Datasets:

JoaoJunior

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java_encoded_processed_APR

like 0

pref.putBoolean(SHOWADVANCEDSETTINGS, showAdvancedSettingsBox.isSelected());

PreferencesEntry.SHOWADVANCEDSETTINGS.setValue(getController(), showAdvancedSettingsBox.isSelected());

public void save() { Preferences pref = getController().getPreferences(); // Write properties into core writeTrigger.triggerCommit(); // Set locale if (languageChooser.getSelectedItem() instanceof Locale) { Locale locale = (Locale) languageChooser.getSelectedItem(); // Check if we need to restart needsRestart |= !Util.equals(locale.getLanguage(), Translation .getActiveLocale().getLanguage()); // Save settings Translation.saveLocalSetting(locale); } else { // Remove setting Translation.saveLocalSetting(null); } // Set folder base String folderbase = (String) localBaseHolder.getValue(); ConfigurationEntry.FOLDER_BASEDIR.setValue(getController(), folderbase); // Store ui theme if (UIManager.getLookAndFeel() instanceof PlasticXPLookAndFeel) { PlasticTheme theme = PlasticXPLookAndFeel.getPlasticTheme(); pref.put("uitheme", theme.getClass().getName()); if (!Util.equals(theme, oldTheme)) { // FIXME: Themechange does not repaint SimpleInternalFrames. // thus restart required needsRestart = true; } } // Nickname if (!StringUtils.isBlank(nickField.getText())) { getController().changeNick(nickField.getText(), false); } // setAdvanced pref.putBoolean(SHOWADVANCEDSETTINGS, showAdvancedSettingsBox.isSelected()); }

51438 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/51438/4990d958eaf34a7653f68f1002faf36b3aaa862b/GeneralSettingsTab.java/clean/src/main/de/dal33t/powerfolder/ui/preferences/GeneralSettingsTab.java

throw new ParseException( "Content-Type not application/msword: "+contentType);

return new ParseStatus(ParseStatus.FAILED, ParseStatus.FAILED_INVALID_FORMAT, "Content-Type not application/msword: " + contentType).getEmptyParse();

public Parse getParse(Content content) throws ParseException { // check that contentType is one we can handle String contentType = content.getContentType(); if (contentType != null && !contentType.startsWith("application/msword")) throw new ParseException( "Content-Type not application/msword: "+contentType); String text = null; String title = null; Properties properties = null; try { byte[] raw = content.getContent(); String contentLength = content.get("Content-Length"); if (contentLength != null && raw.length != Integer.parseInt(contentLength)) { throw new ParseException("Content truncated at "+raw.length +" bytes. Parser can't handle incomplete msword file."); } WordExtractor extractor = new WordExtractor(); // collect text text = extractor.extractText(new ByteArrayInputStream(raw)); // collect meta info properties = extractor.extractProperties(new ByteArrayInputStream(raw)); extractor = null; } catch (ParseException e) { throw e; } catch (FastSavedException e) { throw new ParseException(e); } catch (PasswordProtectedException e) { throw new ParseException(e); } catch (Exception e) { // run time exception throw new ParseException("Can't be handled as msword document. "+e); } finally { // nothing so far } // collect meta data Properties metadata = new Properties(); metadata.putAll(content.getMetadata()); // copy through if(properties != null) { title = properties.getProperty("Title"); properties.remove("Title"); metadata.putAll(properties); } if (text == null) text = ""; if (title == null) title = ""; // collect outlink Outlink[] outlinks = new Outlink[0]; ParseData parseData = new ParseData(title, outlinks, metadata); return new ParseImpl(text, parseData); // any filter? //return HtmlParseFilters.filter(content, parse, root); }

57484 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57484/29bea6a24ea978596c3c1880a520b24bdeb2252d/MSWordParser.java/clean/src/plugin/parse-msword/src/java/org/apache/nutch/parse/msword/MSWordParser.java

gcpG = new GCPoint(Convert.toDouble(parts[2]), Convert.toDouble(parts[3]));

gcpG = new GCPoint(Convert.toDouble(parts[3]), Convert.toDouble(parts[2]));

public boolean importMap(){ Extractor ext; String rawFileName = new String(); FileChooser fc = new FileChooser(FileChooser.DIRECTORY_SELECT, File.getProgramDirectory()); fc.addMask("*.png"); fc.setTitle((String)lr.get(4100,"Select Directory:")); if(fc.execute() != fc.IDCANCEL){ File inDir = fc.getChosenFile(); File dir = new File(mapsPath); File mapFile; if (!dir.exists()) { dir.createDir(); } try{ //User selected a map, but maybe there are more png(s) //copy all of them! //at the same time try to find associated .map files! //These are georeference files targeted for OziExplorer. //So lets check if we have more than 1 png file: String[] files; String line = new String(); InputStream in; OutputStream out; FileReader inMap; byte[] buf; int len; String[] parts; files = inDir.list("*.png", File.LIST_FILES_ONLY); InfoBox inf = new InfoBox("Info", (String)lr.get(4109,"Loading maps...")); inf.show(); Vm.showWait(true); for(int i = 0; i<files.length;i++){ inf.setInfo((String)lr.get(4110,"Loading:")+ " " + files[i]); //Copy the file //Vm.debug("Copy: " + inDir.getFullPath() + "/" +files[i]); //Vm.debug("to: " + mapsPath + files[i]); in = new FileInputStream(inDir.getFullPath() + "/" +files[i]); out = new FileOutputStream(mapsPath + files[i]); buf = new byte[1024]; while ((len = in.read(buf)) > 0) { out.write(buf, 0, len); } in.close(); out.close(); //Check for a .map file ext = new Extractor(files[i], "", ".", 0, true); rawFileName = ext.findNext(); mapFile = new File(inDir.getFullPath() + "/" + rawFileName + ".map"); if(mapFile.exists()){ GCPoint gcp1 = new GCPoint(); GCPoint gcp2 = new GCPoint(); GCPoint gcp3 = new GCPoint(); GCPoint gcp4 = new GCPoint(); GCPoint gcpG = new GCPoint(); //Vm.debug("Found file: " + inDir.getFullPath() + "/" + rawFileName + ".map"); inMap = new FileReader(inDir.getFullPath() + "/" + rawFileName + ".map"); while((line = inMap.readLine()) != null){ if(line.equals("MMPNUM,4")){ line = inMap.readLine(); parts = mString.split(line, ','); gcp1.bitMapX = Convert.toInt(parts[2]); gcp1.bitMapY = Convert.toInt(parts[3]); line = inMap.readLine(); parts = mString.split(line, ','); gcp2.bitMapX = Convert.toInt(parts[2]); gcp2.bitMapY = Convert.toInt(parts[3]); line = inMap.readLine(); parts = mString.split(line, ','); gcp3.bitMapX = Convert.toInt(parts[2]); gcp3.bitMapY = Convert.toInt(parts[3]); imageWidth = gcp3.bitMapX; imageHeight = gcp3.bitMapY; line = inMap.readLine(); parts = mString.split(line, ','); gcp4.bitMapX = Convert.toInt(parts[2]); gcp4.bitMapY = Convert.toInt(parts[3]); line = inMap.readLine(); parts = mString.split(line, ','); gcpG = new GCPoint(Convert.toDouble(parts[2]), Convert.toDouble(parts[3])); gcpG.bitMapX = gcp1.bitMapX; gcpG.bitMapY = gcp1.bitMapY; addGCP(gcpG); line = inMap.readLine(); parts = mString.split(line, ','); gcpG = new GCPoint(Convert.toDouble(parts[2]), Convert.toDouble(parts[3])); gcpG.bitMapX = gcp2.bitMapX; gcpG.bitMapY = gcp2.bitMapY; addGCP(gcpG); line = inMap.readLine(); parts = mString.split(line, ','); gcpG = new GCPoint(Convert.toDouble(parts[2]), Convert.toDouble(parts[3])); gcpG.bitMapX = gcp3.bitMapX; gcpG.bitMapY = gcp3.bitMapY; addGCP(gcpG); line = inMap.readLine(); parts = mString.split(line, ','); gcpG = new GCPoint(Convert.toDouble(parts[2]), Convert.toDouble(parts[3])); gcpG.bitMapX = gcp4.bitMapX; gcpG.bitMapY = gcp4.bitMapY; addGCP(gcpG); evalGCP(); //Vm.debug("Saving .map file to: " + mapsPath + "/" + rawFileName + ".wfl"); saveWFL(mapsPath + "/" + rawFileName + ".wfl"); } } inMap.close(); } } inf.close(0); Vm.showWait(false); return true; }catch(Exception ex){ Vm.debug("Error:" + ex.toString()); } } return false; }

51026 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/51026/39c46900ebba19c68621cdca63912a2190b0f811/Map.java/buggy/src/CacheWolf/Map.java

IMethod primaryCandidate= JavaModelUtil.findMethod(getGetterName(field, EMPTY), new String[0], false, field.getDeclaringType());

IMethod primaryCandidate= JavaModelUtil.findMethod(getGetterName(field, EMPTY, true), new String[0], false, field.getDeclaringType());

public static IMethod getGetter(IField field) throws JavaModelException{ IMethod primaryCandidate= JavaModelUtil.findMethod(getGetterName(field, EMPTY), new String[0], false, field.getDeclaringType()); if (! JavaModelUtil.isBoolean(field) || (primaryCandidate != null && primaryCandidate.exists())) return primaryCandidate; //bug 30906 describes why we need to look for other alternatives here String secondCandidateName= getGetterName(field.getJavaProject(), field.getElementName(), field.getFlags(), false, EMPTY); return JavaModelUtil.findMethod(secondCandidateName, new String[0], false, field.getDeclaringType()); }

9698 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/9698/b4da61a3d57255f6e89b5cd1698b70f088958e3a/GetterSetterUtil.java/buggy/org.eclipse.jdt.ui/core extension/org/eclipse/jdt/internal/corext/codemanipulation/GetterSetterUtil.java

MylarTaskListPlugin.setCurrentPriorityLevel(Task.PriorityLevel.P4); PRIORITY_FILTER.displayPrioritiesAbove(PRIORITY_LEVELS[3]);

MylarTaskListPlugin.setCurrentPriorityLevel(Task.PriorityLevel.P2); PRIORITY_FILTER.displayPrioritiesAbove(PRIORITY_LEVELS[1]);

public void run() { MylarTaskListPlugin.setCurrentPriorityLevel(Task.PriorityLevel.P4); PRIORITY_FILTER.displayPrioritiesAbove(PRIORITY_LEVELS[3]); getViewer().refresh(); }

51151 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/51151/6740590a4c4acd414bc94a9174b5cca97c99d56b/TaskListView.java/clean/org.eclipse.mylyn.tasks.ui/src/org/eclipse/mylyn/internal/tasklist/ui/views/TaskListView.java

if (isInitNameChar(content.charAt(0))) { for (int i = 1; i < len; i++) { if (!isNameChar(content.charAt(i))) { seenErr = true; break; } } } else { seenErr = true; }

seenErr = !XMLCharacterProperties.validName(content);

protected static void validateToken(String tokenType, String content) throws InvalidDatatypeValueException { int len; if (content == null || (len = content.length()) == 0) { throw new InvalidDatatypeValueException("The length of the content must be greater than 0"); } boolean seenErr = false; if (tokenType == SPECIAL_TOKEN_NMTOKEN) { // PATTERN "\\c+" for (int i = 0; i < len; i++) { if (!isNameChar(content.charAt(i))) { seenErr = true; break; } } } else if (tokenType == SPECIAL_TOKEN_NAME || tokenType == SPECIAL_TOKEN_IDNAME || tokenType == SPECIAL_TOKEN_IDREFNAME) { // PATTERN "\\i\\c*" if (isInitNameChar(content.charAt(0))) { for (int i = 1; i < len; i++) { if (!isNameChar(content.charAt(i))) { seenErr = true; break; } } } else { seenErr = true; } } else if (tokenType == SPECIAL_TOKEN_NCNAME || tokenType == SPECIAL_TOKEN_IDNCNAME || tokenType == SPECIAL_TOKEN_IDREFNCNAME || tokenType == SPECIAL_TOKEN_ENTITY) { // PATTERN "[\\i-[:]][\\c-[:]]*" if (isNCInitNameChar(content.charAt(0))) { for (int i = 1; i < len; i++) { if (!isNCNameChar(content.charAt(i))) { seenErr = true; break; } } } else { seenErr = true; } } if (seenErr) { throw new InvalidDatatypeValueException("Value '"+content+"' is not a valid " + tokenType); } }

4434 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/4434/8426e76c1efaf189a0a808a432c7029bbddbca04/AbstractStringValidator.java/buggy/src/org/apache/xerces/validators/datatype/AbstractStringValidator.java

if ( ( factory == null && cssRule.getType() == CSSRule.STYLE_RULE ) ||

if ( /*( factory == null && cssRule.getType() == CSSRule.STYLE_RULE ) ||*/

public static Iterator fromCSSPropertyDecl( CSSRule cssRule, CSSStyleDeclaration style, String propName, int sequence ) { // HACK: special cases for RuleNormalizer...need to work this out cleanly PropertyFactory factory = (PropertyFactory)PRP_FACTORIES.get( propName ); if ( ( factory == null && cssRule.getType() == CSSRule.STYLE_RULE ) || propName.indexOf( "color" ) >= 0 && !propName.equals( "border" ) ) { RULE_NORMALIZER.normalize( (CSSStyleRule)cssRule ); style = ( (CSSStyleRule)cssRule ).getStyle(); } List list = new ArrayList(); switch ( style.getPropertyCSSValue( propName ).getCssValueType() ) { case CSSValue.CSS_PRIMITIVE_VALUE: if ( factory == null ) { XRProperty prop = new XRPropertyImpl( style, propName, sequence ); list.add( prop ); } else { Iterator iter = factory.explodeProperties( style, propName, sequence ); while ( iter.hasNext() ) { list.add( iter.next() ); } } break; case CSSValue.CSS_VALUE_LIST: if ( factory == null ) { XRProperty prop = new XRPropertyImpl( style, propName, sequence ); list.add( prop ); // HACK--right now, BP is allowed to not have a factory if ( !propName.equals( CSSName.BACKGROUND_POSITION ) && !propName.equals( CSSName.FONT_FAMILY ) ) { System.err.println( "! Property '" + propName + "' was assigned multiple values but no factory is assigned to it." ); } } else { Iterator iter = factory.explodeProperties( style, propName, sequence ); while ( iter.hasNext() ) { list.add( iter.next() ); } } break; default: System.err.println( "Property '" + propName + "' is neither primitive nor value list, can't handle." ); break; } return list.iterator(); }

