rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k | meta stringlengths 141 403 |
|---|---|---|---|
return pos; | return this; | public IRubyObject seek(RubyFixnum pos) { this.pos = (int) pos.getLongValue(); return pos; } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/af80e8f70b3c6d7fab314143b5f1e641350602b1/RubyDir.java/buggy/src/org/jruby/RubyDir.java |
return (new ArticleActionURIHandler()).getHandlerIdentifier(); | return ArticleActionURIHandler.HANDLER_IDENTIFIER; | public String getIWActionURIHandlerIdentifier() { return (new ArticleActionURIHandler()).getHandlerIdentifier(); } | 57000 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57000/44c7553551d463f44b7cb7cf5d0a43b62412701b/ArticleListManagedBean.java/buggy/src/java/com/idega/block/article/bean/ArticleListManagedBean.java |
public void open() { quickLaunchBtn.doClick(); } | public void open() { quickLaunchBtn.doClick(); } | public void open() { quickLaunchBtn.doClick(); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/cf83d7e74fdf42d9c4357c3e575c08395991a878/TopWindow.java/clean/SRC/org/openmicroscopy/shoola/env/ui/TopWindow.java |
public void postHandleDisplay() { } | public void postHandleDisplay() {} | public void postHandleDisplay() { } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/cf83d7e74fdf42d9c4357c3e575c08395991a878/TopWindow.java/clean/SRC/org/openmicroscopy/shoola/env/ui/TopWindow.java |
public ManageableTopWindow(String s) { super(s); | public ManageableTopWindow() { super(); | public ManageableTopWindow(String s) { super(s); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/cf83d7e74fdf42d9c4357c3e575c08395991a878/ManageableTopWindow.java/buggy/SRC/org/openmicroscopy/shoola/env/ui/ManageableTopWindow.java |
String id = articleItemBean[i].getFolderLocation()+"/"+articleItemBean[i].getHeadline()+".xml"; | String id = articleItemBean[i].getFolderLocation()+"/"+articleItemBean[i].getHeadline()+ArticleItemBean.ARTICLE_SUFFIX; | public void updateDataModel(Integer start, Integer rows) { if (_dataModel == null) { _dataModel = new WFDataModel(); } try {// ArticleItemBean[] articleItemBean = (ArticleItemBean[]) ArticleListBean.loadAllArticlesInFolder("/files/content").toArray(new ArticleItemBean[0]); ArticleItemBean[] articleItemBean = ... | 57000 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57000/e75e5a35d9b917c44d8a58d117a43ccf5ad660b4/ListArticlesBean.java/clean/src/java/com/idega/block/article/bean/ListArticlesBean.java |
setQuantumStrategy(QuantumFactory.DEPTH_8BIT); setCodomainInterval(0, QuantumFactory.DEPTH_8BIT); | resetDefaults(rndDef, getMetadata(), iPixels); setModel(rndDef.getModel()); | public void resetDefaults() { // Reset the bit resolution. setQuantumStrategy(QuantumFactory.DEPTH_8BIT); // NB: Java locks are setCodomainInterval(0, QuantumFactory.DEPTH_8BIT); // re-entrant. // Set the each channel's window to the channel's [min, max]. // Make active only th... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/64e6d912272b039f986c1a36d1ca930cc5578578/Renderer.java/buggy/components/rendering/src/omeis/providers/re/Renderer.java |
ChannelBinding[] cb = getChannelBindings(); boolean active = false; RenderingModel model = PlaneFactory.getRenderingModel(iPixels, MODEL_GREYSCALE); List channels = getMetadata().getChannels(); int w = 0; for (Iterator i = channels.iterator(); i.hasNext();) { Channel channel = (Channel) i.next(); if (channel.getPix... | if (getCodomainChain() != null) getCodomainChain().remove(); iPixels.saveRndSettings(rndDef); | public void resetDefaults() { // Reset the bit resolution. setQuantumStrategy(QuantumFactory.DEPTH_8BIT); // NB: Java locks are setCodomainInterval(0, QuantumFactory.DEPTH_8BIT); // re-entrant. // Set the each channel's window to the channel's [min, max]. // Make active only th... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/64e6d912272b039f986c1a36d1ca930cc5578578/Renderer.java/buggy/components/rendering/src/omeis/providers/re/Renderer.java |
case M_HASH: return hash(); | public RubyObject callIndexed(int index, RubyObject[] args) { switch (index) { case M_TO_F: return to_f(); case M_TO_S: return to_s(); case M_OP_LSHIFT: return op_lshift(args[0]); case M_OP_RSHIFT: return op_rshift(args[0]); case ... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/7f0907240b4b4a4379424377e971ed0ca23f1dcb/RubyFixnum.java/clean/org/jruby/RubyFixnum.java | |
fixnumClass.defineMethod("hash", IndexedCallback.create(M_HASH, 0)); | public static RubyClass createFixnumClass(Ruby ruby) { RubyClass fixnumClass = ruby.defineClass("Fixnum", ruby.getClasses().getIntegerClass()); fixnumClass.includeModule(ruby.getClasses().getPrecisionModule()); fixnumClass.defineSingletonMethod("induced_from", CallbackFactory.getSingletonMethod... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/7f0907240b4b4a4379424377e971ed0ca23f1dcb/RubyFixnum.java/clean/org/jruby/RubyFixnum.java | |
bindStreams(inputStream, outputStream); | try { handler = new IOHandlerSocket(getRuntime(), inputStream, outputStream); } catch (IOException e) { throw getRuntime().newIOError(e.getMessage()); } registerIOHandler(handler); modes = handler.getModes(); | public IRubyObject initialize(IRubyObject[] args) { IRubyObject input = args[0]; IRubyObject output = args[1]; InputStream inputStream = (InputStream) extractStream(input); OutputStream outputStream = (OutputStream) extractStream(output); bindStreams(inputStream, outputS... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/955df6c6347fe40e2cb6502680208323eef890e2/RubyBasicSocket.java/clean/src/org/jruby/RubyBasicSocket.java |
catch (Exception e) { throw new PropertyException ("Unable to iterate list", e); } | public void write(FastWriter out, Context context) throws PropertyException, IOException { Object l, limit, from; int loopLimit=-1, loopStart=1, loopIndex=0; l = list; while (l instanceof Macro) l = ((Macro) l).evaluate(context); if (limitExpr != null) { limit = limitExpr; while (li... | 52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/f6d51f5ec2ae25d44756c8da8932f1833850935a/ForeachDirective.java/clean/webmacro/src/org/webmacro/directive/ForeachDirective.java | |
String pageName = wc.getForm ("save"); | String pageName = getWikiPageName(wiki, wc); | protected WikiPage createNewPage (WikiSystem wiki, WebContext wc, WikiUser user) throws Exception { // get the page elements from the request String editor = user.getIdentifier(); String text = wc.getForm ("TEXT"); boolean moderated = wc.getForm ("MODERATED") != null && wc.getForm("MODER... | 52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/63e182a593c47d9b882560d480b0bab109616dc8/SavePageAction.java/clean/wiki/src/org/tcdi/opensource/wiki/servlet/SavePageAction.java |
return wc.getForm ("save"); | String pageName = wc.getForm ("save"); pageName = WikiUtil.formatAsWikiTitle(pageName); return pageName; | public String getWikiPageName(WikiSystem wiki, WebContext wc) { return wc.getForm ("save"); } | 52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/63e182a593c47d9b882560d480b0bab109616dc8/SavePageAction.java/clean/wiki/src/org/tcdi/opensource/wiki/servlet/SavePageAction.java |
