id int64 1 49k | buggy stringlengths 34 37.5k | fixed stringlengths 2 37k |
|---|---|---|
45,801 | sysLog("ImportOLD: " + Config.importOld);
if (Config.nurSenderLaden != null) {
sysLog("Nur Sender laden: " + StringUtils.join(Config.nurSenderLaden, ','));
}
sysLog("");
<BUG>sysLog("##################################################################################");
}</BUG>
public static synchronized void endMsg() {
sysLog("");
sysLog("");
| [DELETED] |
45,802 | strEx = " ";
}
retList.add(strEx + e.cl + " Fehlernummer: " + e.nr + " Anzahl: " + e.count);
}
}
<BUG>retList.add("##################################################################################");
return retList;</BUG>
}
public static synchronized void errorLog(int fehlerNummer, Exception ex) {
fehlermeldung_(fehlerNummer, ex, new String[]{});
| retList.add(LILNE);
return retList;
|
45,803 | public final static int VON_NR = 0;
public final static String NACH = "nach";
public final static int NACH_NR = 1;
public final static String[] COLUMN_NAMES = {VON, NACH};
public static final int MAX_ELEM = 2;
<BUG>public LinkedList<String[]> list = new LinkedList<>();
public void init() {
</BUG>
list.clear();
| public static LinkedList<String[]> list = new LinkedList<>();
public static void init() {
|
45,804 | public void init() {
</BUG>
list.clear();
list.add(new String[]{" ", "_"});
}
<BUG>public String replace(String strCheck, boolean pfad) {
</BUG>
Iterator<String[]> it = list.iterator();
while (it.hasNext()) {
String[] strReplace = it.next();
| public final static int VON_NR = 0;
public final static String NACH = "nach";
public final static int NACH_NR = 1;
public final static String[] COLUMN_NAMES = {VON, NACH};
public static final int MAX_ELEM = 2;
public static LinkedList<String[]> list = new LinkedList<>();
public static void init() {
public static String replace(String strCheck, boolean pfad) {
|
45,805 | import org.springframework.cloud.sleuth.log.SpanLogger;
import org.springframework.cloud.sleuth.sampler.AlwaysSampler;
import org.springframework.cloud.sleuth.sampler.NeverSampler;
import org.springframework.cloud.sleuth.trace.DefaultTracer;
import org.springframework.cloud.sleuth.trace.TestSpanContextHolder;
<BUG>import org.springframework.cloud.sleuth.util.ArrayListSpanAccumulator;
import org.springframework.http.HttpStatus;</BUG>
import org.springframework.http.MediaType;
import org.springframework.mock.web.MockFilterChain;
import org.springframework.mock.web.MockHttpServletRequest;
| import org.springframework.cloud.sleuth.util.ExceptionUtils;
import org.springframework.http.HttpStatus;
|
45,806 | public void should_set_random_spanid_if_header_value_is_invalid() {
BDDMockito.given(this.request.getHeader(Span.TRACE_ID_NAME))
.willReturn(String.valueOf(new Random().nextLong()));
BDDMockito.given(this.request.getHeader(Span.SPAN_ID_NAME))
.willReturn("invalid");
<BUG>try {
this.extractor.joinTrace(this.request);
fail("should throw an exception");
} catch (IllegalArgumentException e) {
then(e).hasMessageContaining("Malformed id");
}</BUG>
}
| then(this.extractor.joinTrace(this.request)).isNull();
|
45,807 | .willReturn(String.valueOf(new Random().nextLong()));
BDDMockito.given(this.request.getHeader(Span.SPAN_ID_NAME))
.willReturn(String.valueOf(new Random().nextLong()));
BDDMockito.given(this.request.getHeader(Span.PARENT_ID_NAME))
.willReturn("invalid");
<BUG>try {
this.extractor.joinTrace(this.request);
fail("should throw an exception");
} catch (IllegalArgumentException e) {
then(e).hasMessageContaining("Malformed id");
}</BUG>
}
| then(this.extractor.joinTrace(this.request)).isNull();
|
45,808 | }
@Override
public Span joinTrace(HttpServletRequest carrier) {
if (carrier.getHeader(Span.TRACE_ID_NAME) == null) {
return null;
<BUG>}
String uri = this.urlPathHelper.getPathWithinApplication(carrier);</BUG>
boolean skip = this.skipPattern.matcher(uri).matches()
|| Span.SPAN_NOT_SAMPLED.equals(carrier.getHeader(Span.SAMPLED_NAME));
long traceId = Span
| try {
String uri = this.urlPathHelper.getPathWithinApplication(carrier);
|
45,809 | boolean skip = this.skipPattern.matcher(uri).matches()
|| Span.SPAN_NOT_SAMPLED.equals(carrier.getHeader(Span.SAMPLED_NAME));
long traceId = Span
.hexToId(carrier.getHeader(Span.TRACE_ID_NAME));
long spanId = spanId(carrier, traceId);
<BUG>return buildParentSpan(carrier, uri, skip, traceId, spanId);
}</BUG>
private long spanId(HttpServletRequest carrier, long traceId) {
String spanId = carrier.getHeader(Span.SPAN_ID_NAME);
if (spanId == null) {
| } catch (Exception e) {
log.error("Exception occurred while trying to extract span from carrier", e);
return null;
}
}
|
45,810 | <BUG>package org.springframework.cloud.sleuth.instrument.messaging;
import org.springframework.cloud.sleuth.Span;</BUG>
import org.springframework.cloud.sleuth.SpanExtractor;
import org.springframework.cloud.sleuth.SpanInjector;
import org.springframework.cloud.sleuth.TraceKeys;
| import java.lang.invoke.MethodHandles;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.springframework.cloud.sleuth.Span;
|
45,811 | import org.springframework.messaging.support.ChannelInterceptorAdapter;
import org.springframework.messaging.support.ExecutorChannelInterceptor;
import org.springframework.messaging.support.MessageBuilder;
import org.springframework.util.ClassUtils;
abstract class AbstractTraceChannelInterceptor extends ChannelInterceptorAdapter
<BUG>implements ExecutorChannelInterceptor {
protected static final String MESSAGE_COMPONENT = "message";</BUG>
private final Tracer tracer;
private final TraceKeys traceKeys;
private final SpanExtractor<Message<?>> spanExtractor;
| private static final Log log = LogFactory.getLog(MethodHandles.lookup().lookupClass());
protected static final String MESSAGE_COMPONENT = "message";
|
45,812 | import org.dom4j.Node;
import org.orbeon.oxf.common.OXFException;
import org.orbeon.oxf.pipeline.api.PipelineContext;
import org.orbeon.oxf.pipeline.api.XMLReceiver;
import org.orbeon.oxf.processor.*;
<BUG>import org.orbeon.oxf.resources.ResourceManagerWrapper;
import org.orbeon.oxf.resources.URLFactory;
import org.orbeon.oxf.util.NumberUtils;</BUG>
import org.orbeon.oxf.xml.ContentHandlerHelper;
import org.orbeon.oxf.xml.XPathUtils;
| import org.orbeon.oxf.util.DateUtils;
import org.orbeon.oxf.util.NetUtils;
import org.orbeon.oxf.util.NumberUtils;
|
45,813 | import org.orbeon.oxf.pipeline.api.PipelineContext;
import org.orbeon.oxf.processor.ProcessorImpl;
import org.orbeon.oxf.processor.ProcessorInputOutputInfo;
import org.orbeon.oxf.processor.ProcessorUtils;
import org.orbeon.oxf.processor.serializer.FileSerializer;
<BUG>import org.orbeon.oxf.util.LoggerFactory;
import org.orbeon.oxf.xml.XPathUtils;</BUG>
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
| import org.orbeon.oxf.util.NetUtils;
import org.orbeon.oxf.xml.XPathUtils;
|
45,814 | try {
final Document config = readCacheInputAsDOM4J(context, INPUT_CONFIG);
for (Iterator i = XPathUtils.selectIterator(config, "/*/*"); i.hasNext();) {
final Element currentElement = (Element) i.next();
if (currentElement.getName().equals("delete")) {
<BUG>final File file = FileSerializer.getFile(
XPathUtils.selectStringValueNormalize(currentElement, "directory"),
XPathUtils.selectStringValueNormalize(currentElement, "file"),</BUG>
XPathUtils.selectStringValueNormalize(currentElement, "url"),