8125 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/8125/303478cb2d50ec8a2e30b215b0e54607a0ae9a68/XRPropertyImpl.java/clean/src/java/org/xhtmlrenderer/css/impl/XRPropertyImpl.java

add(new CharGenerator("Hello World2!")); add(new SplitJoin()

this.add(new CharGenerator("Hello World2!")); this.add(new SplitJoin()

public void init() { add(new CharGenerator("Hello World2!")); add(new SplitJoin() { public void init() { setSplitter(ROUND_ROBIN ()); add(new Identity (Character.TYPE)); add(new Identity (Character.TYPE)); setJoiner (ROUND_ROBIN ()); } }); add (new Pipeline () { public void init () { add (new Pipeline () { public void init () { add (new SplitJoin () { public void init () { setSplitter (WEIGHTED_ROUND_ROBIN (2, 1, 4, 2)); add (new Filter () { Channel input = new Channel(Character.TYPE, 1); Channel output = new Channel (Character.TYPE, 2); public void initIO () { streamInput = input; streamOutput = output; } public void work() { input.popChar (); output.pushChar (input.popChar ()); } }); add (new Filter () { Channel input = new Channel(Character.TYPE, 1); Channel output = new Channel (Character.TYPE, 8); public void initIO () { streamInput = input; streamOutput = output; } public void work() { char c = input.popChar (); output.pushChar (c); output.pushChar (c); output.pushChar (c); output.pushChar (c); output.pushChar (c); output.pushChar (c); output.pushChar (c); output.pushChar (c); } }); add (new Identity (Character.TYPE)); add(new CharPrinter()); setJoiner (WEIGHTED_ROUND_ROBIN (1, 2, 1, 0)); } }); } }); } }); add (new CharPrinter ()); }

5955 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/5955/1537aac832f399becfeb312d0251fb8431191491/HelloWorld2.java/clean/streams/apps/tests/hello-splits/HelloWorld2.java

Bundle b = m_context.installBundle(tabBundle); b.start(); System.out.println(msg+" Bundle started");

Bundle b = m_context.installBundle(tabBundle); b.start(); System.out.println(" - Bundle started: \""+name.toString()+"\" - "+tabBundle);

public void propertyChange(PropertyChangeEvent event) { if (event.getPropertyName().equals(Plugin.PLUGIN_ADDED)) { Plugin cp=(Plugin) event.getNewValue(); this.add(cp.getName(), cp.getGUI()); System.out.println("Add gui \""+cp.getName()+"\" into NodePanel"/*+" :: "+cp.getGUI()*/); this.a.addPropertyChangeListener(cp); this.pluginList.put(cp.pluginLocation(), cp); }else if(event.getPropertyName().equals(Plugin.PLUGIN_REMOVED)) { Plugin cp = (Plugin) event.getNewValue(); this.remove(cp.getGUI()); this.a.removePropertyChangeListener(cp); // this.pluginList.remove(cp.pluginLocation()); }else if(event.getPropertyName().equals(Plugin.EMPTY_NODE)) { System.out.println("******* Debug No node selected"); this.clean(); }else if (event.getPropertyName().equals(Plugin.NEW_NODE_SELECTED)) { //System.out.println("Event NEW_NODE_SELECTED"); /* Update the tabs (Plugin) in the JTabbedPane (NodePanel) */ MBeanServerConnection mbsc = (MBeanServerConnection)event.getNewValue(); try { this.clean(); Set ons = mbsc.queryNames( null, null ); String msg=""; for( Iterator i=ons.iterator(); i.hasNext(); ) { ObjectName name = ( ObjectName )i.next(); msg="Queried name: "+name.toString(); if ( "TabUI".equals(name.getDomain()) ) { msg+=" New tab: "+name.toString(); /* Get the plugin implementation via a bundle */ String tabBundle = (String) mbsc.getAttribute(name, "BundleName"); msg+=" Bundle name for current Plugin: "+tabBundle; if (tabBundle!=null){ Plugin p = (Plugin) this.pluginList.get(tabBundle); if (p == null){ Bundle b = m_context.installBundle(tabBundle); b.start(); System.out.println(msg+" Bundle started"); //Thread.sleep(5000); }else{ System.out.println(msg+" Register service plugin: " + p); p.registerServicePlugin(); }// ServiceReference[] sr = b.getRegisteredServices();// System.out.println(sr);// Plugin p;// for (int j=0 ; j < sr.length ; j++) {// p=(Plugin)m_context.getService(sr[j]);// this.add(p.getName(), p.getGUI());// this.a.addPropertyChangeListener(p);// }// System.out.println("Delegation for this");// printcl = this.getClass().getClassLoader();// while (printcl != null) {// System.out.println(printcl);// printcl = printcl.getParent();// }// System.out.println("{bootstrap loader}");// System.out.println(""); /* Get the tab object */// Object tabObj = mbsc.getAttribute(name, "Tab");// // System.out.println("Delegation for tabObj: " + tabObj);// printcl = tabObj.getClass().getClassLoader();// while (printcl != null) {// System.out.println(printcl);// printcl = printcl.getParent();// }// System.out.println("{bootstrap loader}");// System.out.println(""); // System.out.println("tabObj.getName(): " + ((fr.inria.ares.managedelements.testprobe.tab.TestProbeTabUI) tabObj).getName()); /* Cast the tab */ // Plugin tab = (Plugin)tabObj; /* register the tab on the JTabbedPane */// this.add(tab.getName(), tab.getGUI()); }else{ System.out.println(msg+" No "+tabBundle+" property defined. I cannot install "+tabBundle+" tab"); } } } a.firePropertyChangedEvent(Plugin.NEW_NODE_READY, null, mbsc); a.firePropertyChangedEvent(Plugin.PLUGIN_ACTIVATED, null, this.getComponentAt(0).getName()); } catch (MBeanException e) { System.err.println("MBeanException : "+e);// } catch (MalformedObjectNameException e) {// System.err.println(e); } catch (AttributeNotFoundException e) { System.err.println("AttributeNotFoundException : "+e); } catch (InstanceNotFoundException e) { System.err.println("InstanceNotFoundException : "+e); } catch (ReflectionException e) { System.err.println("ReflectionException : "+e); } catch (IOException e) { System.err.println("IOException : "+e); } catch (BundleException e) { System.err.println("BundleException : "+e); } catch (Exception e) { System.err.println("Exception : "+e); }// } catch (java.lang.InterruptedException e) {// System.err.println(e);// } } }

45948 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/45948/ba1be79cba7fef5ae7fca4aac5fd530bdea243f5/NodePanel.java/buggy/mosgi.console.gui/src/main/java/org/apache/felix/mosgi/console/gui/NodePanel.java

String[] files = PluginUtils.findSources( sourceDir, "**/*.mmld" );

ClassLoader oldCl = Thread.currentThread().getContextClassLoader(); try { Thread.currentThread().setContextClassLoader(MarmaladeMojoDescriptorExtractor.class.getClassLoader()); String[] files = PluginUtils.findSources( sourceDir, "**/*.mmld" );

public Set execute( String sourceDir, MavenProject project ) throws Exception { String[] files = PluginUtils.findSources( sourceDir, "**/*.mmld" ); Set descriptors = new HashSet(); File dir = new File( sourceDir ); for ( int i = 0; i < files.length; i++ ) { String file = files[i]; Map context = new TreeMap(); context.put( MarmaladeMojoExecutionDirectives.SCRIPT_BASEPATH_INVAR, sourceDir ); File scriptFile = new File( dir, file ); context = LazyMansAccess.executeFromFile( scriptFile, context ); MojoDescriptor descriptor = (MojoDescriptor) context.get( MarmaladeMojoExecutionDirectives.METADATA_OUTVAR ); descriptor.setImplementation( file ); descriptors.add( descriptor ); } return descriptors; }

11530 /local/tlutelli/issta_data/temp/all_java1context/java/2006_temp/2006/11530/95d01ff57237629f48cc62e515ebc75aff870cc6/MarmaladeMojoDescriptorExtractor.java/clean/maven-plugin-tools/maven-plugin-tools-marmalade/src/main/java/org/apache/maven/tools/plugin/extractor/marmalade/MarmaladeMojoDescriptorExtractor.java

public SimpleCycleBasis (UndirectedGraph graph) { this.cycles = new ArrayList(); this.edgeList = new ArrayList();

public SimpleCycleBasis (List cycles, List edgeList, UndirectedGraph graph) { this.edgeList = edgeList; this.cycles = cycles;

public SimpleCycleBasis (UndirectedGraph graph) { this.cycles = new ArrayList(); this.edgeList = new ArrayList(); this.graph = graph; createMinimalCycleBase(); }

45167 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/45167/377171c5907bab11cc813de19845b0f9ae108f55/SimpleCycleBasis.java/buggy/src/org/openscience/cdk/ringsearch/cyclebasis/SimpleCycleBasis.java

public void cancelTimer(MessageAddress node) {

private void cancelTimer(MessageAddress node) {

public void cancelTimer(MessageAddress node) { Timer theMaskingTimer = (Timer) nodeTimerMap.get(node); theMaskingTimer.cancel(); nodeTimerMap.remove(node); }

7981 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/7981/08e9bdbce8d4cae387f03013c4fda7a925fce848/TrafficMaskingGeneratorAspect.java/buggy/core/src/org/cougaar/core/mts/TrafficMaskingGeneratorAspect.java

readyToRun = false; blackboard.closeTransaction(); primed = true;

readyToRun = false; } catch (Throwable t) { System.err.println("Error: Uncaught exception in "+this+": "+t); t.printStackTrace(); } finally { blackboard.closeTransaction(); primed = true; }

protected void precycle() { blackboard.openTransaction(); setupSubscriptions(); // run execute here so subscriptions don't miss out on the first // batch in their subscription addedLists execute(); readyToRun = false; // don't need to run execute again blackboard.closeTransaction(); primed = true; }

7981 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/7981/baf5f99723f9a67c04d9aceb95c9c025ae9033c8/ComponentPlugin.java/buggy/core/src/org/cougaar/core/plugin/ComponentPlugin.java

log.debug(fullName);

getLogger().debug(fullName);

protected final boolean checkTTC(FontFileReader in, String name) throws IOException { String tag = in.readTTFString(4); if ("ttcf".equals(tag)) { // This is a TrueType Collection in.skip(4); // Read directory offsets int numDirectories = (int)in.readTTFULong(); // int numDirectories=in.readTTFUShort(); long[] dirOffsets = new long[numDirectories]; for (int i = 0; i < numDirectories; i++) { dirOffsets[i] = in.readTTFULong(); } log.debug("This is a TrueType collection file with" + numDirectories + " fonts"); log.debug("Containing the following fonts: "); // Read all the directories and name tables to check // If the font exists - this is a bit ugly, but... boolean found = false; // Iterate through all name tables even if font // Is found, just to show all the names long dirTabOffset = 0; for (int i = 0; (i < numDirectories); i++) { in.seek_set(dirOffsets[i]); readDirTabs(in); readName(in); if (fullName.equals(name)) { found = true; dirTabOffset = dirOffsets[i]; log.debug("* " + fullName); } else { log.debug(fullName); } // Reset names notice = ""; fullName = ""; familyName = ""; fontName = ""; subFamilyName = ""; } in.seek_set(dirTabOffset); return found; } else { in.seek_set(0); return true; } }

5268 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/5268/2e2226dd0dd6733fdab0c36331723114a46eddd8/TTFFile.java/buggy/src/org/apache/fop/fonts/TTFFile.java

return false;

return otherValue.equals(myValue);

public boolean equal(org.omg.CORBA.Any any) { if (any == null) { throw new BAD_PARAM ("Null passed to Any equal operation"); } if (!typeCode.equal (any.type())) { return false; } int kind = originalType().kind().value(); switch (kind) { case TCKind._tk_null: case TCKind._tk_void: return true; case TCKind._tk_short: return extract_short() == any.extract_short(); case TCKind._tk_long: return extract_long() == any.extract_long(); case TCKind._tk_longlong: return extract_longlong() == any.extract_longlong(); case TCKind._tk_ushort: return extract_ushort() == any.extract_ushort(); case TCKind._tk_ulong: return extract_ulong() == any.extract_ulong(); case TCKind._tk_ulonglong: return extract_ulonglong() == any.extract_ulonglong(); case TCKind._tk_float: return extract_float() == any.extract_float(); case TCKind._tk_double: return extract_double() == any.extract_double(); case TCKind._tk_fixed: return extract_fixed().equals( any.extract_fixed() ); case TCKind._tk_boolean: return extract_boolean() == any.extract_boolean(); case TCKind._tk_char: return extract_char() == any.extract_char(); case TCKind._tk_wchar: return extract_wchar() == any.extract_wchar(); case TCKind._tk_octet: return extract_octet() == any.extract_octet(); case TCKind._tk_any: return extract_any().equals( any.extract_any() ); case TCKind._tk_TypeCode: return extract_TypeCode().equal( any.extract_TypeCode() ); case TCKind._tk_Principal: throw new org.omg.CORBA.NO_IMPLEMENT ("Principal deprecated"); case TCKind._tk_objref: return extract_Object().equals( any.extract_Object() ); case TCKind._tk_string: return extract_string().equals( any.extract_string() ); case TCKind._tk_wstring: return extract_wstring().equals( any.extract_wstring() ); case TCKind._tk_array: case TCKind._tk_sequence: case TCKind._tk_struct: case TCKind._tk_except: case TCKind._tk_enum: case TCKind._tk_union: case TCKind._tk_value: case TCKind._tk_value_box: { CDROutputStream out1, out2; if( !( orb instanceof org.jacorb.orb.ORB )) { out1 = new CDROutputStream(); out2 = new CDROutputStream(); } else { out1 = new CDROutputStream(orb); out2 = new CDROutputStream(orb); } write_value( out1 ); any.write_value( out2 ); if( out1.size() != out2.size() ) { return false; } return Arrays.equals( out1.getBufferCopy(), out2.getBufferCopy()); } default: throw new BAD_TYPECODE("Cannot compare anys with TypeCode kind " + kind); } }

46355 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/46355/dcd731487996f10323f454bdda69836e266fc67f/Any.java/buggy/src/org/jacorb/orb/Any.java