println("<method nameAndSignature=\"" + methodNameAndSignature + "\">"); | println("<method nameAndSignature=\"" + xmlEscape(methodNameAndSignature) + "\">"); | private void dumpMethods(CoverageData instrumentation) { Iterator iter = instrumentation.getMethodNamesAndDescriptors() .iterator(); while (iter.hasNext()) { String methodNameAndSignature = (String)iter.next(); println("<method nameAndSignature=\"" + methodNameAndSignature + "\">"); increaseIndentation... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/e99865317a5efeb3b1f3deb3463354ec351d77a4/XMLReport.java/buggy/cobertura/src/net/sourceforge/cobertura/reporting/xml/XMLReport.java |
return t; | return null; | final public Template getTemplate(String fileName) { File tFile = findTemplate (fileName); Template t = null; try { t = new FileTemplate (_broker, tFile); t.parse (); _lastModifiedCache.put (fileName, new Long (tFile.lastModified())); } catch (NullPointerException n... | 52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/e9a3ed7ab80a712ee6fbc4fd902c3cffa556335a/TemplateProvider.java/buggy/webmacro/src/org/webmacro/resource/TemplateProvider.java |
return chatPreferences.getNickname(); | LocalPreferences pref = SettingsManager.getLocalPreferences(); return pref.getNickname(); | public String getNickname() { return chatPreferences.getNickname(); } | 52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/f678f06c6fbc4a84079c230a0a7461759cb20755/ChatRoom.java/clean/src/java/org/jivesoftware/spark/ui/ChatRoom.java |
chatPreferences = (ChatPreferences)SparkManager.getPreferenceManager().getPreferenceData(ChatPreference.NAMESPACE); | private void init() { setLayout(new GridBagLayout()); add(splitPane, new GridBagConstraints(0, 1, 1, 1, 1.0, 1.0, GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0, 0, 0, 0), 0, 0)); add(notificationLabel, new GridBagConstraints(0, 2, 1, 1, 0.0, 0.0, GridBagConstraints.WEST, Grid... | 52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/f678f06c6fbc4a84079c230a0a7461759cb20755/ChatRoom.java/clean/src/java/org/jivesoftware/spark/ui/ChatRoom.java | |
return "Image"+(imageId==null ? ":Hash"+this.hashCode() : ":"+imageId); | return "Image"+(imageId==null ? ":Hash_"+this.hashCode() : ":Id_"+imageId); | public String toString(){ return "Image"+(imageId==null ? ":Hash"+this.hashCode() : ":"+imageId); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/51a3c546dfc7a7a98b29771a459df19094fc5b51/Image.java/buggy/components/common/src/ome/model/Image.java |
setImages(new HashSet( c.eachLinkedImage( block ))); | setImages( makeSet( c.sizeOfImageLinks(), c.eachLinkedImage( block ))); | public void copy(IObject model, ModelMapper mapper) { if (model instanceof Category) { Category c = (Category) model; super.copy(model,mapper); // Details Details details = c.getDetails(); if (details!=null){ this.setOwner((ExperimenterData) mapper.findTarget(... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9638b50efec05ce0b3d19bbef1c149c757b964aa/CategoryData.java/buggy/components/shoola-adapter/src/pojos/CategoryData.java |
log.info(getData()); | OMEData data = new OMEPerformanceData(); OMEData old = getData(); Set imgs = new HashSet(); imgs.add(new Integer(101)); imgs.add(new Integer(12)); imgs.add(new Integer(5393)); imgs.add(new Integer(4954)); imgs.add(new Integer(3919)); imgs.add(new Integer(1273)); data.imgsCGCI=imgs; setData(data); Object o = this.testFi... | public void testHessian(){ log.info(getData()); Utils.structureSize(this.testFindCGCIHierarchies()); Utils.structureSize(this.testFindDatasetAnnotationsSet()); Utils.structureSize(this.testFindDatasetAnnotationsSetForExperimenter()); Utils.structureSize(this.testFindImageAnnotatio... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9570ef74198a070d72e77c417c9d25244a942de2/OmeroServiceTest.java/buggy/components/server/test/org/openmicroscopy/omero/server/itests/OmeroServiceTest.java |
log.debug("Null date."); | static public Timestamp convertDate(Date date){ if (null==date){ log.debug("Null date."); return null; } return new Timestamp(date.getTime()); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9cc885fa28a62ed7b7bf1dbcf110c443345339d1/AdapterUtils.java/buggy/components/shoola-adapter/src/org/openmicroscopy/omero/shoolaadapter/AdapterUtils.java | |
log.debug(nullId+p); | if (log.isDebugEnabled())log.debug(nullId+p); | static public ProjectData go(Project p, Map cache) { if (check(cache,p)) { return (ProjectData) from(cache, p); } ProjectData pd = new ProjectData(); to(cache, p, pd); if (null == p.getProjectId()) { log.debug(nullId+p); } else { pd.... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9cc885fa28a62ed7b7bf1dbcf110c443345339d1/AdapterUtils.java/buggy/components/shoola-adapter/src/org/openmicroscopy/omero/shoolaadapter/AdapterUtils.java |
log.debug(nullExp + p); | if (log.isDebugEnabled())log.debug(nullExp + p); | static public ProjectData go(Project p, Map cache) { if (check(cache,p)) { return (ProjectData) from(cache, p); } ProjectData pd = new ProjectData(); to(cache, p, pd); if (null == p.getProjectId()) { log.debug(nullId+p); } else { pd.... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9cc885fa28a62ed7b7bf1dbcf110c443345339d1/AdapterUtils.java/buggy/components/shoola-adapter/src/org/openmicroscopy/omero/shoolaadapter/AdapterUtils.java |
log.debug(nullDs + p); | if (log.isDebugEnabled())log.debug(nullDs + p); | static public ProjectData go(Project p, Map cache) { if (check(cache,p)) { return (ProjectData) from(cache, p); } ProjectData pd = new ProjectData(); to(cache, p, pd); if (null == p.getProjectId()) { log.debug(nullId+p); } else { pd.... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9cc885fa28a62ed7b7bf1dbcf110c443345339d1/AdapterUtils.java/buggy/components/shoola-adapter/src/org/openmicroscopy/omero/shoolaadapter/AdapterUtils.java |
File file = new File("target/SpringLoaderTest.jar"); | File file = new File(basedir, "target/SpringLoaderTest.jar"); | private static File createJarFile() throws IOException { File file = new File("target/SpringLoaderTest.jar"); FileOutputStream out = new FileOutputStream(file); JarOutputStream jarOut = new JarOutputStream(out); jarOut.putNextEntry(new JarEntry(CLASS_NAME + ".class")); jarOut.writ... | 52533 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52533/c06ecd608700a5a1d16363b667e5a08286b3438a/SpringLoaderTest.java/buggy/server/src/test/org/xbean/server/spring/loader/SpringLoaderTest.java |
