc4f28a62114d47079e1b3765d9e3b2b0891 | Java | 1,072 | 42 | package org.broadinstitute.dropseqrna.annotation.functionaldata.disambiguate;
import com.google.common.base.Objects;
import org.broadinstitute.dropseqrna.annotation.functionaldata.FunctionalData;
public class GeneWithFunction {
private final String gene;
private final FunctionalData.Type category;
publi... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.