}

}

public byte [] getSourceBytes(){ byte [] result = null; myFactory.throwExceptionIfNotInitialized(); String HTMLContent = new String(); String currURL = getCurrentURL(); System.out.println("\nThe Current URL is -- " + currURL); try { URL aURL = new URL(currURL); URLConnection connection = aURL.openConnection(); connection.connect(); BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream())); boolean more = true; while (more) { String line = in.readLine(); if (line == null) more = false; else { HTMLContent = HTMLContent + line; } } } catch (Throwable e) { System.out.println("Error occurred while establishing connection -- \n ERROR - " + e); } result = HTMLContent.getBytes(); return result;}

47609 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/47609/afee19ff581e3d13844917014bf035cd25e515ae/CurrentPageImpl.java/buggy/java/webclient/classes_spec/org/mozilla/webclient/wrapper_native/CurrentPageImpl.java

String value = randomValueForSetter();

String value = "\"" + randomValueForDbUnit() + "\"";

public String formSetterWithValue() throws XDocletException { XMethod method = super.getCurrentMethod(); XMethod setter = method.getMutator(); String value = randomValueForSetter(); if (setter.getPropertyType().getType().isA("java.util.Date")) { value = "\"" + getDate(new Date(), uiDatePattern) + "\""; } rootClassName = classNameLower(); return rootClassName + "Form." + curprefix + setter.getName() + "(" + value + ");"; }

3521 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/3521/1596a9e2151b45f8d8b68dc66bbab6cc9bfd0ea4/MethodExTagsHandler.java/clean/extras/appgen/src/org/example/antbook/xdoclet/MethodExTagsHandler.java

fErrorHandler.handleError(error);

fErrorHandler.getErrorHandler().handleError(error);

XMLInputSource dom2xmlInputSource (LSInput is) { // need to wrap the LSInput with an XMLInputSource XMLInputSource xis = null; // check whether there is a Reader // according to DOM, we need to treat such reader as "UTF-16". if (is.getCharacterStream () != null) { xis = new XMLInputSource (is.getPublicId (), is.getSystemId (), is.getBaseURI (), is.getCharacterStream (), "UTF-16"); } // check whether there is an InputStream else if (is.getByteStream () != null) { xis = new XMLInputSource (is.getPublicId (), is.getSystemId (), is.getBaseURI (), is.getByteStream (), is.getEncoding ()); } // if there is a string data, use a StringReader // according to DOM, we need to treat such data as "UTF-16". else if (is.getStringData () != null && is.getStringData().length() > 0) { xis = new XMLInputSource (is.getPublicId (), is.getSystemId (), is.getBaseURI (), new StringReader (is.getStringData ()), "UTF-16"); } // otherwise, just use the public/system/base Ids else if ((is.getSystemId() != null && is.getSystemId().length() > 0) || (is.getPublicId() != null && is.getPublicId().length() > 0)) { xis = new XMLInputSource (is.getPublicId (), is.getSystemId (), is.getBaseURI ()); } else { // all inputs are null if (fErrorHandler != null) { DOMErrorImpl error = new DOMErrorImpl(); error.fType = "no-input-specified"; error.fMessage = "no-input-specified"; error.fSeverity = DOMError.SEVERITY_FATAL_ERROR; fErrorHandler.handleError(error); } throw new LSException(LSException.PARSE_ERR, "no-input-specified"); } return xis; }

6373 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/6373/057f39ad905b6f8c6a6864e0591a9ba69d0ea78c/DOMParserImpl.java/buggy/src/org/apache/xerces/parsers/DOMParserImpl.java

tooltip.setVisible(false); ListIterator li = actionList.listIterator(0); ActionListener al; while (li.hasNext()) { al = (ActionListener) li.next(); al.actionPerformed(new ActionEvent(e.getSource(), ActionEvent.ACTION_PERFORMED, "PressAction", e.getWhen(), 0)); }

if(tooltip != null) tooltip.setVisible(false); SwingUtilities.invokeLater(new Runnable(){ public void run() { Thread actionThread = new Thread(new Runnable(){ public void run() { ListIterator li = actionList.listIterator(0); while (li.hasNext()) { ActionListener al; al = (ActionListener) li.next(); al.actionPerformed(new ActionEvent(GnomeTrayIconService.this, ActionEvent.ACTION_PERFORMED, "PressAction", e.getWhen(), 0)); } } }); actionThread.start(); } });

void mousePressed(MouseEvent e) { if (menu != null) { if (e.isPopupTrigger()) { tooltip.setVisible(false); Dimension d = menu.getPreferredSize(); Dimension s = Toolkit.getDefaultToolkit().getScreenSize(); Point p = e.getPoint(); SwingUtilities.convertPointToScreen(p, (Component) e.getSource()); p.x = p.x + d.width > s.width ? p.x - d.width : p.x; p.y = p.y + d.height > s.height ? p.y - d.height : p.y; SwingUtilities.convertPointFromScreen(p, popupMenuParent); menu.show(popupMenuParent, p.x, p.y); } else { tooltip.setVisible(false); ListIterator li = actionList.listIterator(0); ActionListener al; while (li.hasNext()) { al = (ActionListener) li.next(); al.actionPerformed(new ActionEvent(e.getSource(), ActionEvent.ACTION_PERFORMED, "PressAction", e.getWhen(), 0)); } } } }

4416 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/4416/f2a6ecf973acf6bbc0afbdbdec2eb8eec0112ce4/GnomeTrayIconService.java/buggy/src/jdic/src/unix/classes/org/jdesktop/jdic/tray/internal/impl/GnomeTrayIconService.java

boolean reverse) { int fill = points.length; for (int i = 0; i < points.length / 2; i++) { if (!reverse) { shape[index++] = x + points[2 * i]; shape[index++] = y + points[2 * i + 1]; } else { shape[index + fill - 2 - 2 * i] = x + points[2 * i]; shape[index + fill - 1 - 2 * i] = y + points[2 * i + 1]; } } if (reverse) { index += fill; } return index; }

boolean reverse) { int fill = points.length; for (int i = 0; i < points.length / 2; i++) { if (!reverse) { shape[index++] = x + points[2 * i]; shape[index++] = y + points[2 * i + 1]; } else { shape[index + fill - 2 - 2 * i] = x + points[2 * i]; shape[index + fill - 1 - 2 * i] = y + points[2 * i + 1]; } } if (reverse) { index += fill; } return index; }

private int fillShape(int[] shape, int[] points, int index, int x, int y, boolean reverse) { int fill = points.length; for (int i = 0; i < points.length / 2; i++) { if (!reverse) { shape[index++] = x + points[2 * i]; shape[index++] = y + points[2 * i + 1]; } else { shape[index + fill - 2 - 2 * i] = x + points[2 * i]; shape[index + fill - 1 - 2 * i] = y + points[2 * i + 1]; } } if (reverse) { index += fill; } return index; }

13822 /local/tlutelli/issta_data/temp/all_java1context/java/2006_temp/2006/13822/1b18c4111a9bdd6d059092d4cb5971693a9544b2/IntroLaunchBar.java/clean/org.eclipse.ui.intro/src/org/eclipse/ui/internal/intro/impl/presentations/IntroLaunchBar.java

log.error("***** Draw.run(): received invalid draw command " + comm.mode);

System.err.println("***** Draw.run(): received invalid draw command " + comm.mode);

public void mainLoop() { Object tmp; Message msg=null; DrawCommand comm; boolean fl=true; while(fl) { try { tmp=channel.receive(0); if(tmp == null) continue; if(tmp instanceof View) { View v=(View)tmp; if(v instanceof MergeView) System.out.println("** MergeView=" + v); else System.out.println("** View=" + v); member_size=v.size(); if(mainFrame != null) setTitle(); continue; } if(tmp instanceof ExitEvent) { System.out.println("-- Draw.main(): received EXIT, waiting for ChannelReconnected callback"); setTitle(" Draw Demo - shunned "); break; } if(!(tmp instanceof Message)) continue; msg=(Message)tmp; comm=null; Object obj=msg.getObject(); if(obj instanceof DrawCommand) comm=(DrawCommand)obj; else if(obj instanceof Message) { System.out.println("*** Draw.run(): message is " + Util.printMessage((Message)obj)); Util.dumpStack(false); continue; } else { if(obj != null) System.out.println("*** Draw.run(): obj is " + obj.getClass() + ", hdrs are" + msg.printObjectHeaders()); else System.out.println("*** Draw.run(): hdrs are " + msg.printObjectHeaders()); Util.dumpStack(false); continue; } switch(comm.mode) { case DrawCommand.DRAW: if(panel != null) panel.drawPoint(comm); break; case DrawCommand.CLEAR: clearPanel(); continue; default: log.error("***** Draw.run(): received invalid draw command " + comm.mode); break; } } catch(ChannelNotConnectedException not) { log.error("Draw: " + not); break; } catch(ChannelClosedException closed) { break; } catch(Exception e) { log.error(e); continue; } } }

3550 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/3550/13de68466e3cf7fde6ee0bde0cee09a33e837e89/Draw.java/buggy/src/org/jgroups/demos/Draw.java

Node testNode2Session2 = (Node) session2.getItem(testNode2Session1.getPath());

try { Node testNode2Session2 = (Node) session2.getItem(testNode2Session1.getPath());

public void testRefreshBooleanTrue() throws RepositoryException { // get default workspace test root node using superuser session Node defaultRootNode = (Node) superuser.getItem(testRootNode.getPath()); // create a node Node testNode1Session1 = defaultRootNode.addNode(nodeName1, testNodeType); // create a second node Node testNode2Session1 = defaultRootNode.addNode(nodeName2, testNodeType); // save the new nodes defaultRootNode.save(); // add child node to test node 1 using session 1 testNode1Session1.addNode(nodeName2, testNodeType); // get session 2 Session session2 = helper.getReadWriteSession(); // get the second node Node testNode2Session2 = (Node) session2.getItem(testNode2Session1.getPath()); // adds a child node testNode2Session2.addNode(nodeName3, testNodeType); // save the changes session2.save(); // call refresh on session 1 defaultRootNode.refresh(true); // check if session 1 flag has been cleared assertTrue("Session should still have pending changes recorded after Node.refresh(true)!", superuser.hasPendingChanges()); // check if added child node for node 1 by session 1 is still there assertTrue("Node Modifications are lost after Node.refresh(true)", testNode1Session1.hasNodes()); // check if added child node for node 2 by session 2 has become visible in session 1 assertTrue("Node modified by a different session has not been updated after Node.refresh(true)", testNode2Session1.hasNodes()); }

49304 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/49304/5ccda17da27a5f4b68cd1402b8d936c724c7aa46/NodeTest.java/buggy/src/test/org/apache/jackrabbit/test/api/NodeTest.java

SocketAppender(String host, int port) { this.port = port; this.address = getAddressByName(host); this.remoteHost = host; connect(address, port);

public SocketAppender() {

SocketAppender(String host, int port) { this.port = port; this.address = getAddressByName(host); this.remoteHost = host; connect(address, port); }

45952 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/45952/1134214910cde23075dafa03ee90fde97a5223c7/SocketAppender.java/buggy/src/java/org/apache/log4j/net/SocketAppender.java

catch (InvocationTargetException e) { if (e.getTargetException() instanceof CoreException) throw (CoreException) e.getTargetException(); if (e.getTargetException() instanceof RuntimeException) throw (RuntimeException) e.getTargetException(); if (e.getTargetException() instanceof Error) throw (Error) e.getTargetException(); e.getTargetException().printStackTrace(); } }

protected void execute(IProgressMonitor monitor) throws CoreException, InterruptedException { try { content.run(monitor); } catch (InvocationTargetException e) { if (e.getTargetException() instanceof CoreException) throw (CoreException) e.getTargetException(); if (e.getTargetException() instanceof RuntimeException) throw (RuntimeException) e.getTargetException(); if (e.getTargetException() instanceof Error) throw (Error) e.getTargetException(); e.getTargetException().printStackTrace(); }}

55805 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/55805/7b50a348ec9564b04f52eb73450ed9b2ffddff74/WorkspaceModifyDelegatingOperation.java/clean/bundles/org.eclipse.ui.ide/extensions/org/eclipse/ui/actions/WorkspaceModifyDelegatingOperation.java

this.clipboard = clipboard; }

this.clipboard = clipboard; }

void setClipboard(Clipboard clipboard) { this.clipboard = clipboard; }

55805 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/55805/cd30df30dfb88f9bda2fa203f31e3dd26ff697b7/ActionCopyMarker.java/buggy/bundles/org.eclipse.ui.ide/src/org/eclipse/ui/views/markers/internal/ActionCopyMarker.java