File baseDir = new File("src/test/org/xbean/server/spring/loader/").getAbsoluteFile(); System.setProperty("xbean.base.dir", baseDir.getAbsolutePath()); | File xbeanDir = new File(basedir, "src/test/org/xbean/server/spring/loader/").getAbsoluteFile(); System.setProperty("xbean.base.dir", xbeanDir.getAbsolutePath()); | public void testLoad() throws Exception{ Kernel kernel = KernelFactory.newInstance().createKernel("test"); try { File baseDir = new File("src/test/org/xbean/server/spring/loader/").getAbsoluteFile(); System.setProperty("xbean.base.dir", baseDir.getAbsolutePath()); File... | 52533 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52533/c06ecd608700a5a1d16363b667e5a08286b3438a/SpringLoaderTest.java/buggy/server/src/test/org/xbean/server/spring/loader/SpringLoaderTest.java |
FileSystemRepository repository = new FileSystemRepository(new File(".").getAbsoluteFile()); | FileSystemRepository repository = new FileSystemRepository(new File(basedir).getAbsoluteFile()); | public void testLoad() throws Exception{ Kernel kernel = KernelFactory.newInstance().createKernel("test"); try { File baseDir = new File("src/test/org/xbean/server/spring/loader/").getAbsoluteFile(); System.setProperty("xbean.base.dir", baseDir.getAbsolutePath()); File... | 52533 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52533/c06ecd608700a5a1d16363b667e5a08286b3438a/SpringLoaderTest.java/buggy/server/src/test/org/xbean/server/spring/loader/SpringLoaderTest.java |
springLoader.setBaseDir(baseDir); | springLoader.setBaseDir(xbeanDir); | public void testLoad() throws Exception{ Kernel kernel = KernelFactory.newInstance().createKernel("test"); try { File baseDir = new File("src/test/org/xbean/server/spring/loader/").getAbsoluteFile(); System.setProperty("xbean.base.dir", baseDir.getAbsolutePath()); File... | 52533 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52533/c06ecd608700a5a1d16363b667e5a08286b3438a/SpringLoaderTest.java/buggy/server/src/test/org/xbean/server/spring/loader/SpringLoaderTest.java |
File baseDir = new File("src/test/org/xbean/server/spring/loader/").getAbsoluteFile(); System.setProperty("xbean.base.dir", baseDir.getAbsolutePath()); | File xbeanDir = new File(basedir, "src/test/org/xbean/server/spring/loader/").getAbsoluteFile(); System.setProperty("xbean.base.dir", xbeanDir.getAbsolutePath()); | public void testReload() throws Exception{ Kernel kernel = KernelFactory.newInstance().createKernel("test"); try { File baseDir = new File("src/test/org/xbean/server/spring/loader/").getAbsoluteFile(); System.setProperty("xbean.base.dir", baseDir.getAbsolutePath()); Fi... | 52533 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52533/c06ecd608700a5a1d16363b667e5a08286b3438a/SpringLoaderTest.java/buggy/server/src/test/org/xbean/server/spring/loader/SpringLoaderTest.java |
FileSystemRepository repository = new FileSystemRepository(new File(".").getAbsoluteFile()); | FileSystemRepository repository = new FileSystemRepository(new File(basedir).getAbsoluteFile()); | public void testReload() throws Exception{ Kernel kernel = KernelFactory.newInstance().createKernel("test"); try { File baseDir = new File("src/test/org/xbean/server/spring/loader/").getAbsoluteFile(); System.setProperty("xbean.base.dir", baseDir.getAbsolutePath()); Fi... | 52533 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52533/c06ecd608700a5a1d16363b667e5a08286b3438a/SpringLoaderTest.java/buggy/server/src/test/org/xbean/server/spring/loader/SpringLoaderTest.java |
springLoader.setBaseDir(baseDir); | springLoader.setBaseDir(xbeanDir); | public void testReload() throws Exception{ Kernel kernel = KernelFactory.newInstance().createKernel("test"); try { File baseDir = new File("src/test/org/xbean/server/spring/loader/").getAbsoluteFile(); System.setProperty("xbean.base.dir", baseDir.getAbsolutePath()); Fi... | 52533 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52533/c06ecd608700a5a1d16363b667e5a08286b3438a/SpringLoaderTest.java/buggy/server/src/test/org/xbean/server/spring/loader/SpringLoaderTest.java |
public FileSystemRepository(File root) { this.root = root; | public FileSystemRepository() { | public FileSystemRepository(File root) { this.root = root; } | 52533 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52533/438aa707be746e2381b40041b37ebd6b00c23429/FileSystemRepository.java/buggy/server/src/java/org/xbean/server/repository/FileSystemRepository.java |
d.setPermissions( new Permissions() ); | public void testAllowLoad() { prepareMocksWithUserDetails(); Details d = new Details(); d.setOwner(new Experimenter(2L)); d.setGroup(new ExperimenterGroup(2L)); sec.setCurrentDetails(); assertTrue(sec.allowLoad(Image.class,d)); d.setPermissions(new Permissions().revoke(WORLD,READ)); assertFalse(sec.allowLo... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0172174c25a126f3473655022bb846c98e246c25/SecuritySystemTest.java/buggy/components/server/test/ome/server/utests/sec/SecuritySystemTest.java | |
point = new PlanePoint(x, v); | point = new PlanePoint(x, v); | private Object[] getGraphicDataZ(Map xAxis, Map yAxis) { Object[] result = new Object[5]; Iterator i = (yAxis.keySet()).iterator(); Iterator j; Integer key; PlanePoint point;//Coordinate ArrayList list; TreeMap values = new TreeMap(); double v, maxY = 0, m... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3db37517e6873d11567ee5822e769ab058e1abed/StatsResultsPaneMng.java/buggy/SRC/org/openmicroscopy/shoola/agents/roi/results/stats/StatsResultsPaneMng.java |
graphicCanvas.acrossT(tSelected, ((Integer) result[0]).intValue(), | graphicCanvas.acrossZ(tSelected, ((Integer) result[0]).intValue(), | public void showGraphic(int statsIndex, int axis, Map zSelected, Map tSelected) { this.statsIndex = statsIndex; resultIndex = GRAPHIC_RESULT; graphicCanvas = new GraphicCanvas(this, StatsResultsPane.zAndtFieldNames[statsIndex]); Obje... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3db37517e6873d11567ee5822e769ab058e1abed/StatsResultsPaneMng.java/buggy/SRC/org/openmicroscopy/shoola/agents/roi/results/stats/StatsResultsPaneMng.java |
while (i.hasNext()) { agentInfo = (AgentInfo) i.next(); a = agentInfo.getAgent(); a.setContext(agentInfo.getRegistry()); | try { while (i.hasNext()) { agentInfo = (AgentInfo) i.next(); a = agentInfo.getAgent(); a.setContext(agentInfo.getRegistry()); } i = agents.iterator(); while (i.hasNext()) { agentInfo = (AgentInfo) i.next(); a = agentInfo.getAgent(); a.activate(); } RenderingEngine re = RenderingEngine.getInstance(this); re.activa... | public void startService() { List agents = (List) singleton.registry.lookup(LookupNames.AGENTS); Iterator i = agents.iterator(); AgentInfo agentInfo; Agent a; //Agents linking phase. while (i.hasNext()) { agentInfo = (AgentInfo) i.next(); a = agentInfo.getAgent(); a.setContext(agentInfo.getRegistry()); ... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/a8120868e0e5ade5c98b188e8361f7deb0d651d3/Container.java/clean/SRC/org/openmicroscopy/shoola/env/Container.java |