| final File file = NetUtils.getFile(
getDirectory(currentElement, "directory"),
XPathUtils.selectStringValueNormalize(currentElement, "file"),
|
45,815 |
XPathUtils.selectStringValueNormalize(currentElement, "directory"),
XPathUtils.selectStringValueNormalize(currentElement, "file"),</BUG>
XPathUtils.selectStringValueNormalize(currentElement, "url"),
getLocationData(),
<BUG>false,
getPropertySet()</BUG>
);
if (file.exists() && file.canWrite()) {
final boolean deleted = file.delete();
| try {
final Document config = readCacheInputAsDOM4J(context, INPUT_CONFIG);
for (Iterator i = XPathUtils.selectIterator(config, "/*/*"); i.hasNext();) {
final Element currentElement = (Element) i.next();
if (currentElement.getName().equals("delete")) {
final File file = NetUtils.getFile(
getDirectory(currentElement, "directory"),
XPathUtils.selectStringValueNormalize(currentElement, "file"),
false
|
45,816 | final boolean deleted = file.delete();
if (!deleted)
throw new OXFException("Can't delete file: " + file);
}
} else if (currentElement.getName().equals("move")) {
<BUG>final File fromFile = FileSerializer.getFile(
XPathUtils.selectStringValueNormalize(currentElement, "from/directory"),
XPathUtils.selectStringValueNormalize(currentElement, "from/file"),</BUG>
XPathUtils.selectStringValueNormalize(currentElement, "from/url"),
| final File fromFile = NetUtils.getFile(
getDirectory(currentElement, "from/directory"),
XPathUtils.selectStringValueNormalize(currentElement, "from/file"),
|
45,817 |
XPathUtils.selectStringValueNormalize(currentElement, "from/directory"),
XPathUtils.selectStringValueNormalize(currentElement, "from/file"),</BUG>
XPathUtils.selectStringValueNormalize(currentElement, "from/url"),
getLocationData(),
<BUG>false,
getPropertySet()</BUG>
);
if (!fromFile.exists() || ! fromFile.canRead()) {
throw new OXFException("Can't move file: " + fromFile);
| final boolean deleted = file.delete();
if (!deleted)
throw new OXFException("Can't delete file: " + file);
}
} else if (currentElement.getName().equals("move")) {
final File fromFile = NetUtils.getFile(
getDirectory(currentElement, "from/directory"),
XPathUtils.selectStringValueNormalize(currentElement, "from/file"),
false
|
45,818 | final boolean deleted = fromFile.delete();
if (!deleted)
throw new OXFException("Can't delete file " + fromFile + " after copying it to " + toFile);
}
} else if (currentElement.getName().equals("copy")) {
<BUG>final File fromFile = FileSerializer.getFile(
XPathUtils.selectStringValueNormalize(currentElement, "from/directory"),
XPathUtils.selectStringValueNormalize(currentElement, "from/file"),</BUG>
XPathUtils.selectStringValueNormalize(currentElement, "from/url"),
| final File fromFile = NetUtils.getFile(
getDirectory(currentElement, "from/directory"),
XPathUtils.selectStringValueNormalize(currentElement, "from/file"),
|
45,819 |
XPathUtils.selectStringValueNormalize(currentElement, "from/directory"),
XPathUtils.selectStringValueNormalize(currentElement, "from/file"),</BUG>
XPathUtils.selectStringValueNormalize(currentElement, "from/url"),
getLocationData(),
<BUG>false,
getPropertySet()</BUG>
);
if (!fromFile.exists() || ! fromFile.canRead()) {
throw new OXFException("Can't copy file: " + fromFile);
| final boolean deleted = fromFile.delete();
if (!deleted)
throw new OXFException("Can't delete file " + fromFile + " after copying it to " + toFile);
}
} else if (currentElement.getName().equals("copy")) {
final File fromFile = NetUtils.getFile(
getDirectory(currentElement, "from/directory"),
XPathUtils.selectStringValueNormalize(currentElement, "from/file"),
false
|
45,820 | import org.orbeon.oxf.pipeline.api.PipelineContext;
import org.orbeon.oxf.pipeline.api.XMLReceiver;
import org.orbeon.oxf.processor.*;
import org.orbeon.oxf.processor.serializer.store.ResultStore;
import org.orbeon.oxf.processor.serializer.store.ResultStoreOutputStream;
<BUG>import org.orbeon.oxf.properties.PropertySet;
import org.orbeon.oxf.resources.ResourceManagerWrapper;
import org.orbeon.oxf.resources.URLFactory;</BUG>
import org.orbeon.oxf.util.LoggerFactory;
import org.orbeon.oxf.util.NetUtils;
| [DELETED] |
45,821 | final Config config = readCacheInputAsObject(context, getInputByName(INPUT_CONFIG), new CacheableInputReader<Config>() {
public Config read(PipelineContext context, ProcessorInput input) {
return new Config(readInputAsDOM4J(context, input));
}
});
<BUG>final ProcessorInput dataInput = getInputByName(INPUT_DATA);
final File file = getFile(config.getDirectory(), config.getFile(), config.getUrl(), getLocationData(), config.isMakeDirectories(), getPropertySet());
</BUG>
if (!config.isAppend() && file.exists()) {
final boolean deleted = file.delete();
| final String directory = config.getDirectory() != null ? config.getDirectory() : getPropertySet().getString(DIRECTORY_PROPERTY);
final File file = NetUtils.getFile(directory, config.getFile(), config.getUrl(), getLocationData(), config.isMakeDirectories());
|
45,822 | if (!volume.getVolumeType().isSupported()) {
logUtil.logAuditMessage(volume.getClusterId(),
volume,
null,
AuditLogType.GLUSTER_VOLUME_TYPE_UNSUPPORTED,
<BUG>new HashMap<String, String>() {
{
put(GlusterConstants.VOLUME_TYPE, volume.getVolumeType().toString());
}
});</BUG>
}
| Collections.singletonMap(GlusterConstants.VOLUME_TYPE, volume.getVolumeType().toString()));
|
45,823 | log.info("Detected brick '{}' removed from volume '{}'. Removing it from engine DB as well.",
existingBrick.getQualifiedName(),
existingVolume.getName());
logUtil.logAuditMessage(existingVolume.getClusterId(), existingVolume, null,
AuditLogType.GLUSTER_VOLUME_BRICK_REMOVED_FROM_CLI,
<BUG>new HashMap<String, String>() {
{
put(GlusterConstants.BRICK, existingBrick.getQualifiedName());
}
});</BUG>
}
| Collections.singletonMap(GlusterConstants.BRICK, existingBrick.getQualifiedName()));
|
45,824 | if (volumeTypeUnSupported) {
logUtil.logAuditMessage(fetchedVolume.getClusterId(),
fetchedVolume,
null,
AuditLogType.GLUSTER_VOLUME_TYPE_UNSUPPORTED,
<BUG>new HashMap<String, String>() {
{
put(GlusterConstants.VOLUME_TYPE, fetchedVolume.getVolumeType().toString());
}
});</BUG>
}
| Collections.singletonMap(GlusterConstants.VOLUME_TYPE, fetchedVolume.getVolumeType().toString()));
|
45,825 | if (invalidExtensions != null)
{
throw new WebApplicationException(Response.status(Status.BAD_REQUEST).entity("Unsupported Extensions within this context: " + StringUtils.join(invalidExtensions, ",")).build());
}
}
<BUG>private HSimpleComment createComment(HTextFlowTarget target)
</BUG>
{
String authorname;
HDocument document = target.getTextFlow().getDocument();
| private String createComment(HTextFlowTarget target)
|
45,826 | package com.projecttango.examples.java.augmentedreality;
import com.google.atap.tangoservice.Tango;
import com.google.atap.tangoservice.Tango.OnTangoUpdateListener;
import com.google.atap.tangoservice.TangoCameraIntrinsics;
import com.google.atap.tangoservice.TangoConfig;
<BUG>import com.google.atap.tangoservice.TangoCoordinateFramePair;
import com.google.atap.tangoservice.TangoEvent;</BUG>
import com.google.atap.tangoservice.TangoOutOfDateException;
import com.google.atap.tangoservice.TangoPoseData;
import com.google.atap.tangoservice.TangoXyzIjData;
| import com.google.atap.tangoservice.TangoErrorException;
import com.google.atap.tangoservice.TangoEvent;
|
45,827 | super.onResume();