AspectJPreferences.setAJDTPrefConfigDone(true);

public void testWithOutJarSwitch3() throws Exception { AspectJPreferences.setAJDTPrefConfigDone(true); IProject projectY = Utils.getPredefinedProject("project.java.Y", true); projectY.build(IncrementalProjectBuilder.FULL_BUILD, null); ProjectDependenciesUtils.waitForJobsToComplete(projectY); IProject projectX = Utils.getPredefinedProject("project.java.X", true); projectX.build(IncrementalProjectBuilder.FULL_BUILD, null); ProjectDependenciesUtils.waitForJobsToComplete(projectX); // sanity check: at this point there should be no error markers, both // projects should build as they're both java projects, project X should // should have a project dependency on project Y assertFalse("project Y should build with no errors", ProjectDependenciesUtils.projectIsMarkedWithError(projectY,null)); assertFalse("project X should build with no errors", ProjectDependenciesUtils.projectIsMarkedWithError(projectX,null)); assertTrue("project X should have a project dependency on project Y", ProjectDependenciesUtils.projectHasProjectDependency(projectX, projectY)); assertFalse("project Y should not be an AJ project", projectY.hasNature(AspectJUIPlugin.ID_NATURE)); assertFalse("project X should not be an AJ project", projectX.hasNature(AspectJUIPlugin.ID_NATURE)); // convert project Y to be an AJ project and check setup is correct AJDTUtils.addAspectJNature(projectY); ProjectDependenciesUtils.waitForJobsToComplete(projectY); assertFalse("project Y should build with no errors", ProjectDependenciesUtils.projectIsMarkedWithError(projectY,null)); assertFalse("project X should build with no errors", ProjectDependenciesUtils.projectIsMarkedWithError(projectX,null)); assertTrue("project X should still have a project dependency on project Y", ProjectDependenciesUtils.projectHasProjectDependency(projectX, projectY)); assertFalse("project X should NOT have a class folder dependency on project Y", ProjectDependenciesUtils.projectHasClassFolderDependency(projectX,projectY)); // set project Y to send output to jar file mainWork.jar // setup the outjar String outJar = ProjectDependenciesUtils.setupOutJar("firstJar.jar",projectY); projectY.setPersistentProperty(BuildOptionsAdapter.OUTPUTJAR, outJar); ProjectDependenciesUtils.waitForJobsToComplete(projectY); assertFalse("Output jar should NOT exist! (path=" + outJar + ")",new File(outJar).exists()); // build the project so it picks up the outjar and sends // output there BlockingProgressMonitor monitor = new BlockingProgressMonitor(); monitor.reset(); projectY.build(IncrementalProjectBuilder.FULL_BUILD,"org.eclipse.ajdt.ui.ajbuilder", null, monitor); monitor.waitForCompletion(); ProjectDependenciesUtils.waitForJobsToComplete(projectY); assertTrue("Output jar should exist! (path=" + outJar + ")",new File(outJar).exists()); assertFalse("project Y should build with no errors", ProjectDependenciesUtils.projectIsMarkedWithError(projectY,null)); assertFalse("project X should build with no errors", ProjectDependenciesUtils.projectIsMarkedWithError(projectX,null)); assertTrue("project X should have project Y's outjar on it's classpath", ProjectDependenciesUtils.projectHasOutJarOnClasspath(projectX,projectY, outJar)); assertTrue("project X should have a project dependency on project Y", ProjectDependenciesUtils.projectHasProjectDependency(projectX, projectY)); assertFalse("project X should not have a class folder dependency on project Y", ProjectDependenciesUtils.projectHasClassFolderDependency(projectX,projectY)); // set project Y to send output to jar file newJar.jar // setup the outjar String outJar2 = ProjectDependenciesUtils.setupOutJar("newJar.jar",projectY); projectY.setPersistentProperty(BuildOptionsAdapter.OUTPUTJAR, outJar2); ProjectDependenciesUtils.waitForJobsToComplete(projectY); assertFalse("Output jar should NOT exist! (path=" + outJar2 + ")",new File(outJar2).exists()); // build the project so it picks up the outjar and sends // output there monitor.reset(); projectY.build(IncrementalProjectBuilder.FULL_BUILD,"org.eclipse.ajdt.ui.ajbuilder", null, monitor); monitor.waitForCompletion(); ProjectDependenciesUtils.waitForJobsToComplete(projectY); assertTrue("Output jar should exist! (path=" + outJar2 + ")",new File(outJar2).exists()); assertFalse("project Y should build with no errors", ProjectDependenciesUtils.projectIsMarkedWithError(projectY,null)); assertFalse("project X should build with no errors", ProjectDependenciesUtils.projectIsMarkedWithError(projectX,null)); assertTrue("project X should have project Y's NEW outjar on it's classpath", ProjectDependenciesUtils.projectHasOutJarOnClasspath(projectX,projectY, outJar2)); assertFalse("project X should NOT have project Y's old outjar on it's classpath", ProjectDependenciesUtils.projectHasOutJarOnClasspath(projectX,projectY, outJar)); assertTrue("project X should have a project dependency on project Y", ProjectDependenciesUtils.projectHasProjectDependency(projectX, projectY)); assertFalse("project X should not have a class folder dependency on project Y", ProjectDependenciesUtils.projectHasClassFolderDependency(projectX,projectY)); StringBuffer sb = new StringBuffer(outJar); IPath path = new Path(sb.substring(sb.lastIndexOf(projectY.getName()))); IResource jarFile = projectY.getWorkspace().getRoot().findMember(path.makeAbsolute()); monitor.reset(); jarFile.delete(true,monitor); monitor.waitForCompletion(); ProjectDependenciesUtils.waitForJobsToComplete(projectY); assertFalse("Output jar should NOT exist! (path=" + outJar + ")",new File(outJar).exists()); projectY.setPersistentProperty(BuildOptionsAdapter.OUTPUTJAR, ""); ProjectDependenciesUtils.waitForJobsToComplete(projectY); monitor.reset(); projectY.build(IncrementalProjectBuilder.FULL_BUILD,"org.eclipse.ajdt.ui.ajbuilder", null, monitor); monitor.waitForCompletion(); ProjectDependenciesUtils.waitForJobsToComplete(projectY); StringBuffer sb2 = new StringBuffer(outJar2); IPath path2 = new Path(sb2.substring(sb2.lastIndexOf(projectY.getName()))); IResource jarFile2 = projectY.getWorkspace().getRoot().findMember(path2.makeAbsolute()); monitor.reset(); jarFile2.delete(true,monitor); monitor.waitForCompletion(); ProjectDependenciesUtils.waitForJobsToComplete(projectY); assertFalse("Second Output jar should NOT exist! (path=" + outJar2 + ")" ,new File(outJar2).exists()); projectX.build(IncrementalProjectBuilder.FULL_BUILD, null); ProjectDependenciesUtils.waitForJobsToComplete(projectX); assertFalse("project X should build with no errors", ProjectDependenciesUtils.projectIsMarkedWithError(projectX,null)); assertFalse("project X should not have outjar on classpath", ProjectDependenciesUtils.projectHasOutJarOnClasspath(projectX,projectY,outJar2)); // reset projects to their original state: AJDTUtils.removeAspectJNature(projectY); ProjectDependenciesUtils.waitForJobsToComplete(projectY); projectY.build(IncrementalProjectBuilder.FULL_BUILD, null); ProjectDependenciesUtils.waitForJobsToComplete(projectY); assertFalse("project Y should build with no errors", ProjectDependenciesUtils.projectIsMarkedWithError(projectY,null)); assertFalse("project X should build with no errors", ProjectDependenciesUtils.projectIsMarkedWithError(projectX,null)); assertTrue("project X should have a project dependency on project Y", ProjectDependenciesUtils.projectHasProjectDependency(projectX, projectY)); assertFalse("project Y should not be an AJ project", projectY.hasNature(AspectJUIPlugin.ID_NATURE)); assertFalse("project X should not be an AJ project", projectX.hasNature(AspectJUIPlugin.ID_NATURE)); // close all the projects so that they don't hang around and hold // up the build for other tests monitor.reset(); projectX.close(monitor); monitor.waitForCompletion(); monitor.reset(); projectY.close(monitor); monitor.waitForCompletion(); AspectJPreferences.setAJDTPrefConfigDone(false); }

13558 /local/tlutelli/issta_data/temp/all_java1context/java/2006_temp/2006/13558/1de3a7ddee14a9331ea7bdbd6a2e8b21cdc4019d/ProjectDependenciesWithJarFilesTest.java/clean/org.eclipse.ajdt.ui.tests/src/org/eclipse/ajdt/internal/builder/ProjectDependenciesWithJarFilesTest.java

String keyPass = props.getProperty(prop, "");

String keyPass = Preferences.getPreference(prop, "");

private void configureHTTPClient(Properties props) { HTTPClientFactory factory = HTTPClientFactory.getInstance(); String prop = null; String value; int colon; try { // FIXME for some reason, we get "" instead of null for value, // and do not use our default value??? prop = "WebScarab.httpProxy"; value = props.getProperty(prop, ":80"); colon = value.indexOf(":"); factory.setHttpProxy(value.substring(0,colon), Integer.parseInt(value.substring(colon+1))); prop = "WebScarab.httpsProxy"; value = props.getProperty(prop, ":80"); colon = value.indexOf(":"); factory.setHttpsProxy(value.substring(0,colon), Integer.parseInt(value.substring(colon+1))); prop = "WebScarab.noProxy"; value = props.getProperty(prop, ""); factory.setNoProxy(value.split(" *, *")); prop = "WebScarab.clientCertificateFile"; String file = props.getProperty(prop, ""); prop = "WebScarab.keyStorePassword"; String keystorePass = props.getProperty(prop, ""); prop = "WebScarab.keyPassword"; String keyPass = props.getProperty(prop, ""); factory.setClientCertificateFile(file, keystorePass, keyPass); } catch (NumberFormatException nfe) { _logger.warning("Error parsing property " + prop + ": " + nfe); } catch (Exception e) { _logger.warning("Error configuring the HTTPClient property " + prop + ": " + e); } }

31053 /local/tlutelli/issta_data/temp/all_java3context/java/2006_temp/2006/31053/a5906aa3ab3214cfaa5b20624c4421944b454f3c/Framework.java/clean/src/org/owasp/webscarab/plugin/Framework.java

rewrite.markAsReplaced(ifStatement.getElseStatement(), newElseBlock);

rewrite.markAsReplaced(ifStatement.getElseStatement(), newElseBlock, null);

public void testIfStatementReplaceElse3() throws Exception { IPackageFragment pack1= fSourceFolder.createPackageFragment("test1", false, null); StringBuffer buf= new StringBuffer(); buf.append("package test1;\n"); buf.append("public class E {\n"); buf.append(" public void foo() {\n"); buf.append(" if (i == 0)\n"); buf.append(" System.beep();\n"); buf.append(" else\n"); buf.append(" hoo(11);\n"); buf.append(" if (i == 0) {\n"); buf.append(" System.beep();\n"); buf.append(" } else\n"); buf.append(" hoo(11);\n"); buf.append(" if (i == 0)\n"); buf.append(" System.beep();\n"); buf.append(" else {\n"); buf.append(" hoo(11);\n"); buf.append(" }\n"); buf.append(" if (i == 0) {\n"); buf.append(" System.beep();\n"); buf.append(" } else {\n"); buf.append(" hoo(11);\n"); buf.append(" }\n"); buf.append(" }\n"); buf.append("}\n"); ICompilationUnit cu= pack1.createCompilationUnit("E.java", buf.toString(), false, null); CompilationUnit astRoot= createAST(cu); NewASTRewrite rewrite= new NewASTRewrite(astRoot.getAST()); AST ast= astRoot.getAST(); assertTrue("Parse errors", (astRoot.getFlags() & ASTNode.MALFORMED) == 0); TypeDeclaration type= findTypeDeclaration(astRoot, "E"); MethodDeclaration methodDecl= findMethodDeclaration(type, "foo"); Block block= methodDecl.getBody(); List statements= block.statements(); assertTrue("Number of statements not 4", statements.size() == 4); { // replace then statement by block , replace else with if statement (no block) IfStatement ifStatement= (IfStatement) statements.get(0); ASTNode statement= ifStatement.getThenStatement(); Block newBody= ast.newBlock(); ASTNode newStatement= rewrite.createMovePlaceholder(statement); newBody.statements().add(newStatement); rewrite.markAsReplaced(statement, newBody); IfStatement newElseBlock= ast.newIfStatement(); newElseBlock.setExpression(ast.newBooleanLiteral(true)); Statement newBody2= (Statement) rewrite.createMovePlaceholder(ifStatement.getElseStatement()); newElseBlock.setThenStatement(newBody2); rewrite.markAsReplaced(ifStatement.getElseStatement(), newElseBlock); } { // replace then statement by block, replace else with if statement (no block) IfStatement ifStatement= (IfStatement) statements.get(1); Block body= (Block) ifStatement.getThenStatement(); ASTNode statement= (ASTNode) body.statements().get(0); ASTNode newBody= rewrite.createMovePlaceholder(statement); rewrite.markAsReplaced(body, newBody); IfStatement newElseBlock= ast.newIfStatement(); newElseBlock.setExpression(ast.newBooleanLiteral(true)); Statement newBody2= (Statement) rewrite.createMovePlaceholder(ifStatement.getElseStatement()); newElseBlock.setThenStatement(newBody2); rewrite.markAsReplaced(ifStatement.getElseStatement(), newElseBlock); } { // replace then block by statement, replace else with if statement (block) IfStatement ifStatement= (IfStatement) statements.get(2); ASTNode statement= ifStatement.getThenStatement(); Block newBody= ast.newBlock(); ASTNode newStatement= rewrite.createMovePlaceholder(statement); newBody.statements().add(newStatement); rewrite.markAsReplaced(statement, newBody); IfStatement newElseBlock= ast.newIfStatement(); newElseBlock.setExpression(ast.newBooleanLiteral(true)); Statement newBody2= (Statement) rewrite.createMovePlaceholder(ifStatement.getElseStatement()); newElseBlock.setThenStatement(newBody2); rewrite.markAsReplaced(ifStatement.getElseStatement(), newElseBlock); } { // replace then block by statement, replace else with if statement (block) IfStatement ifStatement= (IfStatement) statements.get(3); Block body= (Block) ifStatement.getThenStatement(); ASTNode statement= (ASTNode) body.statements().get(0); ASTNode newBody= rewrite.createMovePlaceholder(statement); rewrite.markAsReplaced(body, newBody); IfStatement newElseBlock= ast.newIfStatement(); newElseBlock.setExpression(ast.newBooleanLiteral(true)); Statement newBody2= (Statement) rewrite.createMovePlaceholder(ifStatement.getElseStatement()); newElseBlock.setThenStatement(newBody2); rewrite.markAsReplaced(ifStatement.getElseStatement(), newElseBlock); } String preview= evaluateRewrite(cu, rewrite); buf= new StringBuffer(); buf.append("package test1;\n"); buf.append("public class E {\n"); buf.append(" public void foo() {\n"); buf.append(" if (i == 0) {\n"); buf.append(" System.beep();\n"); buf.append(" } else if (true)\n"); buf.append(" hoo(11);\n"); buf.append(" if (i == 0)\n"); buf.append(" System.beep();\n"); buf.append(" else if (true)\n"); buf.append(" hoo(11);\n"); buf.append(" if (i == 0) {\n"); buf.append(" System.beep();\n"); buf.append(" } else if (true) {\n"); buf.append(" hoo(11);\n"); buf.append(" }\n"); buf.append(" if (i == 0)\n"); buf.append(" System.beep();\n"); buf.append(" else if (true) {\n"); buf.append(" hoo(11);\n"); buf.append(" }\n"); buf.append(" }\n"); buf.append("}\n"); assertEqualString(preview, buf.toString()); }