i = agents.iterator(); while (i.hasNext()) { agentInfo = (AgentInfo) i.next(); a = agentInfo.getAgent(); a.activate(); } RenderingEngine re = RenderingEngine.getInstance(this); re.activate(); LoginManager lm = LoginManager.getInstance(this); lm.activate(); AWTExceptionHanlder.configure(this); | public void startService() { List agents = (List) singleton.registry.lookup(LookupNames.AGENTS); Iterator i = agents.iterator(); AgentInfo agentInfo; Agent a; //Agents linking phase. while (i.hasNext()) { agentInfo = (AgentInfo) i.next(); a = agentInfo.getAgent(); a.setContext(agentInfo.getRegistry()); ... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/a8120868e0e5ade5c98b188e8361f7deb0d651d3/Container.java/clean/SRC/org/openmicroscopy/shoola/env/Container.java | |
StringBuffer buf = new StringBuffer(); buf.append("Error message: "+se.getMessage()); buf.append("Originated by: "+se.getOriginator()); UserNotifier un = UIFactory.makeUserNotifier(); un.notifyInitError("Initialization Error", buf.toString(), se); System.exit(1); | AbnormalExitHandler.terminate(se); } catch (Throwable t) { AbnormalExitHandler.terminate(t); | public static void startup(String home) { Initializer initManager = null; if (singleton == null) { try { singleton = new Container(home); initManager = new Initializer(singleton); initManager.configure(); initManager.doInit(); //startService() called by Initializer at end of doInit(). } catch (Sta... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/a8120868e0e5ade5c98b188e8361f7deb0d651d3/Container.java/clean/SRC/org/openmicroscopy/shoola/env/Container.java |
this.setAllPixels((Set) mapper.findCollection(i.collectFromPixels(null))); this.setAnnotations((Set) mapper.findCollection(i.collectFromAnnotations(null))); | public void copy(IObject model, ModelMapper mapper) { if (model instanceof Image) { Image i = (Image) model; super.copy(model,mapper); // Details if (i.getDetails() != null){ Details d = i.getDetails(); this.setCreated(mapper.event2tim... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/a39e29573bdd486ca5c91592a592b445e6d4625e/ImageData.java/buggy/components/shoola-adapter/src/pojos/ImageData.java | |
setAllPixels( new HashSet( i.collectFromPixels( block ))); setAnnotations( new HashSet( i.collectFromAnnotations( block ))); | public void copy(IObject model, ModelMapper mapper) { if (model instanceof Image) { Image i = (Image) model; super.copy(model,mapper); // Details if (i.getDetails() != null){ Details d = i.getDetails(); this.setCreated(mapper.event2tim... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/a39e29573bdd486ca5c91592a592b445e6d4625e/ImageData.java/buggy/components/shoola-adapter/src/pojos/ImageData.java | |
public ASCII_UCodeESC_CharStream(java.io.Reader dstream, int startline, int startcolumn, | private ASCII_UCodeESC_CharStream(java.io.Reader dstream, int startline, int startcolumn, | public ASCII_UCodeESC_CharStream(java.io.Reader dstream, int startline, int startcolumn, int buffersize) { inputStream = dstream; line = startline; column = startcolumn - 1; available = bufsize = buffersize; buffer = new char[buffersize]; bufline = new int[buffersize]; bufcolumn = new int[buffersize]; nextCh... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/56b5525edc49962bc040c60be12062884232fcc7/ASCII_UCodeESC_CharStream.java/buggy/cobertura/src/de/kclee/clemens/javancss/ASCII_UCodeESC_CharStream.java |
static final int hexval(char c) throws java.io.IOException | private static final int hexval(char c) throws java.io.IOException | static final int hexval(char c) throws java.io.IOException { switch (c) { case '0': return 0; case '1': return 1; case '2': return 2; case '3': return 3; case '4': return 4; case '5': return 5; case '6': return 6; case '7': return 7; case '8': return 8; case '9': ret... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/56b5525edc49962bc040c60be12062884232fcc7/ASCII_UCodeESC_CharStream.java/buggy/cobertura/src/de/kclee/clemens/javancss/ASCII_UCodeESC_CharStream.java |
AdjustBuffSize(); | adjustBuffSize(); | public final char readChar() throws java.io.IOException { if (inBuf > 0) { --inBuf; return buffer[(bufpos == bufsize - 1) ? (bufpos = 0) : ++bufpos]; } char c; if (++bufpos == available) AdjustBuffSize(); if (((buffer[bufpos] = c = (char)((char)0xff & ReadByte())) == '\\')) { UpdateLineColumn(c); int ... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/56b5525edc49962bc040c60be12062884232fcc7/ASCII_UCodeESC_CharStream.java/buggy/cobertura/src/de/kclee/clemens/javancss/ASCII_UCodeESC_CharStream.java |
if (((buffer[bufpos] = c = (char)((char)0xff & ReadByte())) == '\\')) | if (((buffer[bufpos] = c = (char)((char)0xff & readByte())) == '\\')) | public final char readChar() throws java.io.IOException { if (inBuf > 0) { --inBuf; return buffer[(bufpos == bufsize - 1) ? (bufpos = 0) : ++bufpos]; } char c; if (++bufpos == available) AdjustBuffSize(); if (((buffer[bufpos] = c = (char)((char)0xff & ReadByte())) == '\\')) { UpdateLineColumn(c); int ... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/56b5525edc49962bc040c60be12062884232fcc7/ASCII_UCodeESC_CharStream.java/buggy/cobertura/src/de/kclee/clemens/javancss/ASCII_UCodeESC_CharStream.java |
UpdateLineColumn(c); | updateLineColumn(c); | public final char readChar() throws java.io.IOException { if (inBuf > 0) { --inBuf; return buffer[(bufpos == bufsize - 1) ? (bufpos = 0) : ++bufpos]; } char c; if (++bufpos == available) AdjustBuffSize(); if (((buffer[bufpos] = c = (char)((char)0xff & ReadByte())) == '\\')) { UpdateLineColumn(c); int ... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/56b5525edc49962bc040c60be12062884232fcc7/ASCII_UCodeESC_CharStream.java/buggy/cobertura/src/de/kclee/clemens/javancss/ASCII_UCodeESC_CharStream.java |
AdjustBuffSize(); | adjustBuffSize(); | public final char readChar() throws java.io.IOException { if (inBuf > 0) { --inBuf; return buffer[(bufpos == bufsize - 1) ? (bufpos = 0) : ++bufpos]; } char c; if (++bufpos == available) AdjustBuffSize(); if (((buffer[bufpos] = c = (char)((char)0xff & ReadByte())) == '\\')) { UpdateLineColumn(c); int ... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/56b5525edc49962bc040c60be12062884232fcc7/ASCII_UCodeESC_CharStream.java/buggy/cobertura/src/de/kclee/clemens/javancss/ASCII_UCodeESC_CharStream.java |
if ((buffer[bufpos] = c = (char)((char)0xff & ReadByte())) != '\\') | if ((buffer[bufpos] = c = (char)((char)0xff & readByte())) != '\\') | public final char readChar() throws java.io.IOException { if (inBuf > 0) { --inBuf; return buffer[(bufpos == bufsize - 1) ? (bufpos = 0) : ++bufpos]; } char c; if (++bufpos == available) AdjustBuffSize(); if (((buffer[bufpos] = c = (char)((char)0xff & ReadByte())) == '\\')) { UpdateLineColumn(c); int ... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/56b5525edc49962bc040c60be12062884232fcc7/ASCII_UCodeESC_CharStream.java/buggy/cobertura/src/de/kclee/clemens/javancss/ASCII_UCodeESC_CharStream.java |