if (!mIsConnected) {
mTango = new Tango(AugmentedRealityActivity.this, new Runnable() {
@Override
public void run() {
<BUG>try {
connectTango();</BUG>
setupRenderer();
mIsConnected = true;
} catch (TangoOutOfDateException e) {
| TangoSupport.initialize();
connectTango();
|
45,828 | if (lastFramePose.statusCode == TangoPoseData.POSE_VALID) {
mRenderer.updateRenderCameraPose(lastFramePose, mExtrinsics);
mCameraPoseTimestamp = lastFramePose.timestamp;</BUG>
} else {
<BUG>Log.w(TAG, "Can't get device pose at time: " + mRgbTimestampGlThread);
}</BUG>
}
}
}
@Override
| mRenderer.updateRenderCameraPose(lastFramePose);
mCameraPoseTimestamp = lastFramePose.timestamp;
Log.w(TAG, "Can't get device pose at time: " +
|
45,829 | import org.rajawali3d.materials.Material;
import org.rajawali3d.materials.methods.DiffuseMethod;
import org.rajawali3d.materials.textures.ATexture;
import org.rajawali3d.materials.textures.StreamingTexture;
import org.rajawali3d.materials.textures.Texture;
<BUG>import org.rajawali3d.math.Matrix4;
import org.rajawali3d.math.vector.Vector3;</BUG>
import org.rajawali3d.primitives.ScreenQuad;
import org.rajawali3d.primitives.Sphere;
import org.rajawali3d.renderer.RajawaliRenderer;
| import org.rajawali3d.math.Quaternion;
import org.rajawali3d.math.vector.Vector3;
|
45,830 | translationMoon.setRepeatMode(Animation.RepeatMode.INFINITE);
translationMoon.setTransformable3D(moon);
getCurrentScene().registerAnimation(translationMoon);
translationMoon.play();
}
<BUG>public void updateRenderCameraPose(TangoPoseData devicePose, DeviceExtrinsics extrinsics) {
Pose cameraPose = ScenePoseCalculator.toOpenGlCameraPose(devicePose, extrinsics);
getCurrentCamera().setRotation(cameraPose.getOrientation());
getCurrentCamera().setPosition(cameraPose.getPosition());
}</BUG>
public int getTextureId() {
| public void updateRenderCameraPose(TangoPoseData cameraPose) {
float[] rotation = cameraPose.getRotationAsFloats();
float[] translation = cameraPose.getTranslationAsFloats();
Quaternion quaternion = new Quaternion(rotation[3], rotation[0], rotation[1], rotation[2]);
getCurrentCamera().setRotation(quaternion.conjugate());
getCurrentCamera().setPosition(translation[0], translation[1], translation[2]);
|
45,831 | package com.projecttango.examples.java.helloareadescription;
import com.google.atap.tangoservice.Tango;
<BUG>import com.google.atap.tangoservice.Tango.OnTangoUpdateListener;
import com.google.atap.tangoservice.TangoConfig;</BUG>
import com.google.atap.tangoservice.TangoCoordinateFramePair;
import com.google.atap.tangoservice.TangoErrorException;
import com.google.atap.tangoservice.TangoEvent;
| import com.google.atap.tangoservice.TangoAreaDescriptionMetaData;
import com.google.atap.tangoservice.TangoConfig;
|
45,832 | public synchronized Annotator get(String name) {
if (!this.annotators.containsKey(name)) {
AnnotatorFactory factory = this.factories.get(name);
if (factory == null) {
throw new IllegalArgumentException("No annotator named " + name);
<BUG>}
this.annotators.put(name, factory.create());
}</BUG>
return this.annotators.get(name);
| [DELETED] |
45,833 | public StanfordCoreNLP(String propsFileNamePrefix, boolean enforceRequirements) {
Properties props = loadProperties(propsFileNamePrefix);
if (props == null) {
throw new RuntimeIOException("ERROR: cannot find properties file \"" + propsFileNamePrefix + "\" in the classpath!");
}
<BUG>construct(props, enforceRequirements, getAnnotatorImplementations());
}</BUG>
protected AnnotatorImplementations getAnnotatorImplementations() {
return new AnnotatorImplementations();
}
| AnnotatorImplementations impl = getAnnotatorImplementations();
construct(props, enforceRequirements, impl, getDefaultAnnotatorPool(props, impl));
|
45,834 | } catch (NoClassDefFoundError ex) {
return false;
}
return true;
}
<BUG>private void construct(Properties props, boolean enforceRequirements, AnnotatorImplementations annotatorImplementations) {
</BUG>
Timing tim = new Timing();
this.numWords = 0;
this.constituentTreePrinter = new TreePrint("penn");
| private void construct(Properties props, boolean enforceRequirements, AnnotatorImplementations annotatorImplementations, AnnotatorPool pool) {
|
45,835 | import org.springframework.web.socket.config.annotation.WebSocketHandlerRegistry;
@Configuration
public class SmoothieConfig implements WebSocketConfigurer {
@Override
public void registerWebSocketHandlers(WebSocketHandlerRegistry registry) {
<BUG>registry.addHandler(cpuDataHandler(), "/smoothieSockJS").withSockJS();
</BUG>
}
@Bean
public WebSocketHandler cpuDataHandler() {
| registry.addHandler(cpuDataHandler(), "/smoothieSockJS").setAllowedOrigins("*").withSockJS();
|
45,836 | import org.springframework.web.socket.config.annotation.WebSocketHandlerRegistry;
@Configuration
public class BrainConfig implements WebSocketConfigurer {
@Override
public void registerWebSocketHandlers(WebSocketHandlerRegistry registry) {
<BUG>registry.addHandler(brainHandler(), "/brainsockjs").withSockJS();
</BUG>
}
@Bean
public WebSocketHandler brainHandler() {
| registry.addHandler(brainHandler(), "/brainsockjs").setAllowedOrigins("*").withSockJS();
|
45,837 | import org.springframework.web.socket.handler.PerConnectionWebSocketHandler;
@Configuration
public class SnakeConfig implements WebSocketConfigurer {
@Override
public void registerWebSocketHandlers(WebSocketHandlerRegistry registry) {
<BUG>registry.addHandler(snakeWebSocketHandler(), "/snakesockjs").withSockJS();
</BUG>
}
@Bean
public WebSocketHandler snakeWebSocketHandler() {
| registry.addHandler(snakeWebSocketHandler(), "/snakesockjs").setAllowedOrigins("*").withSockJS();
|
45,838 | import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.security.DigestOutputStream;
import java.security.MessageDigest;
<BUG>import java.security.NoSuchAlgorithmException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;</BUG>
public final class PatchUtils {
| import java.text.DateFormat;
import java.util.Date;
import java.util.List;
|
45,839 | package org.jboss.as.patching.runner;
<BUG>import org.jboss.as.boot.DirectoryStructure;
import org.jboss.as.patching.LocalPatchInfo;</BUG>
import org.jboss.as.patching.PatchInfo;
import org.jboss.as.patching.PatchLogger;
import org.jboss.as.patching.PatchMessages;
| import static org.jboss.as.patching.runner.PatchUtils.generateTimestamp;
import org.jboss.as.patching.CommonAttributes;
import org.jboss.as.patching.LocalPatchInfo;
|
45,840 | private static final String PATH_DELIMITER = "/";
public static final byte[] NO_CONTENT = PatchingTask.NO_CONTENT;
enum Element {
ADDED_BUNDLE("added-bundle"),
ADDED_MISC_CONTENT("added-misc-content"),
<BUG>ADDED_MODULE("added-module"),
BUNDLES("bundles"),</BUG>
CUMULATIVE("cumulative"),
DESCRIPTION("description"),
MISC_FILES("misc-files"),
| APPLIES_TO_VERSION("applies-to-version"),
BUNDLES("bundles"),
|
45,841 | final int count = reader.getAttributeCount();
for (int i = 0; i < count; i++) {
final String value = reader.getAttributeValue(i);
final Attribute attribute = Attribute.forName(reader.getAttributeLocalName(i));
switch (attribute) {
<BUG>case APPLIES_TO_VERSION:
builder.addAppliesTo(value);
break;</BUG>
case RESULTING_VERSION:
if(type == Patch.PatchType.CUMULATIVE) {
| [DELETED] |
45,842 | final StringBuilder path = new StringBuilder();
for(final String p : item.getPath()) {