9698 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/9698/57e3aa581b2bf9d9c15ee310aa69c71cec638595/ASTRewritingStatementsTest.java/clean/org.eclipse.jdt.ui.tests/ui/org/eclipse/jdt/ui/tests/astrewrite/ASTRewritingStatementsTest.java

if (directoryNames == null) directoryNames = new String[0];

if (directoryNames == null) { directoryNames = new String[0]; }

protected void internalSaveWidgetValues() { // update directory names history IDialogSettings settings = getDialogSettings(); if (settings != null) { String[] directoryNames = settings .getArray(STORE_DESTINATION_NAMES_ID); if (directoryNames == null) directoryNames = new String[0]; directoryNames = addToHistory(directoryNames, getDestinationValue()); settings.put(STORE_DESTINATION_NAMES_ID, directoryNames); settings.put(STORE_CREATE_STRUCTURE_ID, createDirectoryStructureButton.getSelection()); settings.put(STORE_COMPRESS_CONTENTS_ID, compressContentsCheckbox .getSelection()); } }

55805 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/55805/e38d295ea613cf9f08aadb93a84a33d2e91abc5f/WizardArchiveFileResourceExportPage1.java/buggy/bundles/org.eclipse.ui.ide/src/org/eclipse/ui/internal/wizards/datatransfer/WizardArchiveFileResourceExportPage1.java

if (TDEBUG) trace(IN, "blockDecrypt("+in+", "+inOffset+", "+sessionKey+")");

if (TDEBUG) trace(IN, "blockDecrypt("+in+", "+inOffset+", "+sessionKey+ ')');

blockDecrypt (byte[] in, byte[] result, int inOffset, Object sessionKey) {if (TDEBUG) trace(IN, "blockDecrypt("+in+", "+inOffset+", "+sessionKey+")"); Object[] sk = (Object[]) sessionKey; // extract S-box and session key int[] sBox = (int[]) sk[0]; int[] sKey = (int[]) sk[1];if (TDEBUG && (debuglevel > 6)) System.out.println("CT="+toString(in, inOffset, BLOCK_SIZE)); int x2 = (in[inOffset++] & 0xFF) | (in[inOffset++] & 0xFF) << 8 | (in[inOffset++] & 0xFF) << 16 | (in[inOffset++] & 0xFF) << 24; int x3 = (in[inOffset++] & 0xFF) | (in[inOffset++] & 0xFF) << 8 | (in[inOffset++] & 0xFF) << 16 | (in[inOffset++] & 0xFF) << 24; int x0 = (in[inOffset++] & 0xFF) | (in[inOffset++] & 0xFF) << 8 | (in[inOffset++] & 0xFF) << 16 | (in[inOffset++] & 0xFF) << 24; int x1 = (in[inOffset++] & 0xFF) | (in[inOffset++] & 0xFF) << 8 | (in[inOffset++] & 0xFF) << 16 | (in[inOffset++] & 0xFF) << 24; x2 ^= sKey[OUTPUT_WHITEN ]; x3 ^= sKey[OUTPUT_WHITEN + 1]; x0 ^= sKey[OUTPUT_WHITEN + 2]; x1 ^= sKey[OUTPUT_WHITEN + 3];if (TDEBUG && (debuglevel > 6)) System.out.println("CTw="+intToString(x2)+intToString(x3)+intToString(x0)+intToString(x1)); int k = ROUND_SUBKEYS + 2*ROUNDS - 1; int t0, t1; for (int R = 0; R < ROUNDS; R += 2) { t0 = Fe32_0( sBox, x2 ); t1 = Fe32_3( sBox, x3 ); x1 ^= t0 + 2*t1 + sKey[k--]; x1 = x1 >>> 1 | x1 << 31; x0 = x0 << 1 | x0 >>> 31; x0 ^= t0 + t1 + sKey[k--];if (TDEBUG && (debuglevel > 6)) System.out.println("PT"+(ROUNDS-R)+"="+intToString(x2)+intToString(x3)+intToString(x0)+intToString(x1)); t0 = Fe32_0( sBox, x0 ); t1 = Fe32_3( sBox, x1 ); x3 ^= t0 + 2*t1 + sKey[k--]; x3 = x3 >>> 1 | x3 << 31; x2 = x2 << 1 | x2 >>> 31; x2 ^= t0 + t1 + sKey[k--];if (TDEBUG && (debuglevel > 6)) System.out.println("PT"+(ROUNDS-R-1)+"="+intToString(x2)+intToString(x3)+intToString(x0)+intToString(x1)); } x0 ^= sKey[INPUT_WHITEN ]; x1 ^= sKey[INPUT_WHITEN + 1]; x2 ^= sKey[INPUT_WHITEN + 2]; x3 ^= sKey[INPUT_WHITEN + 3];if (TDEBUG && (debuglevel > 6)) System.out.println("PTw="+intToString(x2)+intToString(x3)+intToString(x0)+intToString(x1)); result[0] = (byte) x0; result[1] = (byte)(x0 >>> 8); result[2] = (byte)(x0 >>> 16); result[3] = (byte)(x0 >>> 24); result[4] = (byte) x1; result[5] = (byte)(x1 >>> 8); result[6] = (byte)(x1 >>> 16); result[7] = (byte)(x1 >>> 24); result[8] = (byte) x2; result[9] = (byte)(x2 >>> 8); result[10] = (byte)(x2 >>> 16); result[11] = (byte)(x2 >>> 24); result[12] = (byte) x3; result[13] = (byte)(x3 >>> 8); result[14] = (byte)(x3 >>> 16); result[15] = (byte)(x3 >>> 24);if (TDEBUG && (debuglevel > 6)) {System.out.println("PT="+toString(result));System.out.println();}if (TDEBUG) trace(OUT, "blockDecrypt()"); }

45341 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/45341/62fd59041864b4ed1f43adc676de6bfb5ea977f3/Twofish_Algorithm.java/clean/src/freenet/crypt/ciphers/Twofish_Algorithm.java

setOnclick((String) evalAttr("onclick", getOnclick(),

setOnclick((String) evalAttr("onclick", getOnclickExpr(),

private void evaluateExpressions() throws JspException { try { setAlt((String) evalAttr("alt", getAlt(), String.class)); } catch (NullAttributeException ex) { setAlt(null); } try { setAltKey((String) evalAttr("altKey", getAltKey(), String.class)); } catch (NullAttributeException ex) { setAltKey(null); } try { setDisabled(((Boolean) evalAttr("disabled", getDisabledExpr(), Boolean.class)). booleanValue()); } catch (NullAttributeException ex) { setDisabled(false); } try { setIndexed(((Boolean) evalAttr("indexed", getIndexedExpr(), Boolean.class)). booleanValue()); } catch (NullAttributeException ex) { setIndexed(false); } try { setMultiple((String) evalAttr("multiple", getMultiple(), String.class)); } catch (NullAttributeException ex) { setMultiple(null); } try { setName((String) evalAttr("name", getName(), String.class)); } catch (NullAttributeException ex) { setName(null); } try { setOnblur((String) evalAttr("onblur", getOnblur(), String.class)); } catch (NullAttributeException ex) { setOnblur(null); } try { setOnchange((String) evalAttr("onchange", getOnchange(), String.class)); } catch (NullAttributeException ex) { setOnchange(null); } try { setOnclick((String) evalAttr("onclick", getOnclick(), String.class)); } catch (NullAttributeException ex) { setOnclick(null); } try { setOndblclick((String) evalAttr("ondblclick", getOndblclick(), String.class)); } catch (NullAttributeException ex) { setOndblclick(null); } try { setOnfocus((String) evalAttr("onfocus", getOnfocus(), String.class)); } catch (NullAttributeException ex) { setOnfocus(null); } try { setOnkeydown((String) evalAttr("onkeydown", getOnkeydown(), String.class)); } catch (NullAttributeException ex) { setOnkeydown(null); } try { setOnkeypress((String) evalAttr("onkeypress", getOnkeypress(), String.class)); } catch (NullAttributeException ex) { setOnkeypress(null); } try { setOnkeyup((String) evalAttr("onkeyup", getOnkeyup(), String.class)); } catch (NullAttributeException ex) { setOnkeyup(null); } try { setOnmousedown((String) evalAttr("onmousedown", getOnmousedown(), String.class)); } catch (NullAttributeException ex) { setOnmousedown(null); } try { setOnmousemove((String) evalAttr("onmousemove", getOnmousemove(), String.class)); } catch (NullAttributeException ex) { setOnmousemove(null); } try { setOnmouseout((String) evalAttr("onmouseout", getOnmouseout(), String.class)); } catch (NullAttributeException ex) { setOnmouseout(null); } try { setOnmouseover((String) evalAttr("onmouseover", getOnmouseover(), String.class)); } catch (NullAttributeException ex) { setOnmouseover(null); } try { setOnmouseup((String) evalAttr("onmouseup", getOnmouseup(), String.class)); } catch (NullAttributeException ex) { setOnmouseup(null); } try { setProperty((String) evalAttr("property", getProperty(), String.class)); } catch (NullAttributeException ex) { setProperty(null); } try { setSize((String) evalAttr("size", getSize(), String.class)); } catch (NullAttributeException ex) { setSize(null); } try { setStyle((String) evalAttr("style", getStyle(), String.class)); } catch (NullAttributeException ex) { setStyle(null); } try { setStyleClass((String) evalAttr("styleClass", getStyleClass(), String.class)); } catch (NullAttributeException ex) { setStyleClass(null); } try { setStyleId((String) evalAttr("styleId", getStyleId(), String.class)); } catch (NullAttributeException ex) { setStyleId(null); } try { setTabindex((String) evalAttr("tabindex", getTabindex(), String.class)); } catch (NullAttributeException ex) { setTabindex(null); } try { setTitle((String) evalAttr("title", getTitle(), String.class)); } catch (NullAttributeException ex) { setTitle(null); } try { setTitleKey((String) evalAttr("titleKey", getTitleKey(), String.class)); } catch (NullAttributeException ex) { setTitleKey(null); } try { setValue((String) evalAttr("value", getValue(), String.class)); } catch (NullAttributeException ex) { setValue(null); } }

48068 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/48068/db064e19656421b94aaf753550935d95f44bd5f9/ELSelectTag.java/buggy/contrib/struts-el/src/share/org/apache/strutsel/taglib/html/ELSelectTag.java

public ASTNode processRange(ASTNode element, int startOffset, int endOffset) { FileType fileType = myHelper.getFileType(); if (useNewFormatter(fileType)) { PseudoTextBuilder pseudoTextBuilder = ((LanguageFileType)fileType).getLanguage().getFormatter(); if (pseudoTextBuilder == null) { return element; } else { final long start = System.currentTimeMillis(); try { PseudoText pseudoText = pseudoTextBuilder.build(myHelper.getProject(), mySettings, SourceTreeToPsiMap.treeElementToPsi(element)); GeneralCodeFormatter.createSimpleInstance(pseudoText, mySettings, fileType, startOffset, endOffset).format(); } catch (Exception e) { LOG.error(e); } //System.out.println("Time to reformat: " + (System.currentTimeMillis() - start)); formatComments(element, startOffset, endOffset); return element; } } final TextRange range = element.getTextRange(); final int elementStartOffset = range.getStartOffset(); return processRange(element, new int[]{startOffset - elementStartOffset, endOffset - elementStartOffset}); }

12814 /local/tlutelli/issta_data/temp/all_java1context/java/2006_temp/2006/12814/684e19353819557fb6e0c3dcd127af4d3a5851d8/CodeFormatterFacade.java/buggy/source/com/intellij/psi/impl/source/codeStyle/CodeFormatterFacade.java

Utilities.invokeAndWait(new SRunnable() {

if (! projDocs.isEmpty()) Utilities.invokeAndWait(new SRunnable() {

private File[] _loadProject(ProjectFileIR ir, File projectFile) throws IOException { final DocFile[] srcFiles = ir.getSourceFiles(); final DocFile[] auxFiles = ir.getAuxiliaryFiles(); final File buildDir = ir.getBuildDirectory(); final File workDir = ir.getWorkingDirectory(); final File mainClass = ir.getMainClass(); final File[] projectClassPaths = ir.getClassPaths(); final File createJarFile = ir.getCreateJarFile(); int createJarFlags = ir.getCreateJarFlags(); final String projfilepath = projectFile.getCanonicalPath(); final List<OpenDefinitionsDocument> oldProjDocs = getProjectDocuments(); final FileGroupingState oldState = _state; // Utilities.showDebug("openProject called with file " + projectFile); // Sets up the filters that cause documents to load in differentnsections of the tree. The names of these // sections are set from the methods such as getSourceBinTitle(). Changing this changes what is considered // source, aux, and external. List<Pair<String, INavigatorItemFilter<OpenDefinitionsDocument>>> l = new LinkedList<Pair<String, INavigatorItemFilter<OpenDefinitionsDocument>>>(); l.add(new Pair<String, INavigatorItemFilter<OpenDefinitionsDocument>>(getSourceBinTitle(), new INavigatorItemFilter<OpenDefinitionsDocument>() { public boolean accept(OpenDefinitionsDocument n) { return n.isInProjectPath(); } })); l.add(new Pair<String, INavigatorItemFilter<OpenDefinitionsDocument>>(getAuxiliaryBinTitle(), new INavigatorItemFilter<OpenDefinitionsDocument>() { public boolean accept(OpenDefinitionsDocument n) { return n.isAuxiliaryFile(); } })); l.add(new Pair<String, INavigatorItemFilter<OpenDefinitionsDocument>>(getExternalBinTitle(), new INavigatorItemFilter<OpenDefinitionsDocument>() { public boolean accept(OpenDefinitionsDocument d) { return !(d.inProject() || d.isAuxiliaryFile()) || d.isUntitled(); } })); IDocumentNavigator<OpenDefinitionsDocument> newNav = new AWTContainerNavigatorFactory<OpenDefinitionsDocument>().makeTreeNavigator(projfilepath, getDocumentNavigator(), l); setDocumentNavigator(newNav); synchronized(_auxiliaryFiles) { _auxiliaryFiles.clear(); for (File file: auxFiles) { _auxiliaryFiles.add(file); } } ClassPathVector extraClassPaths = new ClassPathVector(); for (File f : projectClassPaths) { extraClassPaths.add(f); } setFileGroupingState(makeProjectFileGroupingState(mainClass, buildDir, workDir, projectFile, srcFiles, extraClassPaths, createJarFile, createJarFlags)); resetInteractions(getWorkingDirectory()); // Shut down debugger and reset interactions pane in new working directory ArrayList<File> projFiles = new ArrayList<File>(); File active = null; for (DocFile f: srcFiles) { File file = f; if (f.lastModified() > f.getSavedModDate()) file = new File(f.getPath()); if (f.isActive() && active == null) active = file; else projFiles.add(file); } for (DocFile f: auxFiles) { File file = f; if (f.lastModified() > f.getSavedModDate()) file = new File(f.getPath()); if (f.isActive() && active == null) active = file; else projFiles.add(file); } // Insert active file as last file on list. if (active != null) projFiles.add(active); // Utilities.showDebug("Project files are: " + projFiles); final List<OpenDefinitionsDocument> projDocs = getProjectDocuments(); // opened documents in the project source tree // Keep all nonproject files open other than a new file (untitled). External files in the previous // project may become project files in the new project and must be closed while external files in the // previous project that are still external to the new project should be kept open (except for a new file). Utilities.invokeAndWait(new SRunnable() { public void run() { for (OpenDefinitionsDocument d: projDocs) { if (oldState.inProject(d.file())) closeFile(d); else { try { final String path = fixPathForNavigator(d.getFile().getCanonicalPath()); _documentNavigator.refreshDocument(d, path); // this operation must run in event thread } catch(IOException e) { /* Do nothing; findbugs signals a bug unless this catch clause spans more than two lines */ } } } } });// Utilities.showDebug("Preparing to refresh navigator GUI"); // call on the GUI to finish up by opening the files and making necessary gui component changes final File[] filesToOpen = projFiles.toArray(new File[projFiles.size()]); _notifier.projectOpened(projectFile, new FileOpenSelector() { public File[] getFiles() { return filesToOpen; } }); if (_documentNavigator instanceof JTreeSortNavigator) { ((JTreeSortNavigator<?>)_documentNavigator).collapsePaths(ir.getCollapsedPaths()); } return srcFiles; // Unnecessarily returns src files in keeping with the previous interface. }