UpdateLineColumn(c); | updateLineColumn(c); | public final char readChar() throws java.io.IOException { if (inBuf > 0) { --inBuf; return buffer[(bufpos == bufsize - 1) ? (bufpos = 0) : ++bufpos]; } char c; if (++bufpos == available) AdjustBuffSize(); if (((buffer[bufpos] = c = (char)((char)0xff & ReadByte())) == '\\')) { UpdateLineColumn(c); int ... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/56b5525edc49962bc040c60be12062884232fcc7/ASCII_UCodeESC_CharStream.java/buggy/cobertura/src/de/kclee/clemens/javancss/ASCII_UCodeESC_CharStream.java |
UpdateLineColumn(c); | updateLineColumn(c); | public final char readChar() throws java.io.IOException { if (inBuf > 0) { --inBuf; return buffer[(bufpos == bufsize - 1) ? (bufpos = 0) : ++bufpos]; } char c; if (++bufpos == available) AdjustBuffSize(); if (((buffer[bufpos] = c = (char)((char)0xff & ReadByte())) == '\\')) { UpdateLineColumn(c); int ... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/56b5525edc49962bc040c60be12062884232fcc7/ASCII_UCodeESC_CharStream.java/buggy/cobertura/src/de/kclee/clemens/javancss/ASCII_UCodeESC_CharStream.java |
while ((c = (char)((char)0xff & ReadByte())) == 'u') | while ((c = (char)((char)0xff & readByte())) == 'u') | public final char readChar() throws java.io.IOException { if (inBuf > 0) { --inBuf; return buffer[(bufpos == bufsize - 1) ? (bufpos = 0) : ++bufpos]; } char c; if (++bufpos == available) AdjustBuffSize(); if (((buffer[bufpos] = c = (char)((char)0xff & ReadByte())) == '\\')) { UpdateLineColumn(c); int ... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/56b5525edc49962bc040c60be12062884232fcc7/ASCII_UCodeESC_CharStream.java/buggy/cobertura/src/de/kclee/clemens/javancss/ASCII_UCodeESC_CharStream.java |
| hexval((char)((char)0xff & ReadByte())) << 8 | hexval((char)((char)0xff & ReadByte())) << 4 | hexval((char)((char)0xff & ReadByte()))); | | hexval((char)((char)0xff & readByte())) << 8 | hexval((char)((char)0xff & readByte())) << 4 | hexval((char)((char)0xff & readByte()))); | public final char readChar() throws java.io.IOException { if (inBuf > 0) { --inBuf; return buffer[(bufpos == bufsize - 1) ? (bufpos = 0) : ++bufpos]; } char c; if (++bufpos == available) AdjustBuffSize(); if (((buffer[bufpos] = c = (char)((char)0xff & ReadByte())) == '\\')) { UpdateLineColumn(c); int ... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/56b5525edc49962bc040c60be12062884232fcc7/ASCII_UCodeESC_CharStream.java/buggy/cobertura/src/de/kclee/clemens/javancss/ASCII_UCodeESC_CharStream.java |
UpdateLineColumn(c); | updateLineColumn(c); | public final char readChar() throws java.io.IOException { if (inBuf > 0) { --inBuf; return buffer[(bufpos == bufsize - 1) ? (bufpos = 0) : ++bufpos]; } char c; if (++bufpos == available) AdjustBuffSize(); if (((buffer[bufpos] = c = (char)((char)0xff & ReadByte())) == '\\')) { UpdateLineColumn(c); int ... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/56b5525edc49962bc040c60be12062884232fcc7/ASCII_UCodeESC_CharStream.java/buggy/cobertura/src/de/kclee/clemens/javancss/ASCII_UCodeESC_CharStream.java |
junit.textui.TestRunner.run(SpringFacadeTest.class); | junit.textui.TestRunner.run(OmeroPercentTest.class); | public static void main(String[] args) { junit.textui.TestRunner.run(SpringFacadeTest.class); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/SpringFacadeTest.java/clean/components/jars/client/src/test/org/ome/tests/client/SpringFacadeTest.java |
support.unread(); | char tokadd_string(StrTermNode node) { int func = node.getFunc(); int paren = node.getParen(); int term = node.getTerm(); char c; while ((c = support.read()) != EOF) { if (paren != 0 && c == paren) { node.setNest(node.getNest()+1); } ... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/8ce27f029c7dbaced0850b02dedc1e2c73a48589/RubyYaccLexer.java/clean/src/org/jruby/lexer/yacc/RubyYaccLexer.java | |
support.readLine(); | private int yylex() { char c; boolean spaceSeen = false; boolean commandState; if (lex_strterm != null) { if (lex_strterm instanceof HereDocNode) { int token = hereDocument(); if (token == Token.tSTRING_END) { lex_strter... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/8ce27f029c7dbaced0850b02dedc1e2c73a48589/RubyYaccLexer.java/clean/src/org/jruby/lexer/yacc/RubyYaccLexer.java | |
if (was_bol() && whole_match_p("__END__", false)) { | if (was_bol() && whole_match_p("_END__", false)) { | private int yylex() { char c; boolean spaceSeen = false; boolean commandState; if (lex_strterm != null) { if (lex_strterm instanceof HereDocNode) { int token = hereDocument(); if (token == Token.tSTRING_END) { lex_strter... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/8ce27f029c7dbaced0850b02dedc1e2c73a48589/RubyYaccLexer.java/clean/src/org/jruby/lexer/yacc/RubyYaccLexer.java |
list.addAll((int) beg, repList); | list.addAll((int) beg, new ArrayList(repList)); | public void replace(long beg, long len, RubyObject repl) { int length = getLength(); if (len < 0) { throw new RubyIndexException(getRuby(), "Negative array length: " + len); } if (beg < 0) { beg += length; } if (beg < 0) { throw new RubyInde... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/2f13ba47385b7584839c7f6f6f1abfee251cbe53/RubyArray.java/buggy/org/jruby/RubyArray.java |
public RubyBoolean assignable_from_p(IRubyObject other) { if (! (other instanceof JavaClass)) { throw new TypeError(getRuntime(), "assignable_from requires JavaClass (" + other.getType() + " given)"); } Class otherClass = ((JavaClass) other).getValue(); if (javaClass.isAssigna... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/d41a3d6208fe2344a1c9b95a9fd6b38cb78ba69c/JavaClass.java/clean/src/org/jruby/javasupport/JavaClass.java | ||
return RubyBoolean.newBoolean(getRuntime(), javaClass.isPrimitive()); | return RubyBoolean.newBoolean(getRuntime(), isPrimitive()); | public RubyBoolean primitive_p() { return RubyBoolean.newBoolean(getRuntime(), javaClass.isPrimitive()); } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/d41a3d6208fe2344a1c9b95a9fd6b38cb78ba69c/JavaClass.java/clean/src/org/jruby/javasupport/JavaClass.java |
if (System.getProperty("xbean.dir") != null) { File f = new File(System.getProperty("xbean.dir") + uri); try { return new FileInputStream(f); } catch (FileNotFoundException e) { } } | protected InputStream loadResource(String uri) { // lets try the thread context class loader first InputStream in = Thread.currentThread().getContextClassLoader().getResourceAsStream(uri); if (in == null) { in = getClass().getClassLoader().getResourceAsStream(uri); if (in ... | 52533 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52533/11df53b59b983bed2ad4569b2462495157cef4ff/XBeanNamespaceHandler.java/buggy/xbean-spring-v2/src/main/java/org/apache/xbean/spring/context/v2/XBeanNamespaceHandler.java | |
public NoteTree(Shell shell, Composite parent, Listener l) { | public NoteTree(Composite parent, Listener l) { | public NoteTree(Shell shell, Composite parent, Listener l) { // Tree and context menu. tree = new Tree(parent, SWT.MULTI); contextMenu = new TreeContextMenu(shell, tree, l); // Text editor for renaming tree nodes. treeEditor = new TreeEditor(tree); treeEditor.grabHorizontal = true; treeEditor.minimumWidth =... | 57508 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57508/18ce9cf33f3e06fda4addd57f5ae5c9423a990fb/NoteTree.java/buggy/trunk/src/de/berlios/koalanotes/display/NoteTree.java |