path.append(p).append(PATH_DELIMITER);
}
path.append(item.getName());
<BUG>writer.writeAttribute(Attribute.PATH.name, path.toString());
if(type != ModificationType.REMOVE) {</BUG>
writer.writeAttribute(Attribute.HASH.name, bytesToHexString(item.getContentHash()));
}
if(type != ModificationType.ADD) {
| if (item.isDirectory()) {
writer.writeAttribute(Attribute.DIRECTORY.name, "true");
if(type != ModificationType.REMOVE) {
|
45,843 | package org.jboss.as.patching;
import org.jboss.as.controller.OperationFailedException;
import org.jboss.as.patching.runner.PatchingException;
import org.jboss.logging.Messages;
import org.jboss.logging.annotations.Message;
<BUG>import org.jboss.logging.annotations.MessageBundle;
import java.io.IOException;</BUG>
import java.util.List;
@MessageBundle(projectCode = "JBAS")
public interface PatchMessages {
| import org.jboss.logging.annotations.Cause;
import java.io.IOException;
|
45,844 | if (!Orient.instance().isActive())
Orient.instance().startup();
}
@Test
public void testSupportedFreezeTrue() {
<BUG>OLocalPaginatedStorage storage = Mockito.mock(OLocalPaginatedStorage.class);
ODistributedStorage ds = new ODistributedStorage(Mockito.mock(OServer.class), storage);
ds.freeze(true);</BUG>
Mockito.verify(storage).freeze(true);
}
| [DELETED] |
45,845 | private final I18n i18n;
private Filter filter;
ApplicationElement(TodoItemRepository repository, I18n i18n) {
this.repository = repository;
this.i18n = i18n;
<BUG>Elements.Builder builder = new Elements.Builder()
.section().css("todoapp")</BUG>
.header().css("header")
.h(1).innerText(i18n.constants().todos()).end()
.input(text)
| TodoBuilder builder = new TodoBuilder()
.section().css("todoapp")
|
45,846 | import static org.junit.Assert.assertNotNull;
import static org.mockito.Matchers.anyString;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
public class ElementsBuilderTest {
<BUG>private Elements.Builder builder;
</BUG>
@Before
public void setUp() {
Document document = mock(Document.class);
| private TestableBuilder builder;
|
45,847 | when(document.createParagraphElement()).thenAnswer(invocation -> new StandaloneElement("p"));
when(document.createSelectElement()).thenAnswer(invocation -> new StandaloneInputElement("select"));
when(document.createSpanElement()).thenAnswer(invocation -> new StandaloneElement("span"));
when(document.createTextAreaElement()).thenAnswer(invocation -> new StandaloneInputElement("textarea"));
when(document.createUListElement()).thenAnswer(invocation -> new StandaloneElement("ul"));
<BUG>builder = new Elements.Builder(document);
</BUG>
}
@Test
public void headings() {
| builder = new TestableBuilder(document);
|
45,848 | TodoItemRepository repository = new TodoItemRepository(BEAN_FACTORY);
ApplicationElement application = new ApplicationElement(repository, i18n);
Element body = Browser.getDocument().getBody();
body.appendChild(application.asElement());
body.appendChild(new FooterElement(i18n).asElement());
<BUG>Element e = new MyBuilder().ahref( "http://www.google.com" )
.img( "https://www.google.com/images/branding/googlelogo/1x/googlelogo_color_272x92dp.png" ).end()
.end().build();
body.appendChild( e );</BUG>
History.addValueChangeHandler(event -> application.filter(event.getValue()));
| [DELETED] |
45,849 | @Override
public String toString() {
return (container ? "container" : "simple") + " @ " + level + ": " + element.getTagName();
}
}
<BUG>public static class Builder extends CoreBuilder<Builder>
{
public Builder() {
super(Browser.getDocument());
}
protected Builder(Document document) {
super( document );</BUG>
}
| [DELETED] |
45,850 | return start(document.createElement(tag));
}
public B start(Element element) {
elements.push(new ElementInfo(element, true, level));
level++;
<BUG>return (B) this;
}</BUG>
public B end() {
assertCurrent();
if (level == 0) {
| return that();
|
45,851 | Element closingElement = elements.peek().element;
for (ElementInfo child : children) {
closingElement.appendChild(child.element);
}
level--;
<BUG>return (B) this;
}</BUG>
private String dumpElements() {
return elements.toString();
}
| return that();
|
45,852 | }
public B on(EventType type, EventListener listener) {
assertCurrent();
Element element = elements.peek().element;
type.register(element, listener);
<BUG>return (B) this;
}</BUG>
public B rememberAs(String id) {
assertCurrent();
references.put(id, elements.peek().element);
| public B attr(String name, String value) {
elements.peek().element.setAttribute(name, value);
return that();
|
45,853 | import org.apache.sling.jcr.resource.JcrResourceConstants;
import org.apache.sling.jcr.resource.internal.JcrResourceResolverFactoryImpl;
import org.apache.sling.jcr.resource.internal.helper.MapEntries;
import org.apache.sling.jcr.resource.internal.helper.Mapping;
import org.apache.sling.performance.annotation.PerformanceTestSuite;
<BUG>import org.apache.sling.performance.tests.ResolveNonExistingWith10000AliasTest;
import org.apache.sling.performance.tests.ResolveNonExistingWith10000VanityPathTest;
import org.apache.sling.performance.tests.ResolveNonExistingWith1000AliasTest;
import org.apache.sling.performance.tests.ResolveNonExistingWith1000VanityPathTest;
import org.apache.sling.performance.tests.ResolveNonExistingWith5000AliasTest;
import org.apache.sling.performance.tests.ResolveNonExistingWith5000VanityPathTest;</BUG>
import org.junit.runner.RunWith;
| import org.apache.sling.performance.tests.ResolveNonExistingWithManyAliasTest;
import org.apache.sling.performance.tests.ResolveNonExistingWithManyVanityPathTest;
|
45,854 | @PerformanceTestSuite
public ParameterizedTestList testPerformance() throws Exception {
Helper helper = new Helper();
ParameterizedTestList testCenter = new ParameterizedTestList();
testCenter.setTestSuiteTitle("jcr.resource-2.0.10");
<BUG>testCenter.addTestObject(new ResolveNonExistingWith1000VanityPathTest(helper));
testCenter.addTestObject(new ResolveNonExistingWith5000VanityPathTest(helper));
testCenter.addTestObject(new ResolveNonExistingWith10000VanityPathTest(helper));
testCenter.addTestObject(new ResolveNonExistingWith1000AliasTest(helper));
testCenter.addTestObject(new ResolveNonExistingWith5000AliasTest(helper));
testCenter.addTestObject(new ResolveNonExistingWith10000AliasTest(helper));
</BUG>
return testCenter;
| testCenter.addTestObject(new ResolveNonExistingWithManyVanityPathTest("ResolveNonExistingWith1000VanityPathTest",helper, 100, 10));
testCenter.addTestObject(new ResolveNonExistingWithManyVanityPathTest("ResolveNonExistingWith5000VanityPathTest",helper, 100, 50));
testCenter.addTestObject(new ResolveNonExistingWithManyVanityPathTest("ResolveNonExistingWith10000VanityPathTest",helper, 100, 100));
testCenter.addTestObject(new ResolveNonExistingWithManyAliasTest("ResolveNonExistingWithManyAliasTest",helper, 1000));
testCenter.addTestObject(new ResolveNonExistingWithManyAliasTest("ResolveNonExistingWith5000AliasTest",helper, 5000));
testCenter.addTestObject(new ResolveNonExistingWithManyAliasTest("ResolveNonExistingWith10000AliasTest",helper, 10000));
|
45,855 | package org.apache.sling.performance;
<BUG>import static org.mockito.Mockito.*;
import javax.jcr.NamespaceRegistry;</BUG>
import javax.jcr.Session;
import junitx.util.PrivateAccessor;
| import static org.mockito.Mockito.when;
import static org.mockito.Mockito.mock;
import javax.jcr.NamespaceRegistry;