11192 /local/tlutelli/issta_data/temp/all_java1context/java/2006_temp/2006/11192/4e9024f79382344df7a15499ea8826062a420a5f/AbstractGlobalModel.java/clean/drjava/src/edu/rice/cs/drjava/model/AbstractGlobalModel.java

case Token.REF_CALL :

private static void dumpICode(InterpreterData idata) { if (!Token.printICode) { return; } int iCodeLength = idata.itsICodeTop; byte iCode[] = idata.itsICode; String[] strings = idata.itsStringTable; PrintStream out = System.out; out.println("ICode dump, for " + idata.itsName + ", length = " + iCodeLength); out.println("MaxStack = " + idata.itsMaxStack); int indexReg = 0; for (int pc = 0; pc < iCodeLength; ) { out.flush(); out.print(" [" + pc + "] "); int token = iCode[pc]; int icodeLength = bytecodeSpan(token); String tname = bytecodeName(token); int old_pc = pc; ++pc; switch (token) { default: if (icodeLength != 1) Kit.codeBug(); out.println(tname); break; case Icode_GOSUB : case Token.GOTO : case Token.IFEQ : case Token.IFNE : case Icode_IFEQ_POP : case Icode_LEAVEDQ : { int newPC = pc + getShort(iCode, pc) - 1; out.println(tname + " " + newPC); pc += 2; break; } case Icode_VAR_INC_DEC : case Icode_NAME_INC_DEC : case Icode_PROP_INC_DEC : case Icode_ELEM_INC_DEC : case Icode_REF_INC_DEC: { int incrDecrType = iCode[pc]; out.println(tname + " " + incrDecrType); ++pc; break; } case Icode_CALLSPECIAL : { int callType = iCode[pc] & 0xFF; boolean isNew = (iCode[pc + 1] != 0); int line = getShort(iCode, pc+2); out.println(tname+" "+callType+" "+isNew+" "+indexReg+" "+line); pc += 4; break; } case Token.REGEXP : out.println(tname+" "+idata.itsRegExpLiterals[indexReg]); break; case Token.OBJECTLIT : case Icode_SPARE_ARRAYLIT : out.println(tname+" "+idata.literalIds[indexReg]); break; case Icode_CLOSURE_EXPR : case Icode_CLOSURE_STMT : out.println(tname+" "+idata.itsNestedFunctions[indexReg]); break; case Token.CALL : case Token.NEW : case Token.REF_CALL : out.println(tname+' '+indexReg); pc += 2; break; case Token.THROW : { int line = getShort(iCode, pc); out.println(tname + " : " + line); pc += 2; break; } case Icode_SHORTNUMBER : { int value = getShort(iCode, pc); out.println(tname + " " + value); pc += 2; break; } case Icode_INTNUMBER : { int value = getInt(iCode, pc); out.println(tname + " " + value); pc += 4; break; } case Token.NUMBER : { double value = idata.itsDoubleTable[indexReg]; out.println(tname + " " + value); pc += 2; break; } case Icode_LINE : { int line = getShort(iCode, pc); out.println(tname + " : " + line); pc += 2; break; } case Icode_REG_STR1: { String str = strings[0xFF & iCode[pc]]; out.println(tname + " \"" + str + '"'); ++pc; break; } case Icode_REG_STR2: { String str = strings[getIndex(iCode, pc)]; out.println(tname + " \"" + str + '"'); pc += 2; break; } case Icode_REG_STR4: { String str = strings[getInt(iCode, pc)]; out.println(tname + " \"" + str + '"'); pc += 4; break; } case Icode_REG_IND1: { indexReg = 0xFF & iCode[pc]; out.println(tname+" "+indexReg); ++pc; break; } case Icode_REG_IND2: { indexReg = getIndex(iCode, pc); out.println(tname+" "+indexReg); pc += 2; break; } case Icode_REG_IND4: { indexReg = getInt(iCode, pc); out.println(tname+" "+indexReg); pc += 4; break; } case Icode_GETVAR1: case Icode_SETVAR1: indexReg = iCode[pc]; out.println(tname+" "+indexReg); ++pc; break; } if (old_pc + icodeLength != pc) Kit.codeBug(); } int[] table = idata.itsExceptionTable; if (table != null) { out.println("Exception handlers: " +table.length / EXCEPTION_SLOT_SIZE); for (int i = 0; i != table.length; i += EXCEPTION_SLOT_SIZE) { int tryStart = table[i + EXCEPTION_TRY_START_SLOT]; int tryEnd = table[i + EXCEPTION_TRY_END_SLOT]; int catchStart = table[i + EXCEPTION_CATCH_SLOT]; int finallyStart = table[i + EXCEPTION_FINALLY_SLOT]; int withDepth = table[i + EXCEPTION_WITH_DEPTH_SLOT]; int exceptionLocal = table[i + EXCEPTION_LOCAL_SLOT]; out.println(" tryStart="+tryStart+" tryEnd="+tryEnd +" catchStart="+catchStart +" finallyStart="+finallyStart +" withDepth="+withDepth +" exceptionLocal="+exceptionLocal); } } out.flush(); }

19042 /local/tlutelli/issta_data/temp/all_java1context/java/2006_temp/2006/19042/455f6bfb19128ad0a276b4b3c1f15ede63a2041d/Interpreter.java/buggy/src/org/mozilla/javascript/Interpreter.java

while (termDocs.next()) { retArray[termDocs.doc()] = termval;

while (termDocs.next ()) { retArray[termDocs.doc ()] = termval;

static ScoreDocLookupComparator comparator (final IndexReader reader, final TermEnum enumerator, final String field) throws IOException { return new ScoreDocLookupComparator () { protected final float[] fieldOrder = generateSortIndex(); protected final float[] generateSortIndex() throws IOException { float[] retArray = new float[reader.maxDoc()]; TermDocs termDocs = reader.termDocs (); try { do { Term term = enumerator.term(); if (term.field() != field) break; float termval = Float.parseFloat (term.text()); termDocs.seek (enumerator); while (termDocs.next()) { retArray[termDocs.doc()] = termval; } } while (enumerator.next()); } finally { termDocs.close(); } return retArray; } public final int compare (final ScoreDoc i, final ScoreDoc j) { final float fi = fieldOrder[i.doc]; final float fj = fieldOrder[j.doc]; if (fi < fj) return -1; if (fi > fj) return 1; return 0; } public final int compareReverse (final ScoreDoc i, final ScoreDoc j) { final float fi = fieldOrder[i.doc]; final float fj = fieldOrder[j.doc]; if (fi > fj) return -1; if (fi < fj) return 1; return 0; } public final boolean sizeMatches (final int n) { return fieldOrder.length == n; } public Object sortValue (final ScoreDoc i) { return new Float (fieldOrder[i.doc]); } public int sortType() { return SortField.FLOAT; } }; }

1514 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/1514/60f1d192c7fe49cba55432569ed988099f4de5e4/FloatSortedHitQueue.java/buggy/src/java/org/apache/lucene/search/FloatSortedHitQueue.java

decorator.addListener(WorkbenchPlugin.getDefault().getDecoratorManager());

decorator.addListener( WorkbenchPlugin.getDefault().getDecoratorManager());

protected ILabelDecorator internalGetDecorator() throws CoreException { if (labelProviderCreationFailed) return null; final CoreException[] exceptions = new CoreException[1]; if (decorator == null) { Platform.run(new SafeRunnable(WorkbenchMessages.format("DecoratorManager.ErrorActivatingDecorator", new String[] { getName()})) { //$NON-NLS-1$ public void run() { try { decorator = (ILabelDecorator) WorkbenchPlugin.createExtension( definingElement, WizardsRegistryReader.ATT_CLASS); decorator.addListener(WorkbenchPlugin.getDefault().getDecoratorManager()); } catch (CoreException exception) { exceptions[0] = exception; } } }); } else return decorator; if (decorator == null) { this.labelProviderCreationFailed = true; setEnabled(false); } if (exceptions[0] != null) throw exceptions[0]; return decorator; }

56152 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/56152/271b6be5e51f33ef04581c15caa1b63347dc0f14/FullDecoratorDefinition.java/buggy/bundles/org.eclipse.ui.workbench/Eclipse UI/org/eclipse/ui/internal/decorators/FullDecoratorDefinition.java

if (!isUseServantManager()) throw new WrongPolicy();

if (!isUseServantManager()) throw new WrongPolicy();

public void set_servant_manager(org.omg.PortableServer.ServantManager servant_manager) throws WrongPolicy { // Debug.output(Debug.POA | Debug.DEBUG1, "Poa.set_servant_manager <" + // _getQualifiedName() + ">." ); checkDestructionApparent (); if (!isUseServantManager()) throw new WrongPolicy(); if (servantManager != null) throw new org.omg.CORBA.BAD_INV_ORDER(); /* not spec. */ if( isRetain() && !(servant_manager instanceof org.omg.PortableServer.ServantActivator)) throw new WrongPolicy(); if (!isRetain() && !(servant_manager instanceof org.omg.PortableServer.ServantLocator)) throw new WrongPolicy(); servantManager = servant_manager; }

46355 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/46355/a74dc4ac69615c8e503cb9145c3594f1702d4c75/POA.java/buggy/src/org/jacorb/poa/POA.java

Currency newCurrency = (Currency) cache.get(currencyCode); if (newCurrency == null)

/* Attempt to get the currency from the cache */ String code = (String) countryMap.get(country); if (code == null)

public static Currency getInstance(String currencyCode) { Locale[] allLocales; /* * Throw a null pointer exception explicitly if currencyCode is null. * One is not thrown otherwise. It results in an IllegalArgumentException. */ if (currencyCode == null) { throw new NullPointerException("The supplied currency code is null."); } Currency newCurrency = (Currency) cache.get(currencyCode); if (newCurrency == null) { /* Get all locales */ allLocales = Locale.getAvailableLocales(); /* Loop through each locale, looking for the code */ for (int i = 0;i < allLocales.length; i++) { try { Currency testCurrency = getInstance (allLocales[i]); if (testCurrency != null && testCurrency.getCurrencyCode().equals(currencyCode)) { return testCurrency; } } catch (IllegalArgumentException exception) { /* Ignore locales without valid countries */ } } /* * If we get this far, the code is not supported by any of * our locales. */ throw new IllegalArgumentException("The currency code, " + currencyCode + ", is not supported."); } else { return newCurrency; } }

50763 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50763/53b78dd1e4587254262f4618d2aa7551de8e0cbf/Currency.java/buggy/core/src/classpath/java/java/util/Currency.java

artifactList = repoSearcher.search( qry );

artifactList = repoSearchLayer.searchAdvanced( qry );