contextMenu = new TreeContextMenu(shell, tree, l); | contextMenu = new TreeContextMenu(tree, l); | public NoteTree(Shell shell, Composite parent, Listener l) { // Tree and context menu. tree = new Tree(parent, SWT.MULTI); contextMenu = new TreeContextMenu(shell, tree, l); // Text editor for renaming tree nodes. treeEditor = new TreeEditor(tree); treeEditor.grabHorizontal = true; treeEditor.minimumWidth =... | 57508 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57508/18ce9cf33f3e06fda4addd57f5ae5c9423a990fb/NoteTree.java/buggy/trunk/src/de/berlios/koalanotes/display/NoteTree.java |
public void initialiseTreeEditor() { TreeItem ti = tree.getSelection()[0]; if (ti == null) return; // HERE: might have to use a Rectangle for this border. // Also should make it so as soon as the text box loses // focus the editor goes away. Text treeTextEditor = new Text(tree, SWT.NONE); treeTextEditor.set... | 57508 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57508/18ce9cf33f3e06fda4addd57f5ae5c9423a990fb/NoteTree.java/buggy/trunk/src/de/berlios/koalanotes/display/NoteTree.java | ||
public TreeContextMenu(Shell shell, Control parent, Listener l) { | public TreeContextMenu(Control parent, Listener l) { | public TreeContextMenu(Shell shell, Control parent, Listener l) { // menu menu = new Menu(shell, SWT.POP_UP); l.mapEvent(menu, SWT.Show, TreeContextMenuController.INITIALISE_MENU); parent.setMenu(menu); // menu items addNote = createMenuItem(menu, "Add Note", l, TreeContextMenuController.ADD_NOTE); removeNo... | 57508 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57508/18ce9cf33f3e06fda4addd57f5ae5c9423a990fb/TreeContextMenu.java/buggy/trunk/src/de/berlios/koalanotes/display/TreeContextMenu.java |
menu = new Menu(shell, SWT.POP_UP); | menu = new Menu(parent); | public TreeContextMenu(Shell shell, Control parent, Listener l) { // menu menu = new Menu(shell, SWT.POP_UP); l.mapEvent(menu, SWT.Show, TreeContextMenuController.INITIALISE_MENU); parent.setMenu(menu); // menu items addNote = createMenuItem(menu, "Add Note", l, TreeContextMenuController.ADD_NOTE); removeNo... | 57508 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57508/18ce9cf33f3e06fda4addd57f5ae5c9423a990fb/TreeContextMenu.java/buggy/trunk/src/de/berlios/koalanotes/display/TreeContextMenu.java |
} | } | public Set findCGCIHierarchies(final Set arg0) { // CONTRACT if (null == arg0 || arg0.size() == 0) { return new HashSet(); } List result = containerDao.findCGCIHierarchies(arg0); Set imagesAll = new HashSet(result); if (null == imagesAll || imagesAll.size() == 0)... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/2bc67970abd041b6cb8e0252d02a6e27f304bec4/HierarchyBrowsingImpl.java/buggy/components/server/src/org/openmicroscopy/omero/logic/HierarchyBrowsingImpl.java |
public Map findImageAnnotations(final Set arg0) { // CONTRACT if (null == arg0 || arg0.size() == 0) { return new HashMap(); } List result = annotationDao.findImageAnnotations(arg0); return (Map) clean(sortImageAnnotations(result)); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/2bc67970abd041b6cb8e0252d02a6e27f304bec4/HierarchyBrowsingImpl.java/buggy/components/server/src/org/openmicroscopy/omero/logic/HierarchyBrowsingImpl.java | ||
if (log.isDebugEnabled()){ log.debug("findPDIHierarchies() -- no results found:\n"+ arg0.toString()); } | public Set findPDIHierarchies(final Set arg0) { // CONTRACT if (null == arg0 || arg0.size() == 0) { return new HashSet(); } List result = containerDao.findPDIHierarchies(arg0); Set imagesAll = new HashSet(result); if (null == imagesAll || imagesAll.size() == 0) {... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/2bc67970abd041b6cb8e0252d02a6e27f304bec4/HierarchyBrowsingImpl.java/buggy/components/server/src/org/openmicroscopy/omero/logic/HierarchyBrowsingImpl.java | |
} else { | } else { | void hessianClean(Object obj, Set done) { if (null==obj) return; if (done.contains(obj)) return; done.add(obj); if (obj instanceof Map) { Map map = (Map) obj; for (Iterator i = map.values().iterator(); i.hasNext();) { Object value = i.... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/2bc67970abd041b6cb8e0252d02a6e27f304bec4/HierarchyBrowsingImpl.java/buggy/components/server/src/org/openmicroscopy/omero/logic/HierarchyBrowsingImpl.java |
e.printStackTrace(); | re.initCause(e); throw re; | Object invokeGetter(Object target, Method getter){ Object result=null; try { result = getter.invoke(target,new Object[]{}); } catch (IllegalArgumentException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (IllegalAccessException e) {... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/2bc67970abd041b6cb8e0252d02a6e27f304bec4/HierarchyBrowsingImpl.java/buggy/components/server/src/org/openmicroscopy/omero/logic/HierarchyBrowsingImpl.java |
e.printStackTrace(); | re.initCause(e); throw re; | Object invokeGetter(Object target, Method getter){ Object result=null; try { result = getter.invoke(target,new Object[]{}); } catch (IllegalArgumentException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (IllegalAccessException e) {... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/2bc67970abd041b6cb8e0252d02a6e27f304bec4/HierarchyBrowsingImpl.java/buggy/components/server/src/org/openmicroscopy/omero/logic/HierarchyBrowsingImpl.java |
e.printStackTrace(); | re.initCause(e); throw re; | Object invokeGetter(Object target, Method getter){ Object result=null; try { result = getter.invoke(target,new Object[]{}); } catch (IllegalArgumentException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (IllegalAccessException e) {... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/2bc67970abd041b6cb8e0252d02a6e27f304bec4/HierarchyBrowsingImpl.java/buggy/components/server/src/org/openmicroscopy/omero/logic/HierarchyBrowsingImpl.java |
"Class parameter for loadCGCIHierarchy() must be CategoryGroup or Category."); | "Class parameter for loadCGCIHierarchy() must be CategoryGroup or Category, not "+arg0); | public Object loadCGCIHierarchy(final Class arg0, final int arg1) { // CONTRACT if (!CategoryGroup.class.equals(arg0) && !Category.class.equals(arg0)) { throw new IllegalArgumentException( "Class parameter for loadCGCIHierarchy() must be CategoryGroup or Category."); ... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/2bc67970abd041b6cb8e0252d02a6e27f304bec4/HierarchyBrowsingImpl.java/buggy/components/server/src/org/openmicroscopy/omero/logic/HierarchyBrowsingImpl.java |