|
45,856 | import org.apache.sling.jcr.resource.JcrResourceConstants;
import org.apache.sling.jcr.resource.internal.JcrResourceResolverFactoryImpl;
import org.apache.sling.jcr.resource.internal.helper.MapEntries;
import org.apache.sling.jcr.resource.internal.helper.Mapping;
import org.apache.sling.performance.annotation.PerformanceTestSuite;
<BUG>import org.apache.sling.performance.tests.ResolveNonExistingWith10000AliasTest;
import org.apache.sling.performance.tests.ResolveNonExistingWith10000VanityPathTest;
import org.apache.sling.performance.tests.ResolveNonExistingWith1000AliasTest;
import org.apache.sling.performance.tests.ResolveNonExistingWith1000VanityPathTest;
import org.apache.sling.performance.tests.ResolveNonExistingWith5000AliasTest;
import org.apache.sling.performance.tests.ResolveNonExistingWith5000VanityPathTest;</BUG>
import org.junit.runner.RunWith;
| import org.apache.sling.performance.tests.ResolveNonExistingWithManyAliasTest;
import org.apache.sling.performance.tests.ResolveNonExistingWithManyVanityPathTest;
|
45,857 | import org.apache.sling.api.resource.ResourceResolver;
import org.apache.sling.jcr.api.SlingRepository;
import org.apache.sling.jcr.resource.JcrResourceConstants;
import org.apache.sling.jcr.resource.internal.helper.jcr.JcrResourceProviderFactory;
import org.apache.sling.performance.annotation.PerformanceTestSuite;
<BUG>import org.apache.sling.performance.tests.ResolveNonExistingWith10000AliasTest;
import org.apache.sling.performance.tests.ResolveNonExistingWith10000VanityPathTest;
import org.apache.sling.performance.tests.ResolveNonExistingWith1000AliasTest;
import org.apache.sling.performance.tests.ResolveNonExistingWith1000VanityPathTest;
import org.apache.sling.performance.tests.ResolveNonExistingWith5000AliasTest;
import org.apache.sling.performance.tests.ResolveNonExistingWith5000VanityPathTest;</BUG>
import org.apache.sling.resourceresolver.impl.ResourceResolverFactoryActivator;
| import org.apache.sling.performance.tests.ResolveNonExistingWithManyAliasTest;
import org.apache.sling.performance.tests.ResolveNonExistingWithManyVanityPathTest;
|
45,858 | @PerformanceTestSuite
public ParameterizedTestList testPerformance() throws Exception {
Helper helper = new Helper();
ParameterizedTestList testCenter = new ParameterizedTestList();
testCenter.setTestSuiteTitle("jcr.resource-2.2.0");
<BUG>testCenter.addTestObject(new ResolveNonExistingWith1000VanityPathTest(helper));
testCenter.addTestObject(new ResolveNonExistingWith5000VanityPathTest(helper));
testCenter.addTestObject(new ResolveNonExistingWith10000VanityPathTest(helper));
testCenter.addTestObject(new ResolveNonExistingWith1000AliasTest(helper));
testCenter.addTestObject(new ResolveNonExistingWith5000AliasTest(helper));
testCenter.addTestObject(new ResolveNonExistingWith10000AliasTest(helper));
</BUG>
return testCenter;
| testCenter.addTestObject(new ResolveNonExistingWithManyVanityPathTest("ResolveNonExistingWith1000VanityPathTest",helper, 100, 10));
testCenter.addTestObject(new ResolveNonExistingWithManyVanityPathTest("ResolveNonExistingWith5000VanityPathTest",helper, 100, 50));
testCenter.addTestObject(new ResolveNonExistingWithManyVanityPathTest("ResolveNonExistingWith10000VanityPathTest",helper, 100, 100));
testCenter.addTestObject(new ResolveNonExistingWithManyAliasTest("ResolveNonExistingWith1000AliasTest",helper, 1000));
testCenter.addTestObject(new ResolveNonExistingWithManyAliasTest("ResolveNonExistingWith5000AliasTest",helper, 5000));
testCenter.addTestObject(new ResolveNonExistingWithManyAliasTest("ResolveNonExistingWith10000AliasTest",helper, 10000));
|
45,859 | import me.gnat008.perworldinventory.config.PwiProperties;
import me.gnat008.perworldinventory.config.Settings;
import me.gnat008.perworldinventory.data.DataWriter;
import me.gnat008.perworldinventory.groups.Group;
import me.gnat008.perworldinventory.groups.GroupManager;
<BUG>import net.milkbowl.vault.economy.Economy;
import org.bukkit.Bukkit;</BUG>
import org.bukkit.GameMode;
import org.bukkit.entity.Player;
import org.bukkit.potion.PotionEffect;
| import net.milkbowl.vault.economy.EconomyResponse;
import org.bukkit.Bukkit;
|
45,860 | import me.gnat008.perworldinventory.PerWorldInventory;
import me.gnat008.perworldinventory.PwiLogger;
import me.gnat008.perworldinventory.config.PwiProperties;
import me.gnat008.perworldinventory.config.Settings;
import me.gnat008.perworldinventory.data.players.PWIPlayer;
<BUG>import net.milkbowl.vault.economy.Economy;
import org.bukkit.entity.Player;</BUG>
import javax.inject.Inject;
public class PlayerSerializer {
@Inject
| import net.milkbowl.vault.economy.EconomyResponse;
import org.bukkit.entity.Player;
|
45,861 | if (econ == null) {
PwiLogger.warning("Economy saving is turned on, but no economy found!");
return;
}
PwiLogger.debug("[ECON] Withdrawing " + econ.getBalance(player) + " from '" + player.getName() + "'!");
<BUG>econ.withdrawPlayer(player, econ.getBalance(player));
econ.bankWithdraw(player.getName(), econ.bankBalance(player.getName()).amount);
if (data.has("economy")) {
EconomySerializer.deserialize(econ, data.getAsJsonObject("economy"), player);</BUG>
}
| [DELETED] |
45,862 | package com.liferay.portal.kernel.servlet;
import com.liferay.portal.kernel.util.CookieUtil;
<BUG>import com.liferay.portal.kernel.util.HashUtil;
import com.liferay.portal.kernel.util.Validator;
import java.io.Serializable;
import javax.servlet.http.Cookie;</BUG>
import javax.servlet.http.HttpServletResponse;
| import com.liferay.portal.kernel.util.StringPool;
import java.io.Externalizable;
import java.io.IOException;
import java.io.ObjectInput;
import java.io.ObjectOutput;
import javax.servlet.http.Cookie;
|
45,863 | sb.append(serverPort);
sb.append("}");
return sb.toString();
}
protected String contentType;
<BUG>protected Cookie[] cookies;
</BUG>
protected Map<String, Serializable> distributedRequestAttributes;
protected Map<String, List<String>> headerMap;
protected Map<String, FileItem[]> multipartParameterMap;
| protected byte[][] cookiesData;
|
45,864 | log.info("Trying to schedule 24h reminder in the past ("+new Date(reminderTime)+"), no reminder will be sent for eval ("+eval.getTitle()+") ["+eval.getId()+"]");
reminderTime = 0;
} else {
log.info("Scheduling a reminder ("+new Date(reminderTime)+") for 24h before the end ("+new Date(dueTime)+") of the evaluation ("+eval.getTitle()+") ["+eval.getId()+"]");
}
<BUG>}
}</BUG>
return reminderTime;
}
protected void sendAvailableEmail(Long evalId) {
| } else if (reminderDays == -2) {
reminderTime = System.currentTimeMillis() + (1000l * 60l * 5l); // reminders every 5 minutes
log.warn("REMINDERS TESTING ONLY (-2): Scheduling a reminder in the near future ("+new Date(reminderTime)+") for testing: due date ("+new Date(dueTime)+") of the evaluation ("+eval.getTitle()+") ["+eval.getId()+"]");
|
45,865 | } else {
String[] stateList = statusStr.trim().split(" ");
logger.info("GroupMembershipSync.execute() syncing " + statusStr);
for(String state : stateList) {
List<EvalEvaluation> evals = evaluationService.getEvaluationsByState(state);
<BUG>int count = 0;
if(evals != null) {
count = evals.size();
}</BUG>
if(logger.isInfoEnabled()) {
| int count = evals.size();
|
45,866 | import java.text.DateFormat;
import java.util.Calendar;
import java.util.Date;
import java.util.GregorianCalendar;