public void testSearchSingle() throws Exception { createTestIndex(); RepositoryIndexingFactory factory = (RepositoryIndexingFactory) lookup( RepositoryIndexingFactory.ROLE ); PomRepositoryIndex indexer = factory.createPomRepositoryIndex( indexPath, repository ); RepositoryIndexSearcher repoSearcher = factory.createDefaultRepositoryIndexSearcher( indexer ); // search version Query qry = new SinglePhraseQuery( PomRepositoryIndex.FLD_VERSION, "1.0" ); List artifactList = repoSearcher.search( qry ); //assertEquals( 1, artifactList.size() ); for ( Iterator iter = artifactList.iterator(); iter.hasNext(); ) { Artifact artifact = (Artifact) iter.next(); assertEquals( "1.0", artifact.getVersion() ); } // search group id qry = new SinglePhraseQuery( PomRepositoryIndex.FLD_GROUPID, "org.apache.maven" ); artifactList = repoSearcher.search( qry ); assertEquals( 2, artifactList.size() ); Iterator artifacts = artifactList.iterator(); if ( artifacts.hasNext() ) { Artifact artifact = (Artifact) artifacts.next(); assertEquals( "org.apache.maven", artifact.getGroupId() ); } // search artifact id qry = new SinglePhraseQuery( PomRepositoryIndex.FLD_ARTIFACTID, "maven-artifact" ); artifactList = repoSearcher.search( qry ); assertEquals( 1, artifactList.size() ); for ( artifacts = artifactList.iterator(); artifacts.hasNext(); ) { Artifact artifact = (Artifact) artifacts.next(); assertEquals( "maven-artifact", artifact.getArtifactId() ); } // search version qry = new SinglePhraseQuery( PomRepositoryIndex.FLD_VERSION, "2" ); artifactList = repoSearcher.search( qry ); assertEquals( 2, artifactList.size() ); for ( artifacts = artifactList.iterator(); artifacts.hasNext(); ) { Artifact artifact = (Artifact) artifacts.next(); assertTrue( artifact.getVersion().indexOf( "2" ) != -1 ); } // search packaging qry = new SinglePhraseQuery( PomRepositoryIndex.FLD_PACKAGING, "jar" ); artifactList = repoSearcher.search( qry ); assertEquals( 3, artifactList.size() ); for ( artifacts = artifactList.iterator(); artifacts.hasNext(); ) { Artifact artifact = (Artifact) artifacts.next(); assertEquals( "jar", artifact.getType() ); } //search license url qry = new SinglePhraseQuery( PomRepositoryIndex.FLD_LICENSE_URLS, "http://www.apache.org/licenses/LICENSE-2.0.txt" ); artifactList = repoSearcher.search( qry ); assertEquals( 2, artifactList.size() ); for ( artifacts = artifactList.iterator(); artifacts.hasNext(); ) { Artifact artifact = (Artifact) artifacts.next(); License license = (License) getPom( artifact ).getLicenses().get( 0 ); assertEquals( "http://www.apache.org/licenses/LICENSE-2.0.txt", license.getUrl() ); } //search dependencies qry = new SinglePhraseQuery( PomRepositoryIndex.FLD_DEPENDENCIES, "org.codehaus.plexus:plexus-utils:1.0.5" ); artifactList = repoSearcher.search( qry ); assertEquals( 2, artifactList.size() ); for ( artifacts = artifactList.iterator(); artifacts.hasNext(); ) { Artifact artifact = (Artifact) artifacts.next(); Iterator dependencies = getPom( artifact ).getDependencies().iterator(); boolean depFound = false; while ( dependencies.hasNext() ) { Dependency dep = (Dependency) dependencies.next(); if ( "org.codehaus.plexus:plexus-utils:1.0.5".equals( dep.getGroupId() + ":" + dep.getArtifactId() + ":" + dep.getVersion() ) ) { depFound = true; break; } } assertTrue( "Searched dependency not found.", depFound ); } //search build plugin qry = new SinglePhraseQuery( PomRepositoryIndex.FLD_PLUGINS_BUILD, "org.codehaus.modello:modello-maven-plugin:2.0" ); artifactList = repoSearcher.search( qry ); assertEquals( 1, artifactList.size() ); for ( artifacts = artifactList.iterator(); artifacts.hasNext(); ) { Artifact artifact = (Artifact) artifacts.next(); Iterator plugins = getPom( artifact ).getBuild().getPlugins().iterator(); boolean found = false; while ( plugins.hasNext() ) { Plugin plugin = (Plugin) plugins.next(); if ( "org.codehaus.modello:modello-maven-plugin:2.0".equals( plugin.getKey() + ":" + plugin.getVersion() ) ) { found = true; break; } } assertTrue( "Searched plugin not found.", found ); } //search reporting plugin qry = new SinglePhraseQuery( PomRepositoryIndex.FLD_PLUGINS_REPORT, "org.apache.maven.plugins:maven-checkstyle-plugin:2.0" ); artifactList = repoSearcher.search( qry ); assertEquals( 1, artifactList.size() ); for ( artifacts = artifactList.iterator(); artifacts.hasNext(); ) { Artifact artifact = (Artifact) artifacts.next(); Iterator plugins = getPom( artifact ).getReporting().getPlugins().iterator(); boolean found = false; while ( plugins.hasNext() ) { ReportPlugin plugin = (ReportPlugin) plugins.next(); if ( "org.apache.maven.plugins:maven-checkstyle-plugin:2.0".equals( plugin.getKey() + ":" + plugin.getVersion() ) ) { found = true; break; } } assertTrue( "Searched report plugin not found.", found ); } // search sha1 checksum Artifact artifact = getArtifact( "org.apache.maven", "maven-model", "2.0" ); artifact.setFile( new File( repository.getBasedir(), repository.pathOf( artifact ) ) ); String sha1 = digester.createChecksum( artifact.getFile(), Digester.SHA1 ); qry = new SinglePhraseQuery( PomRepositoryIndex.FLD_SHA1, sha1.trim() ); artifactList = repoSearcher.search( qry ); assertEquals( 1, artifactList.size() ); for ( artifacts = artifactList.iterator(); artifacts.hasNext(); ) { Artifact artifact2 = (Artifact) artifacts.next(); String sha1Tmp = digester.createChecksum( getPomFile( artifact2 ), Digester.SHA1 ); assertEquals( sha1, sha1Tmp ); } // search md5 checksum String md5 = digester.createChecksum( getPomFile( artifact ), Digester.MD5 ); qry = new SinglePhraseQuery( PomRepositoryIndex.FLD_MD5, md5.trim() ); artifactList = repoSearcher.search( qry ); assertEquals( 1, artifactList.size() ); for ( artifacts = artifactList.iterator(); artifacts.hasNext(); ) { Artifact artifact2 = (Artifact) artifacts.next(); String md5Tmp = digester.createChecksum( getPomFile( artifact2 ), Digester.MD5 ); assertEquals( md5, md5Tmp ); } indexer.close(); }

28441 /local/tlutelli/issta_data/temp/all_java2context/java/2006_temp/2006/28441/edd8a998aa6006fddaf4d4a404bbdd6ddfd246d7/PomRepositoryIndexingTest.java/clean/maven-repository-indexer/src/test/java/org/apache/maven/repository/indexing/PomRepositoryIndexingTest.java

throw new ArgumentError(runtime, "wrong number of arguments");

throw runtime.newArgumentError("wrong number of arguments");

public static IRubyObject raise(IRubyObject recv, IRubyObject[] args) { // FIXME special case in ruby // recv.checkArgumentCount(args, 0, 2); Ruby runtime = recv.getRuntime(); RubyString string = null; RubyException excptn = null; switch (args.length) { case 0 : IRubyObject defaultException = runtime.getGlobalVariables().get("$!"); if (defaultException.isNil()) { throw new RaiseException(runtime, runtime.getExceptions().getRuntimeError(), "", false); } throw new RaiseException((RubyException) defaultException); case 1 : if (args[0] instanceof RubyException) { throw new RaiseException((RubyException) args[0]); } else if (args[0] instanceof RubyClass) { throw new RaiseException(RubyException.newInstance((RubyClass)args[0], new IRubyObject[0])); } throw new RaiseException(RubyException.newInstance(runtime.getExceptions().getRuntimeError(), args)); case 2 : if (args[0] == runtime.getClasses().getExceptionClass()) { throw new RaiseException((RubyException) args[0].callMethod("exception", args[1])); } string = (RubyString) args[1]; excptn = RubyException.newException(runtime, (RubyClass)args[0], string.getValue()); throw new RaiseException(excptn); case 3: if (args[0] == runtime.getClasses().getExceptionClass()) { throw new RaiseException((RubyException) args[0].callMethod("exception", args[1])); } string = (RubyString) args[1]; excptn = RubyException.newException(runtime, (RubyClass)args[0], string.getValue()); excptn.set_backtrace(args[2]); throw new RaiseException(excptn); default : throw new ArgumentError(runtime, "wrong number of arguments"); } }

47619 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/47619/870e1da9b41bfdbae259e1fc5f18fc8b76686998/RubyKernel.java/buggy/src/org/jruby/RubyKernel.java

int _m488 = mark(); synPredMatched488 = true;

int _m489 = mark(); synPredMatched489 = true;

public final void mNEXT_TOKEN(boolean _createToken) throws RecognitionException, CharStreamException, TokenStreamException { int _ttype; Token _token=null; int _begin=text.length(); _ttype = NEXT_TOKEN; int _saveIndex; Token ncname=null; switch ( LA(1)) { case '{': { mLCURLY(false); if ( inputState.guessing==0 ) { inElementContent= false; inAttributeContent= false; _ttype = LCURLY; } break; } case '}': { mRCURLY(false); if ( inputState.guessing==0 ) { _ttype = RCURLY; } break; } default: boolean synPredMatched472 = false; if (((LA(1)=='(') && (LA(2)==':') && (LA(3)==':') && (LA(4)=='p'))) { int _m472 = mark(); synPredMatched472 = true; inputState.guessing++; try { { match("(::"); } } catch (RecognitionException pe) { synPredMatched472 = false; } rewind(_m472); inputState.guessing--; } if ( synPredMatched472 ) { mPRAGMA(false); if ( inputState.guessing==0 ) { _ttype = Token.SKIP; } } else if ((LA(1)=='(') && (LA(2)==':') && (_tokenSet_6.member(LA(3))) && (_tokenSet_6.member(LA(4)))) { mEXPR_COMMENT(false); if ( inputState.guessing==0 ) { _ttype = Token.SKIP; } } else if ((LA(1)=='<') && (LA(2)=='!') && (LA(3)=='-')) { mXML_COMMENT(false); if ( inputState.guessing==0 ) { String data = new String(text.getBuffer(),_begin,text.length()-_begin); parseLinefeeds(data); _ttype = XML_COMMENT; } } else if ((LA(1)=='<') && (LA(2)=='!') && (LA(3)=='[')) { mXML_CDATA(false); if ( inputState.guessing==0 ) { _ttype = XML_CDATA; } } else { boolean synPredMatched486 = false; if (((_tokenSet_19.member(LA(1))) && (_tokenSet_20.member(LA(2))) && (_tokenSet_21.member(LA(3))) && (true))) { int _m486 = mark(); synPredMatched486 = true; inputState.guessing++; try { { mINTEGER_LITERAL(false); { switch ( LA(1)) { case '.': { match('.'); { if ((_tokenSet_2.member(LA(1)))) { mINTEGER_LITERAL(false); } else if ((LA(1)=='E'||LA(1)=='e')) { } else { throw new NoViableAltForCharException((char)LA(1), getFilename(), getLine(), getColumn()); } } break; } case 'E': case 'e': { break; } default: { throw new NoViableAltForCharException((char)LA(1), getFilename(), getLine(), getColumn()); } } } { switch ( LA(1)) { case 'e': { match('e'); break; } case 'E': { match('E'); break; } default: { throw new NoViableAltForCharException((char)LA(1), getFilename(), getLine(), getColumn()); } } } } } catch (RecognitionException pe) { synPredMatched486 = false; } rewind(_m486); inputState.guessing--; } if ( synPredMatched486 ) { mDOUBLE_LITERAL(false); if ( inputState.guessing==0 ) { _ttype = DOUBLE_LITERAL; } } else if ((LA(1)=='-') && (LA(2)=='-') && (LA(3)=='>') && (true)) { mXML_COMMENT_END(false); if ( inputState.guessing==0 ) { _ttype = XML_COMMENT_END; } } else if ((LA(1)==']') && (LA(2)==']') && (LA(3)=='>') && (true)) { mXML_CDATA_END(false); if ( inputState.guessing==0 ) { _ttype = XML_CDATA_END; } } else { boolean synPredMatched470 = false; if (((LA(1)=='<') && (LA(2)=='?'))) { int _m470 = mark(); synPredMatched470 = true; inputState.guessing++; try { { mXML_PI_START(false); } } catch (RecognitionException pe) { synPredMatched470 = false; } rewind(_m470); inputState.guessing--; } if ( synPredMatched470 ) { mXML_PI(false); if ( inputState.guessing==0 ) { _ttype = XML_PI; } } else if ((LA(1)=='<') && (LA(2)=='/')) { mEND_TAG_START(false); if ( inputState.guessing==0 ) { inElementContent= false; wsExplicit= false; _ttype = END_TAG_START; } } else if ((LA(1)=='<') && (LA(2)=='=')) { mLTEQ(false); if ( inputState.guessing==0 ) { _ttype = LTEQ; } } else if (((LA(1)=='"'||LA(1)=='\'') && ((LA(2) >= '\u0003' && LA(2) <= '\ufffe')) && (true) && (true))&&( parseStringLiterals )) { mSTRING_LITERAL(false); if ( inputState.guessing==0 ) { _ttype = STRING_LITERAL; } } else { boolean synPredMatched474 = false; if ((((LA(1)=='.') && (LA(2)=='.') && (true) && (true))&&( !(inAttributeContent || inElementContent) ))) { int _m474 = mark(); synPredMatched474 = true; inputState.guessing++; try { { match('.'); match('.'); } } catch (RecognitionException pe) { synPredMatched474 = false; } rewind(_m474); inputState.guessing--; } if ( synPredMatched474 ) { mPARENT(false); if ( inputState.guessing==0 ) { _ttype = PARENT; } } else if (((LA(1)=='/') && (LA(2)=='/') && (true) && (true))&&( !(inAttributeContent || inElementContent) )) { mDSLASH(false); if ( inputState.guessing==0 ) { _ttype = DSLASH; } } else if (((LA(1)=='|') && (LA(2)=='=') && (true) && (true))&&( !(inAttributeContent || inElementContent) )) { mOREQ(false); if ( inputState.guessing==0 ) { _ttype = OREQ; } } else if (((LA(1)=='&') && (LA(2)=='=') && (true) && (true))&&( !(inAttributeContent || inElementContent) )) { mANDEQ(false); if ( inputState.guessing==0 ) { _ttype = ANDEQ; } } else if (((LA(1)=='!') && (LA(2)=='=') && (true) && (true))&&( !(inAttributeContent || inElementContent) )) { mNEQ(false); if ( inputState.guessing==0 ) { _ttype = NEQ; } } else if (((LA(1)=='>') && (LA(2)=='=') && (true) && (true))&&( !(inAttributeContent || inElementContent) )) { mGTEQ(false); if ( inputState.guessing==0 ) { _ttype = GTEQ; } } else if ((LA(1)=='?') && (LA(2)=='>') && (true) && (true)) { mXML_PI_END(false); if ( inputState.guessing==0 ) { _ttype = XML_PI_END; } } else if ((LA(1)=='<') && (true)) { mLT(false); if ( inputState.guessing==0 ) { inElementContent= false; _ttype = LT; } } else if (((_tokenSet_13.member(LA(1))) && (true) && (true) && (true))&&( inAttributeContent && attrDelimChar == '"' )) { mQUOT_ATTRIBUTE_CONTENT(false); if ( inputState.guessing==0 ) { _ttype = QUOT_ATTRIBUTE_CONTENT; } } else if (((_tokenSet_14.member(LA(1))) && (true) && (true) && (true))&&( inAttributeContent && attrDelimChar == '\'' )) { mAPOS_ATTRIBUTE_CONTENT(false); if ( inputState.guessing==0 ) { _ttype = APOS_ATTRIBUTE_CONTENT; } } else if (((LA(1)=='"') && (true) && (true) && (true))&&( !(parseStringLiterals || inElementContent) )) { mQUOT(false); if ( inputState.guessing==0 ) { _ttype = QUOT; } } else if (((LA(1)=='\'') && (true) && (true) && (true))&&( !(parseStringLiterals || inElementContent) )) { mAPOS(false); if ( inputState.guessing==0 ) { _ttype = APOS; System.out.println("APOS"); } } else if (((_tokenSet_22.member(LA(1))) && (true) && (true) && (true))&&( inElementContent )) { mELEMENT_CONTENT(false); if ( inputState.guessing==0 ) { _ttype = ELEMENT_CONTENT; } } else if ((LA(1)=='\t'||LA(1)=='\n'||LA(1)=='\r'||LA(1)==' ') && (true) && (true) && (true)) { mWS(false); if ( inputState.guessing==0 ) { if (wsExplicit) { _ttype = WS; text.setLength(_begin); text.append("WS"); } else _ttype = Token.SKIP; } } else if ((_tokenSet_23.member(LA(1))) && (true) && (true) && (true)) { mNCNAME(true); ncname=_returnToken; if ( inputState.guessing==0 ) { _ttype = ncname.getType(); } } else { boolean synPredMatched477 = false; if (((_tokenSet_19.member(LA(1))) && (true) && (true) && (true))) { int _m477 = mark(); synPredMatched477 = true; inputState.guessing++; try { { match('.'); mINTEGER_LITERAL(false); { switch ( LA(1)) { case 'e': { match('e'); break; } case 'E': { match('E'); break; } default: { throw new NoViableAltForCharException((char)LA(1), getFilename(), getLine(), getColumn()); } } } } } catch (RecognitionException pe) { synPredMatched477 = false; } rewind(_m477); inputState.guessing--; } if ( synPredMatched477 ) { mDECIMAL_LITERAL(false); if ( inputState.guessing==0 ) { _ttype = DECIMAL_LITERAL; } } else { boolean synPredMatched479 = false; if (((_tokenSet_19.member(LA(1))) && (true) && (true) && (true))) { int _m479 = mark(); synPredMatched479 = true; inputState.guessing++; try { { match('.'); mINTEGER_LITERAL(false); } } catch (RecognitionException pe) { synPredMatched479 = false; } rewind(_m479); inputState.guessing--; } if ( synPredMatched479 ) { mDECIMAL_LITERAL(false); if ( inputState.guessing==0 ) { _ttype = DECIMAL_LITERAL; } } else { boolean synPredMatched481 = false; if (((LA(1)=='.') && (true) && (true) && (true))) { int _m481 = mark(); synPredMatched481 = true; inputState.guessing++; try { { match('.'); } } catch (RecognitionException pe) { synPredMatched481 = false; } rewind(_m481); inputState.guessing--; } if ( synPredMatched481 ) { mSELF(false); if ( inputState.guessing==0 ) { _ttype = SELF; } } else { boolean synPredMatched488 = false; if (((_tokenSet_19.member(LA(1))) && (true) && (true) && (true))) { int _m488 = mark(); synPredMatched488 = true; inputState.guessing++; try { { mINTEGER_LITERAL(false); match('.'); } } catch (RecognitionException pe) { synPredMatched488 = false; } rewind(_m488); inputState.guessing--; } if ( synPredMatched488 ) { mDECIMAL_LITERAL(false); if ( inputState.guessing==0 ) { _ttype = DECIMAL_LITERAL; } } else if ((_tokenSet_2.member(LA(1))) && (true) && (true) && (true)) { mINTEGER_LITERAL(false); if ( inputState.guessing==0 ) { _ttype = INTEGER_LITERAL; } } else if ((LA(1)=='/') && (true) && (true) && (true)) { mSLASH(false); if ( inputState.guessing==0 ) { _ttype = SLASH; } } else if ((LA(1)==':') && (true) && (true) && (true)) { mCOLON(false); if ( inputState.guessing==0 ) { _ttype = COLON; } } else if ((LA(1)==',') && (true) && (true) && (true)) { mCOMMA(false); if ( inputState.guessing==0 ) { _ttype = COMMA; } } else if ((LA(1)==';') && (true) && (true) && (true)) { mSEMICOLON(false); if ( inputState.guessing==0 ) { _ttype = SEMICOLON; } } else if ((LA(1)=='*') && (true) && (true) && (true)) { mSTAR(false); if ( inputState.guessing==0 ) { _ttype = STAR; } } else if ((LA(1)=='?') && (true) && (true) && (true)) { mQUESTION(false); if ( inputState.guessing==0 ) { _ttype = QUESTION; } } else if ((LA(1)=='+') && (true) && (true) && (true)) { mPLUS(false); if ( inputState.guessing==0 ) { _ttype = PLUS; } } else if ((LA(1)=='-') && (true) && (true) && (true)) { mMINUS(false); if ( inputState.guessing==0 ) { _ttype = MINUS; } } else if ((LA(1)=='[') && (true) && (true) && (true)) { mLPPAREN(false); if ( inputState.guessing==0 ) { _ttype = LPPAREN; } } else if ((LA(1)==']') && (true) && (true) && (true)) { mRPPAREN(false); if ( inputState.guessing==0 ) { _ttype = RPPAREN; } } else if ((LA(1)=='(') && (true) && (true) && (true)) { mLPAREN(false); if ( inputState.guessing==0 ) { _ttype = LPAREN; } } else if ((LA(1)==')') && (true) && (true) && (true)) { mRPAREN(false); if ( inputState.guessing==0 ) { _ttype = RPAREN; } } else if ((LA(1)=='|') && (true) && (true) && (true)) { mUNION(false); if ( inputState.guessing==0 ) { _ttype = UNION; } } else if ((LA(1)=='@') && (true) && (true) && (true)) { mAT(false); if ( inputState.guessing==0 ) { _ttype = AT; } } else if ((LA(1)=='$') && (true) && (true) && (true)) { mDOLLAR(false); if ( inputState.guessing==0 ) { _ttype = DOLLAR; } } else if ((LA(1)=='=') && (true) && (true) && (true)) { mEQ(false); if ( inputState.guessing==0 ) { _ttype = EQ; } } else if ((LA(1)=='>') && (true) && (true) && (true)) { mGT(false); if ( inputState.guessing==0 ) { _ttype = GT; } } else { throw new NoViableAltForCharException((char)LA(1), getFilename(), getLine(), getColumn()); } }}}}}}}} if ( _createToken && _token==null && _ttype!=Token.SKIP ) { _token = makeToken(_ttype); _token.setText(new String(text.getBuffer(), _begin, text.length()-_begin)); } _returnToken = _token; }