"Class parameter for loadPDIHierarchy() must be Project or Dataset."); | "Class parameter for loadPDIHierarchy() must be Project or Dataset, not "+arg0); | public Object loadPDIHierarchy(final Class arg0, final int arg1) { // CONTRACT if (!Project.class.equals(arg0) && !Dataset.class.equals(arg0)) { throw new IllegalArgumentException( "Class parameter for loadPDIHierarchy() must be Project or Dataset."); } retu... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/2bc67970abd041b6cb8e0252d02a6e27f304bec4/HierarchyBrowsingImpl.java/buggy/components/server/src/org/openmicroscopy/omero/logic/HierarchyBrowsingImpl.java |
RuntimeException re = new RuntimeException("Error trying to set to null"); | RuntimeException re = new RuntimeException("Error trying to set to null."); | void setToNull(Object obj, Method setter){ RuntimeException re = new RuntimeException("Error trying to set to null"); try { setter.invoke(obj,new Object[]{null}); } catch (IllegalArgumentException e) { // TODO Auto-generated catch block e.printStackTrace(); ... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/2bc67970abd041b6cb8e0252d02a6e27f304bec4/HierarchyBrowsingImpl.java/buggy/components/server/src/org/openmicroscopy/omero/logic/HierarchyBrowsingImpl.java |
e.printStackTrace(); | re.initCause(e); | void setToNull(Object obj, Method setter){ RuntimeException re = new RuntimeException("Error trying to set to null"); try { setter.invoke(obj,new Object[]{null}); } catch (IllegalArgumentException e) { // TODO Auto-generated catch block e.printStackTrace(); ... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/2bc67970abd041b6cb8e0252d02a6e27f304bec4/HierarchyBrowsingImpl.java/buggy/components/server/src/org/openmicroscopy/omero/logic/HierarchyBrowsingImpl.java |
e.printStackTrace(); | re.initCause(e); | void setToNull(Object obj, Method setter){ RuntimeException re = new RuntimeException("Error trying to set to null"); try { setter.invoke(obj,new Object[]{null}); } catch (IllegalArgumentException e) { // TODO Auto-generated catch block e.printStackTrace(); ... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/2bc67970abd041b6cb8e0252d02a6e27f304bec4/HierarchyBrowsingImpl.java/buggy/components/server/src/org/openmicroscopy/omero/logic/HierarchyBrowsingImpl.java |
e.printStackTrace(); | re.initCause(e); | void setToNull(Object obj, Method setter){ RuntimeException re = new RuntimeException("Error trying to set to null"); try { setter.invoke(obj,new Object[]{null}); } catch (IllegalArgumentException e) { // TODO Auto-generated catch block e.printStackTrace(); ... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/2bc67970abd041b6cb8e0252d02a6e27f304bec4/HierarchyBrowsingImpl.java/buggy/components/server/src/org/openmicroscopy/omero/logic/HierarchyBrowsingImpl.java |
Set result = new HashSet(l); | Set result = new HashSet(l); | Map sortDatasetAnnotations(final List l) { Set result = new HashSet(l); // TODO this everywhere if (null == result || result.size() == 0) { return new HashMap(); } Map map = new HashMap(); // SORT Iterator i = result.iterator(); while (i.hasNext()) { ... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/2bc67970abd041b6cb8e0252d02a6e27f304bec4/HierarchyBrowsingImpl.java/buggy/components/server/src/org/openmicroscopy/omero/logic/HierarchyBrowsingImpl.java |
Set result = new HashSet(l); | Set result = new HashSet(l); | Map sortImageAnnotations(final List l) { Set result = new HashSet(l); // TODO this everywhere if (null == result || result.size() == 0) { return new HashMap(); } Map map = new HashMap(); // SORT Iterator i = result.iterator(); while (i.hasNext()) { ... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/2bc67970abd041b6cb8e0252d02a6e27f304bec4/HierarchyBrowsingImpl.java/buggy/components/server/src/org/openmicroscopy/omero/logic/HierarchyBrowsingImpl.java |
suite.addTest(new TestSuite(TestNativeException.class)); | public static Test suite() { TestSuite suite = new TestSuite(); suite.addTest(new TestSuite(TestBSF.class)); return suite; } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/f5308c71bb6aebeec97981ce3cb34e636a1c531b/JavaSupportTestSuite.java/buggy/test/org/jruby/javasupport/test/JavaSupportTestSuite.java | |
CoverageDataFileHandler.setDefaultDataFile(args[++i]); | dataFile = new File(args[++i]); | private void parseArguments(String[] args) { // Parse our parameters Collection locations = new Vector(); for (int i = 0; i < args.length; i++) { if (args[i].equals("--basedir")) baseDir = new File(args[++i]); else if (args[i].equals("--datafile")) CoverageDataFileHandler.setDefaultDataFile(args[++i]); ... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/8b78aded7bc2195ca2875df15fa36b034194b55e/Main.java/buggy/cobertura/src/net/sourceforge/cobertura/instrument/Main.java |
projectData = ProjectData.getGlobalProjectData(); | projectData = CoverageDataFileHandler.loadCoverageData(dataFile); if (projectData == null) projectData = new ProjectData(); | private void parseArguments(String[] args) { // Parse our parameters Collection locations = new Vector(); for (int i = 0; i < args.length; i++) { if (args[i].equals("--basedir")) baseDir = new File(args[++i]); else if (args[i].equals("--datafile")) CoverageDataFileHandler.setDefaultDataFile(args[++i]); ... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/8b78aded7bc2195ca2875df15fa36b034194b55e/Main.java/buggy/cobertura/src/net/sourceforge/cobertura/instrument/Main.java |
ProjectData.saveGlobalProjectData(); | CoverageDataFileHandler.saveCoverageData(projectData, dataFile); | private void parseArguments(String[] args) { // Parse our parameters Collection locations = new Vector(); for (int i = 0; i < args.length; i++) { if (args[i].equals("--basedir")) baseDir = new File(args[++i]); else if (args[i].equals("--datafile")) CoverageDataFileHandler.setDefaultDataFile(args[++i]); ... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/8b78aded7bc2195ca2875df15fa36b034194b55e/Main.java/buggy/cobertura/src/net/sourceforge/cobertura/instrument/Main.java |
recv.getRubyClass().call(recv, getMId(), new RubyObject[] {value}, 0); | recv.getRubyClass().call(recv, getMId(), new RubyPointer(new RubyObject[] {value}), 0); | public void assign(Ruby ruby, RubyObject self, RubyObject value, boolean check) { RubyObject recv = getRecvNode().eval(ruby, self); if (getArgsNode() == null) { /* attr set */ recv.getRubyClass().call(recv, getMId(), new RubyObject[] {value}, 0); } else { RubyAr... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/f629550c5947df9c1dbe414645f3dc76bcb70df4/CallNode.java/clean/org/jruby/nodes/CallNode.java |
recv.getRubyClass().call(recv, getMId(), args.toJavaArray(), 0); | recv.getRubyClass().call(recv, getMId(), new RubyPointer(args.getList()), 0); | public void assign(Ruby ruby, RubyObject self, RubyObject value, boolean check) { RubyObject recv = getRecvNode().eval(ruby, self); if (getArgsNode() == null) { /* attr set */ recv.getRubyClass().call(recv, getMId(), new RubyObject[] {value}, 0); } else { RubyAr... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/f629550c5947df9c1dbe414645f3dc76bcb70df4/CallNode.java/clean/org/jruby/nodes/CallNode.java |