import java.util.List;
<BUG>import java.util.Locale;
import org.sakaiproject.evaluation.constant.EvalConstants;</BUG>
import org.sakaiproject.evaluation.logic.EvalAuthoringService;
import org.sakaiproject.evaluation.logic.EvalCommonLogic;
import org.sakaiproject.evaluation.logic.EvalEvaluationService;
| import org.azeckoski.reflectutils.ArrayUtils;
import org.sakaiproject.evaluation.constant.EvalConstants;
|
45,867 | readOnly = config.getEditMode() != UserStorageProvider.EditMode.WRITABLE;
}
return ProviderConfigurationBuilder.create()
.property().name(LDAPConstants.EDIT_MODE)
.type(ProviderConfigProperty.STRING_TYPE)
<BUG>.add()
.property().name(LDAPConstants.SYNC_REGISTRATIONS)</BUG>
.type(ProviderConfigProperty.BOOLEAN_TYPE)
.defaultValue("false")
.add()
| .property().name(UserStorageProviderModel.IMPORT_ENABLED)
.defaultValue("true")
.property().name(LDAPConstants.SYNC_REGISTRATIONS)
|
45,868 | import org.keycloak.component.ComponentValidationException;
import org.keycloak.models.KeycloakSession;
import org.keycloak.models.RealmModel;
import org.keycloak.provider.ProviderConfigProperty;
import org.keycloak.provider.ProviderConfigurationBuilder;
<BUG>import org.keycloak.storage.UserStorageProvider;
import org.keycloak.storage.ldap.LDAPConfig;</BUG>
import org.keycloak.storage.ldap.LDAPStorageProvider;
import java.util.List;
public class UserAttributeLDAPStorageMapperFactory extends AbstractLDAPStorageMapperFactory implements LDAPConfigDecorator {
| import org.keycloak.storage.UserStorageProviderModel;
import org.keycloak.storage.ldap.LDAPConfig;
|
45,869 | protected static final List<ProviderConfigProperty> configProperties;
static {
List<ProviderConfigProperty> props = getConfigProps(null);
configProperties = props;
}
<BUG>private static List<ProviderConfigProperty> getConfigProps(ComponentModel parent) {
String readOnly = "false";
if (parent != null) {
LDAPConfig ldapConfig = new LDAPConfig(parent.getConfig());</BUG>
readOnly = ldapConfig.getEditMode() == UserStorageProvider.EditMode.WRITABLE ? "false" : "true";
| [DELETED] |
45,870 | import org.keycloak.component.SubComponentFactory;
import org.keycloak.models.KeycloakSession;
import org.keycloak.models.KeycloakSessionFactory;
import org.keycloak.models.RealmModel;
import org.keycloak.provider.ProviderConfigProperty;
<BUG>import org.keycloak.representations.idm.UserFederationMapperSyncConfigRepresentation;
import java.util.Collections;</BUG>
import java.util.List;
public interface LDAPStorageMapperFactory<T extends LDAPStorageMapper> extends SubComponentFactory<T, LDAPStorageMapper> {
T create(KeycloakSession session, ComponentModel model);
| import org.keycloak.storage.UserStorageProviderModel;
import java.util.Collections;
|
45,871 | return this.ldapIdentityStore;
}
public EditMode getEditMode() {
return editMode;
}
<BUG>public ComponentModel getModel() {
return model;</BUG>
}
public LDAPStorageMapperManager getMapperManager() {
return mapperManager;
| public UserStorageProviderModel getModel() {
return model;
|
45,872 | v.vibrate(pattern, vibrateIndefinitely);
return v;</BUG>
}catch(Exception e){
if(LOG_ENABLE)
<BUG>Log.w(TAG, "Vibration exception (" + e.getMessage() + "). Remember to set permission android.permission.VIBRATE in your manifest application file.");
</BUG>
}
return null;
}
@SuppressWarnings("deprecation")
| }else{
Log.i(TAG, "Device can not vibrate.");
return v;
Log.e(TAG, "Vibration exception (" + e.getMessage() + "). Remember to set permission android.permission.VIBRATE in your manifest application file.");
|
45,873 | private boolean dataSaved = true;
private double bubbleScale = 1;
private static boolean useLogFile = true;
private LastSelectedFolder lastSelectedFolder;
private PTMFactory ptmFactory;
<BUG>private EnzymeFactory enzymeFactory = EnzymeFactory.getInstance();
private UtilitiesUserPreferences utilitiesUserPreferences;</BUG>
private ProcessingPreferences processingPreferences = new ProcessingPreferences();
private ProgressDialogX progressDialog;
private OverviewPanel overviewPanel;
| private EnzymeFactory enzymeFactory;
private UtilitiesUserPreferences utilitiesUserPreferences;
|
45,874 | SearchParameters searchParameters = getIdentificationParameters().getSearchParameters();
if (searchParameters == null) {
setDefaultPreferences();
searchParameters = getIdentificationParameters().getSearchParameters();
}
<BUG>if (searchParameters.getEnzyme() == null) {
searchParameters.setEnzyme(EnzymeFactory.getInstance().getEnzyme("Trypsin"));
}</BUG>
new SearchSettingsDialog(this, searchParameters,
Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")),
| [DELETED] |
45,875 | forwardIonsDeNovoCheckBoxMenuItem.setText("b-ions");
} else if (searchParameters.getIonSearched1() == PeptideFragmentIon.C_ION) {
forwardIonsDeNovoCheckBoxMenuItem.setText("c-ions");</BUG>
}
forwardIonsDeNovoCheckBoxMenuItem.repaint();
<BUG>if (searchParameters.getIonSearched2() == PeptideFragmentIon.X_ION) {
rewindIonsDeNovoCheckBoxMenuItem.setText("x-ions");
} else if (searchParameters.getIonSearched2() == PeptideFragmentIon.Y_ION) {
rewindIonsDeNovoCheckBoxMenuItem.setText("y-ions");
} else if (searchParameters.getIonSearched2() == PeptideFragmentIon.Z_ION) {
</BUG>
rewindIonsDeNovoCheckBoxMenuItem.setText("z-ions");
| if (searchParameters.getForwardIons().contains(PeptideFragmentIon.C_ION)) {
forwardIonsDeNovoCheckBoxMenuItem.setText("c-ions");
if (searchParameters.getRewindIons().contains(PeptideFragmentIon.X_ION)) {
if (searchParameters.getRewindIons().contains(PeptideFragmentIon.Y_ION)) {
|
45,876 | peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumAnnotatedMirroredPeakColor());
}
}
if (identification.matchExists(spectrumKey)) {
SearchParameters searchParameters = peptideShakerGUI.getIdentificationParameters().getSearchParameters();
<BUG>int forwardIon = searchParameters.getIonSearched1();
int rewindIon = searchParameters.getIonSearched2();
</BUG>
PtmSettings modificationProfile = searchParameters.getPtmSettings();
| Integer forwardIon = searchParameters.getForwardIons().get(0);
Integer rewindIon = searchParameters.getRewindIons().get(0);
|
45,877 | prideSearchParameters.setPrecursorAccuracy(peptideIonMassTolerance);
prideParametersReport += peptideIonMassTolerance + " " + prideSearchParameters.getPrecursorAccuracyType();
} else {
prideParametersReport += prideSearchParameters.getPrecursorAccuracy() + " " + prideSearchParameters.getPrecursorAccuracyType() + " (default)";
}
<BUG>prideParametersReport += "<br><br><b>Enzyme:</b> ";
if (!enzymes.isEmpty()) {</BUG>
if (enzymes.size() == 1) {
Enzyme mappedEnzyme = EnzymeFactory.getInstance().getUtilitiesEnzyme(enzymes.get(0));
if (mappedEnzyme == null) {
| DigestionPreferences prideDigestionPreferences = DigestionPreferences.getDefaultPreferences();
prideSearchParameters.setDigestionPreferences(prideDigestionPreferences);
if (!enzymes.isEmpty()) {
|
45,878 | prideParametersReport += enzymes.get(0) + " (unknown)<br>";
}
} else {
prideParametersReport += mappedEnzyme.getName() + "<br>";
}
<BUG>prideSearchParameters.setEnzyme(mappedEnzyme);
} else {</BUG>
String enzymesAsText = "";
for (int i = 0; i < enzymes.size(); i++) {
if (i > 0) {
| if (mappedEnzyme != null) {
prideDigestionPreferences.clearEnzymes();
prideDigestionPreferences.addEnzyme(mappedEnzyme);
|
45,879 | this.setIconImage(Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")));
EnzymeSelectionDialog enzymeSelectionDialog = new EnzymeSelectionDialog(this, true, enzymesAsText, true);
Enzyme selectedEnzyme = enzymeSelectionDialog.getEnzyme();
if (selectedEnzyme != null) {
prideParametersReport += selectedEnzyme.getName() + "<br>";
<BUG>prideSearchParameters.setEnzyme(selectedEnzyme);
} else {
prideSearchParameters.setEnzyme(null);
prideParametersReport += enzymesAsText + " (unknown)<br>";</BUG>
}
| prideDigestionPreferences.clearEnzymes();
prideDigestionPreferences.addEnzyme(selectedEnzyme);
prideDigestionPreferences.clearEnzymes();
prideParametersReport += enzymesAsText + " (unknown)<br>";
|
45,880 | br.write(getCurrentTabSpace() + "</SearchModification>" + lineBreak);
}
tabCounter--;
br.write(getCurrentTabSpace() + "</ModificationParams>" + lineBreak);
DigestionPreferences digestionPreferences = searchParameters.getDigestionPreferences();
<BUG>if (digestionPreferences.isNoEnzymeSpecificity()) {
br.write(getCurrentTabSpace() + "<Enzymes independent=\"false\">" + lineBreak);</BUG>
tabCounter++;
br.write(getCurrentTabSpace() + "<Enzyme name=\"unspecific cleavage\">"
+ lineBreak);
| if (digestionPreferences.getCleavagePreference() == DigestionPreferences.CleavagePreference.unSpecific) {
br.write(getCurrentTabSpace() + "<Enzymes independent=\"false\">" + lineBreak);
|
45,881 | writeCvTerm(enzymeCvTerm);
tabCounter--;
br.write(getCurrentTabSpace() + "</EnzymeName>" + lineBreak);
tabCounter--;
br.write(getCurrentTabSpace() + "</Enzyme>" + lineBreak);
<BUG>} else if (digestionPreferences.isWholeProtein()) {
br.write(getCurrentTabSpace() + "<Enzymes independent=\"false\">" + lineBreak);</BUG>
tabCounter++;
br.write(getCurrentTabSpace() + "<Enzyme name=\"NoEnzyme\">"
+ lineBreak);
| } else if (digestionPreferences.getCleavagePreference() == DigestionPreferences.CleavagePreference.wholeProtein) {
br.write(getCurrentTabSpace() + "<Enzymes independent=\"false\">" + lineBreak);
|
45,882 | spectrumPanel.setPeakWaterMarkColor(peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumBackgroundPeakColor());
spectrumPanel.setPeakWidth(peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumAnnotatedPeakWidth());
spectrumPanel.setBackgroundPeakWidth(peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumBackgroundPeakWidth());
spectrumPanel.showAnnotatedPeaksOnly(!annotationPreferences.showAllPeaks());
spectrumPanel.setYAxisZoomExcludesBackgroundPeaks(annotationPreferences.yAxisZoomExcludesBackgroundPeaks());
<BUG>int forwardIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getIonSearched1();
int rewindIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getIonSearched2();
</BUG>
spectrumPanel.addAutomaticDeNovoSequencing(peptides.get(i), allAnnotations.get(i),
| Integer forwardIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getForwardIons().get(0);
Integer rewindIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getRewindIons().get(0);
|
45,883 | spectrumPanel.addMirroredSpectrum(allSpectra.get(i).getMzValuesAsArray(), allSpectra.get(i).getIntensityValuesNormalizedAsArray(),
500, "2", "", false, peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumAnnotatedMirroredPeakColor(),
peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumAnnotatedMirroredPeakColor());
spectrumPanel.setAnnotateHighestPeak(!annotationPreferences.isHighResolutionAnnotation());
spectrumPanel.setAnnotationsMirrored(SpectrumAnnotator.getSpectrumAnnotation(allAnnotations.get(i)));
<BUG>int forwardIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getIonSearched1();
int rewindIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getIonSearched2();
</BUG>
spectrumPanel.addAutomaticDeNovoSequencing(peptides.get(i), allAnnotations.get(i),
| Integer forwardIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getForwardIons().get(0);
Integer rewindIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getRewindIons().get(0);
|
45,884 | ArrayList<IonMatch> annotations = spectrumAnnotator.getSpectrumAnnotation(annotationPreferences, specificAnnotationPreferences, currentSpectrum, currentPeptide);
spectrumPanel.setAnnotations(SpectrumAnnotator.getSpectrumAnnotation(annotations), !annotationPreferences.isHighResolutionAnnotation());
spectrumPanel.rescale(lowerMzZoomRange, upperMzZoomRange);
spectrumPanel.showAnnotatedPeaksOnly(!annotationPreferences.showAllPeaks());
spectrumPanel.setYAxisZoomExcludesBackgroundPeaks(annotationPreferences.yAxisZoomExcludesBackgroundPeaks());
<BUG>int forwardIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getIonSearched1();
int rewindIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getIonSearched2();
</BUG>
spectrumPanel.addAutomaticDeNovoSequencing(currentPeptide, annotations,
| Integer forwardIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getForwardIons().get(0);
Integer rewindIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getRewindIons().get(0);
|
45,885 | nSequences = 50000;
nSpectra = 10000;
} else {
nSequences = 10000;
nSpectra = 100;
<BUG>}
PTMFactory.getInstance();</BUG>
SequenceFactory.getInstance(nSequences);
SpectrumFactory.getInstance(nSpectra);
}
| EnzymeFactory.getInstance();
PTMFactory.getInstance();
|
45,886 | setVisible(true);
}
private void addData() {
ArrayList<String> spectrumFiles = peptideShakerGUI.getIdentification().getOrderedSpectrumFileNames();
spectrumFileNameMap = new HashMap<String, String>();
<BUG>HashMap<String, XYDataPoint> expectedMolecularWeightRanges = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getFractionMolecularWeightRanges();
</BUG>
for (int i = 0; i < spectrumFiles.size(); i++) {
Double lower = 0.0;
Double upper = 0.0;
| HashMap<String, XYDataPoint> expectedMolecularWeightRanges = peptideShakerGUI.getIdentificationParameters().getFractionSettings().getFractionMolecularWeightRanges();
|
45,887 | peptideShakerGUI.setUpdated(PeptideShakerGUI.PROTEIN_FRACTIONS_TAB_INDEX, false);
if (peptideShakerGUI.getSelectedTab() == PeptideShakerGUI.PROTEIN_FRACTIONS_TAB_INDEX) {
peptideShakerGUI.getProteinFractionsPanel().displayResults();
}
peptideShakerGUI.getIdentification().setOrderedListOfSpectrumFileNames(spectrumFiles);
<BUG>peptideShakerGUI.getIdentificationParameters().getSearchParameters().setFractionMolecularWeightRanges(fractionRanges);
</BUG>
this.setVisible(false);
this.dispose();
}//GEN-LAST:event_okButtonActionPerformed
| peptideShakerGUI.getIdentificationParameters().getFractionSettings().setFractionMolecularWeightRanges(fractionRanges);
|
45,888 | ArrayList<IonMatch> annotations = peptideShakerGUI.getSpectrumAnnotator().getSpectrumAnnotation(annotationPreferences, specificAnnotationPreferences, currentSpectrum, peptide);
spectrum.setAnnotations(SpectrumAnnotator.getSpectrumAnnotation(annotations), !annotationPreferences.isHighResolutionAnnotation());
spectrum.showAnnotatedPeaksOnly(!annotationPreferences.showAllPeaks());
spectrum.setYAxisZoomExcludesBackgroundPeaks(annotationPreferences.yAxisZoomExcludesBackgroundPeaks());
SearchParameters searchParameters = peptideShakerGUI.getIdentificationParameters().getSearchParameters();
<BUG>int forwardIon = searchParameters.getIonSearched1();
int rewindIon = searchParameters.getIonSearched2();
</BUG>
spectrum.addAutomaticDeNovoSequencing(peptide, annotations,
| Integer forwardIon = searchParameters.getForwardIons().get(0);