RubyObject[] args = ArgsUtil.setupArgs(ruby, self, getArgsNode()); | RubyPointer args = ArgsUtil.setupArgs(ruby, self, getArgsNode()); | public RubyObject eval(Ruby ruby, RubyObject self) { // TMP_PROTECT; RubyBlock tmpBlock = ArgsUtil.beginCallArgs(ruby); RubyObject recv = getRecvNode().eval(ruby, self); RubyObject[] args = ArgsUtil.setupArgs(ruby, self, getArgsNode()); ArgsUtil.endCallArgs... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/f629550c5947df9c1dbe414645f3dc76bcb70df4/CallNode.java/clean/org/jruby/nodes/CallNode.java |
return new ProcDefinition(ruby).getType(); | RubyClass result = ruby.defineClass("Proc", ruby.getClasses().getObjectClass()); CallbackFactory callbackFactory = ruby.callbackFactory(); result.defineMethod("arity", callbackFactory.getMethod(RubyProc.class, "arity")); result.defineMethod("call", callbackFactory.getOptMethod(RubyProc.class, "call")); result.defineMe... | public static RubyClass createProcClass(Ruby ruby) { return new ProcDefinition(ruby).getType(); } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/1c602493a83e2050f401fa6925ec7e9269b45e4e/RubyProc.java/clean/src/org/jruby/RubyProc.java |
ContactList contactList = SparkManager.getWorkspace().getContactList(); | final ContactList contactList = SparkManager.getWorkspace().getContactList(); | public void run() { ContactList contactList = SparkManager.getWorkspace().getContactList(); ChatRoom chatRoom = null; try { chatRoom = getChatContainer().getChatRoom(StringUtils.parseBareAddress(from)); if (chatRoom != null &... | 52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/37d2c9c1910f8cad82e65ab912959a96c5121978/ChatManager.java/buggy/src/java/org/jivesoftware/spark/ChatManager.java |
((ChatRoomImpl)chatRoom).showTyping(false); | ((ChatRoomImpl)chatRoom).showTyping(true); | public void run() { ContactList contactList = SparkManager.getWorkspace().getContactList(); ChatRoom chatRoom = null; try { chatRoom = getChatContainer().getChatRoom(StringUtils.parseBareAddress(from)); if (chatRoom != null &... | 52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/37d2c9c1910f8cad82e65ab912959a96c5121978/ChatManager.java/buggy/src/java/org/jivesoftware/spark/ChatManager.java |
contactList.useDefaults(from); customList.remove(StringUtils.parseBareAddress(from)); | contactList.setIconFor(from, SparkRes.getImageIcon(SparkRes.SMALL_MESSAGE_EDIT_IMAGE)); customList.add(StringUtils.parseBareAddress(from)); | public void run() { ContactList contactList = SparkManager.getWorkspace().getContactList(); ChatRoom chatRoom = null; try { chatRoom = getChatContainer().getChatRoom(StringUtils.parseBareAddress(from)); if (chatRoom != null &... | 52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/37d2c9c1910f8cad82e65ab912959a96c5121978/ChatManager.java/buggy/src/java/org/jivesoftware/spark/ChatManager.java |
scaleBar = new HeatMapScaleBar(); | public HeatMapUI() { super(); treePanel = new HeatMapTreeUI(null); gradPanel = new HeatMapGradientUI(); statusPanel = new HeatMapStatusUI(); modeBar = new HeatMapModeBar(); buildUI(); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/6d45d101f4e831fda33928e252f882d4d16128d2/HeatMapUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/browser/heatmap/HeatMapUI.java | |
controlPanel.add(scalePanel,BorderLayout.SOUTH); | private void buildUI() { Container contentPane = getContentPane(); contentPane.setLayout(new BorderLayout()); JPanel mainPanel = new JPanel(); mainPanel.setLayout(new BorderLayout()); JScrollPane scrollPane = new JScrollPane(treePanel); scrollPane.setPref... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/6d45d101f4e831fda33928e252f882d4d16128d2/HeatMapUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/browser/heatmap/HeatMapUI.java | |
dispatcher = new HeatMapDispatcher(model,statusPanel); | dispatcher = new HeatMapDispatcher(model,statusPanel,gradPanel); dispatcher.setCurrentMode(modeBar.getCurrentMode()); dispatcher.setCurrentScale(scaleBar.getCurrentScaleType()); | public void modelChanged(HeatMapModel model) { if(model == null) { return; } this.model = model; setTitle("HeatMap: " + model.getInfoSource().getDataset().getName()); treePanel.setModel(model.getModel()); treePanel.removeListener(dispatcher); mod... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/6d45d101f4e831fda33928e252f882d4d16128d2/HeatMapUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/browser/heatmap/HeatMapUI.java |
scaleBar.addListener(dispatcher); | public void modelChanged(HeatMapModel model) { if(model == null) { return; } this.model = model; setTitle("HeatMap: " + model.getInfoSource().getDataset().getName()); treePanel.setModel(model.getModel()); treePanel.removeListener(dispatcher); mod... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/6d45d101f4e831fda33928e252f882d4d16128d2/HeatMapUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/browser/heatmap/HeatMapUI.java | |
Block oldBlock = ruby.getBlock().getCurrent().cloneBlock(); | Block oldBlock = ruby.getBlockStack().getCurrent().cloneBlock(); | public RubyObject yieldUnder(RubyModule under) { return under.executeUnder(new Callback() { public RubyObject execute(RubyObject self, RubyObject[] args, Ruby ruby) { // if () { Block oldBlock = ruby.getBlock().getCurrent().cloneBlock(); /*... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/8db42974495981011f558bcce15e2dfc28681a76/RubyObject.java/buggy/org/jruby/RubyObject.java |
ruby.getBlock().getCurrent().getFrame().setNamespace(ruby.getCurrentFrame().getNamespace()); | ruby.getBlockStack().getCurrent().getFrame().setNamespace(ruby.getCurrentFrame().getNamespace()); | public RubyObject yieldUnder(RubyModule under) { return under.executeUnder(new Callback() { public RubyObject execute(RubyObject self, RubyObject[] args, Ruby ruby) { // if () { Block oldBlock = ruby.getBlock().getCurrent().cloneBlock(); /*... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/8db42974495981011f558bcce15e2dfc28681a76/RubyObject.java/buggy/org/jruby/RubyObject.java |
ruby.getBlock().setCurrent(oldBlock); | ruby.getBlockStack().setCurrent(oldBlock); | public RubyObject yieldUnder(RubyModule under) { return under.executeUnder(new Callback() { public RubyObject execute(RubyObject self, RubyObject[] args, Ruby ruby) { // if () { Block oldBlock = ruby.getBlock().getCurrent().cloneBlock(); /*... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/8db42974495981011f558bcce15e2dfc28681a76/RubyObject.java/buggy/org/jruby/RubyObject.java |
Block oldBlock = ruby.getBlock().getCurrent().cloneBlock(); | Block oldBlock = ruby.getBlockStack().getCurrent().cloneBlock(); | public RubyObject execute(RubyObject self, RubyObject[] args, Ruby ruby) { // if () { Block oldBlock = ruby.getBlock().getCurrent().cloneBlock(); /* copy the block to avoid modifying global data. */ ruby.getBlock().getCurrent().getFram... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/8db42974495981011f558bcce15e2dfc28681a76/RubyObject.java/buggy/org/jruby/RubyObject.java |
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