Integer rewindIon = searchParameters.getRewindIons().get(0);
|
45,889 | private LocalBroadcastManager mLocalBroadcastManager;
private String mActiveDownloadUrlString;
@Override
protected void onCreate(Bundle savedInstanceState) {
super.onCreate(savedInstanceState);
<BUG>setContentView(R.layout.activity_app_details2);
Toolbar toolbar = (Toolbar) findViewById(R.id.toolbar);</BUG>
toolbar.setTitle(""); // Nice and clean toolbar
setSupportActionBar(toolbar);
getSupportActionBar().setDisplayHomeAsUpEnabled(true);
| setContentView(R.layout.app_details2);
Toolbar toolbar = (Toolbar) findViewById(R.id.toolbar);
|
45,890 | .inflate(R.layout.app_details2_screenshots, parent, false);
return new ScreenShotsViewHolder(view);
} else if (viewType == VIEWTYPE_WHATS_NEW) {
View view = LayoutInflater.from(parent.getContext())
.inflate(R.layout.app_details2_whatsnew, parent, false);
<BUG>return new WhatsNewViewHolder(view);
} else if (viewType == VIEWTYPE_LINKS) {</BUG>
View view = LayoutInflater.from(parent.getContext())
.inflate(R.layout.app_details2_links, parent, false);
return new ExpandableLinearLayoutViewHolder(view);
| } else if (viewType == VIEWTYPE_DONATE) {
.inflate(R.layout.app_details2_donate, parent, false);
return new DonateViewHolder(view);
} else if (viewType == VIEWTYPE_LINKS) {
|
45,891 | import org.sonar.api.utils.log.Loggers;
import org.sonar.server.computation.component.CrawlerDepthLimit;
import org.sonar.server.computation.component.SettingsRepository;
import org.sonar.server.computation.component.TypeAwareVisitorAdapter;
import org.sonar.server.computation.issue.ComponentIssuesRepository;
<BUG>import org.sonar.server.computation.measure.api.MeasureComputerImplementationContext;
import org.sonar.server.computation.metric.MetricRepository;</BUG>
import static org.sonar.server.computation.component.ComponentVisitor.Order.POST_ORDER;
public class MeasureComputersVisitor extends TypeAwareVisitorAdapter {
| import org.sonar.server.computation.measure.api.MeasureComputerContextImpl;
import org.sonar.server.computation.measure.api.MeasureComputerWrapper;
import org.sonar.server.computation.metric.MetricRepository;
|
45,892 | this.settings = settings;
this.measureComputersHolder = measureComputersHolder;
this.componentIssuesRepository = componentIssuesRepository;
}
@Override
<BUG>public void visitAny(org.sonar.server.computation.component.Component component) {
for (MeasureComputer computer : measureComputersHolder.getMeasureComputers()) {
LOGGER.trace("Measure computer '{}' is computing component {}", computer.getImplementation(), component);
MeasureComputerImplementationContext measureComputerContext = new MeasureComputerImplementationContext(component, computer,
settings, measureRepository, metricRepository, componentIssuesRepository);
computer.getImplementation().compute(measureComputerContext);</BUG>
}
| [DELETED] |
45,893 | package org.sonar.server.computation.measure;
import com.google.common.base.Predicates;
import javax.annotation.CheckForNull;
<BUG>import org.sonar.api.ce.measure.MeasureComputer;
import static com.google.common.base.Preconditions.checkState;</BUG>
import static com.google.common.collect.FluentIterable.from;
import static java.util.Objects.requireNonNull;
public class MeasureComputersHolderImpl implements MutableMeasureComputersHolder {
| import org.sonar.server.computation.measure.api.MeasureComputerWrapper;
import static com.google.common.base.Preconditions.checkState;
|
45,894 | result_ = variableAssignmentExpression(builder_, level_ + 1);
}
else if (root_ == VARIABLE_EXPRESSION) {
result_ = variableExpression(builder_, level_ + 1);
}
<BUG>else {
Marker marker_ = builder_.mark();
enterErrorRecordingSection(builder_, level_, _SECTION_RECOVER_, null);
result_ = parse_root_(root_, builder_, level_);
exitErrorRecordingSection(builder_, level_, result_, true, _SECTION_RECOVER_, TOKEN_ADVANCER);
marker_.done(root_);</BUG>
}
| Marker marker_ = enter_section_(builder_, level_, _NONE_, null);
exit_section_(builder_, level_, marker_, root_, result_, true, TOKEN_ADVANCER);
|
45,895 | return builder_.getTreeBuilt();
}
protected boolean parse_root_(final IElementType root_, final PsiBuilder builder_, final int level_) {
return root(builder_, level_ + 1);
}
<BUG>private static final TokenSet[] EXTENDS_SETS_ = new TokenSet[] {
</BUG>
create_token_set_(BINARY_EXPRESSION, CONDITIONAL_EXPRESSION, EXPRESSION, INDEXED_EXPRESSION,
LITERAL_EXPRESSION, METHOD_CALL_EXPRESSION, NEW_EXPRESSION, PARENTHESIZED_EXPRESSION,
REFERENCE_EXPRESSION, SEQUENCE_EXPRESSION, UNARY_EXPRESSION, VARIABLE_ASSIGNMENT_EXPRESSION,
| public static final TokenSet[] EXTENDS_SETS_ = new TokenSet[] {
|
45,896 | create_token_set_(BINARY_EXPRESSION, CONDITIONAL_EXPRESSION, EXPRESSION, INDEXED_EXPRESSION,
LITERAL_EXPRESSION, METHOD_CALL_EXPRESSION, NEW_EXPRESSION, PARENTHESIZED_EXPRESSION,
REFERENCE_EXPRESSION, SEQUENCE_EXPRESSION, UNARY_EXPRESSION, VARIABLE_ASSIGNMENT_EXPRESSION,
VARIABLE_EXPRESSION),
};
<BUG>public static boolean type_extends_(IElementType child_, IElementType parent_) {
return type_extends_impl_(EXTENDS_SETS_, child_, parent_);
}</BUG>
static boolean arrayConstructorExpression(PsiBuilder builder_, int level_) {
if (!recursion_guard_(builder_, level_, "arrayConstructorExpression")) return false;
| [DELETED] |
45,897 | sequenceExpression(builder_, level_ + 1);
return true;
}
static boolean binaryOperations(PsiBuilder builder_, int level_) {
if (!recursion_guard_(builder_, level_, "binaryOperations")) return false;
<BUG>boolean result_ = false;
Marker marker_ = builder_.mark();
enterErrorRecordingSection(builder_, level_, _SECTION_GENERAL_, "<operator>");</BUG>
result_ = plusMinusOperations(builder_, level_ + 1);
if (!result_) result_ = divideMultiplyOperations(builder_, level_ + 1);
| Marker marker_ = enter_section_(builder_, level_, _NONE_, "<operator>");
|
45,898 | return result_;
}
static boolean bitwiseBooleanOperations(PsiBuilder builder_, int level_) {
if (!recursion_guard_(builder_, level_, "bitwiseBooleanOperations")) return false;
boolean result_ = false;
<BUG>Marker marker_ = builder_.mark();
result_ = consumeToken(builder_, OR);</BUG>
if (!result_) result_ = consumeToken(builder_, XOR);
if (!result_) result_ = consumeToken(builder_, AND);
if (!result_) result_ = consumeToken(builder_, BAND_KEYWORD);
| Marker marker_ = enter_section_(builder_);
result_ = consumeToken(builder_, OR);
|
45,899 | if (offset_ == next_offset_) {
empty_element_parsed_guard_(builder_, offset_, "expressionSequenceRequired_1");
break;
}
offset_ = next_offset_;
<BUG>}
if (!result_) {
marker_.rollbackTo();
}
else {
marker_.drop();
}</BUG>
return result_;
| empty_element_parsed_guard_(builder_, offset_, "referenceExpression_2");
|
45,900 | return consumeToken(builder_, INSTANCEOF_KEYWORD);
}
static boolean methodCallParameters(PsiBuilder builder_, int level_) {
if (!recursion_guard_(builder_, level_, "methodCallParameters")) return false;
boolean result_ = false;
<BUG>Marker marker_ = builder_.mark();
result_ = methodCallParameters_0(builder_, level_ + 1);
result_ = result_ && methodCallParameters_1(builder_, level_ + 1);
if (!result_) {
marker_.rollbackTo();
}
else {
marker_.drop();
}</BUG>
return result_;
| if (offset_ == next_offset_) {
empty_element_parsed_guard_(builder_, offset_, "referenceExpression_2");
break;
|
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