2909 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/2909/10544e5ec103a411822c6180ed81ef38eab15de8/XQueryLexer.java/clean/src/org/exist/xquery/parser/XQueryLexer.java

updateDescription(); }

updateDescription(); }

public void widgetDefaultSelected(SelectionEvent e) { updateDescription(); }

58148 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/58148/901694a204e2e98a8a01b05f67351a3c900227dc/WizardPreferencesPage.java/clean/bundles/org.eclipse.ui.ide/src/org/eclipse/ui/internal/wizards/preferences/WizardPreferencesPage.java

query = new FuzzyQuery(new Term("field", "student"), FuzzyQuery.defaultMinSimilarity, 1); hits = searcher.search(query); assertEquals(1, hits.length()); query = new FuzzyQuery(new Term("field", "stellent"), FuzzyQuery.defaultMinSimilarity, 1); hits = searcher.search(query); assertEquals(1, hits.length()); query = new FuzzyQuery(new Term("field", "student"), FuzzyQuery.defaultMinSimilarity, 2); hits = searcher.search(query); assertEquals(0, hits.length()); query = new FuzzyQuery(new Term("field", "stellent"), FuzzyQuery.defaultMinSimilarity, 2); hits = searcher.search(query); assertEquals(0, hits.length());

public void testFuzzinessLong() throws Exception { RAMDirectory directory = new RAMDirectory(); IndexWriter writer = new IndexWriter(directory, new WhitespaceAnalyzer(), true); addDoc("aaaaaaa", writer); addDoc("segment", writer); writer.optimize(); writer.close(); IndexSearcher searcher = new IndexSearcher(directory); FuzzyQuery query; // not similar enough: query = new FuzzyQuery(new Term("field", "xxxxx")); Hits hits = searcher.search(query); assertEquals(0, hits.length()); // edit distance to "aaaaaaa" = 3, this matches because the string is longer than // in testDefaultFuzziness so a bigger difference is allowed: query = new FuzzyQuery(new Term("field", "aaaaccc")); hits = searcher.search(query); assertEquals(1, hits.length()); assertEquals(hits.doc(0).get("field"), ("aaaaaaa")); // no match, more than half of the characters is wrong: query = new FuzzyQuery(new Term("field", "aaacccc")); hits = searcher.search(query); assertEquals(0, hits.length()); // "student" and "stellent" are indeed similar to "segment" by default: query = new FuzzyQuery(new Term("field", "student")); hits = searcher.search(query); assertEquals(1, hits.length()); query = new FuzzyQuery(new Term("field", "stellent")); hits = searcher.search(query); assertEquals(1, hits.length()); // "student" doesn't match anymore thanks to increased minimum similarity: query = new FuzzyQuery(new Term("field", "student"), 0.6f); hits = searcher.search(query); assertEquals(0, hits.length()); try { query = new FuzzyQuery(new Term("field", "student"), 1.1f); fail("Expected IllegalArgumentException"); } catch (IllegalArgumentException e) { // expecting exception } try { query = new FuzzyQuery(new Term("field", "student"), -0.1f); fail("Expected IllegalArgumentException"); } catch (IllegalArgumentException e) { // expecting exception } searcher.close(); directory.close(); }

1514 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/1514/a433e2c1de45521ddf0b5f08eeab69fb279aff15/TestFuzzyQuery.java/buggy/src/test/org/apache/lucene/search/TestFuzzyQuery.java

+ " and coGene.products.id=coBs2gp.geneProduct.id "

+ " and coGene.products.id=coBs2gp.geneProduct.id "

protected Object handleGetCoexpressedGenes( Gene gene, Collection ees, Integer stringency ) throws Exception { Gene givenG = gene; long id = givenG.getId(); String p2pClassName; if (TaxonUtility.isHuman(givenG.getTaxon())) p2pClassName = "HumanProbeCoExpressionImpl"; else if (TaxonUtility.isMouse(givenG.getTaxon())) p2pClassName = "MouseProbeCoExpressionImpl"; else if (TaxonUtility.isRat(givenG.getTaxon())) p2pClassName = "RatProbeCoExpressionImpl"; else //must be other p2pClassName = "OtherProbeCoExpressionImpl"; Map<Long,CoexpressionValueObject> geneMap = new HashMap<Long,CoexpressionValueObject>(); Map<Long,ExpressionExperimentValueObject> eeMap = new HashMap<Long,ExpressionExperimentValueObject>(); String queryStringFirstVector = // return values "select coGene.id, coGene.name, coGene.officialName,p2pc.firstVector.expressionExperiment.id, p2pc.firstVector.expressionExperiment.shortName, p2pc.firstVector.expressionExperiment.name" // source tables + " from GeneImpl as gene, BioSequence2GeneProductImpl as bs2gp, CompositeSequenceImpl as compositeSequence," // join table + p2pClassName + " as p2pc," // target tables + " GeneImpl as coGene,BioSequence2GeneProductImpl as coBs2gp, CompositeSequenceImpl as coCompositeSequence" + " where gene.products.id=bs2gp.geneProduct.id " + " and compositeSequence.biologicalCharacteristic=bs2gp.bioSequence " + " and compositeSequence.designElementDataVectors.id=p2pc.firstVector.id " + " and coCompositeSequence.designElementDataVectors.id=p2pc.secondVector.id " + " and coCompositeSequence.biologicalCharacteristic=coBs2gp.bioSequence " + " and coGene.products.id=coBs2gp.geneProduct.id " + " and gene.id = :id and coGene.taxon.id = :taxonId"; String queryStringSecondVector = // return values "select coGene.id, coGene.name, coGene.officialName,p2pc.secondVector.expressionExperiment.id, p2pc.secondVector.expressionExperiment.shortName, p2pc.secondVector.expressionExperiment.name " // source tables + "from GeneImpl as gene, BioSequence2GeneProductImpl as bs2gp, CompositeSequenceImpl as compositeSequence," // join table + p2pClassName + " as p2pc," // target tables + "GeneImpl as coGene,BioSequence2GeneProductImpl as coBs2gp, CompositeSequenceImpl as coCompositeSequence" + " where gene.products.id=bs2gp.geneProduct.id " + " and compositeSequence.biologicalCharacteristic=bs2gp.bioSequence " + " and compositeSequence.designElementDataVectors.id=p2pc.secondVector.id " + " and coCompositeSequence.designElementDataVectors.id=p2pc.firstVector.id " + " and coCompositeSequence.biologicalCharacteristic=coBs2gp.bioSequence " + " and coGene.products.id=coBs2gp.geneProduct.id " + " and gene.id = :id and coGene.taxon.id = :taxonId"; // OPTIONAL joins // if there are expressionExperiment arguments Collection<Long> eeIds = new ArrayList<Long>(); CoexpressionCollectionValueObject coexpressions = new CoexpressionCollectionValueObject(); if (ees.size() > 0) { queryStringFirstVector += " and p2pc.firstVector.expressionExperiment.id in (:ees) "; queryStringSecondVector += " and p2pc.secondVector.expressionExperiment.id in (:ees) "; for ( Iterator iter = ees.iterator(); iter.hasNext(); ) { ExpressionExperiment e = ( ExpressionExperiment ) iter.next(); eeIds.add( e.getId() ); } } try { // do query joining coexpressed genes through the firstVector to the secondVector org.hibernate.Query queryObject = super.getSession( false ).createQuery( queryStringFirstVector ); queryObject.setLong( "id", id ); // this is to make the query faster by narrowing down the gene join queryObject.setLong( "taxonId", gene.getTaxon().getId() ); if (ees.size() > 0) { queryObject.setParameterList( "ees", eeIds ); }// queryObject.setInteger( "stringency", stringency ); // put genes in the geneSet ScrollableResults scroll = queryObject.scroll(ScrollMode.FORWARD_ONLY); while (scroll.next()) { CoexpressionValueObject vo; Long geneId = scroll.getLong( 0 ); // check to see if geneId is already in the geneMap if (geneMap.containsKey( geneId )) { vo = geneMap.get( geneId ); } else { vo = new CoexpressionValueObject(); vo.setGeneId( geneId ); vo.setGeneName( scroll.getString( 1 ) ); vo.setGeneOfficialName( scroll.getString( 2 ) ); geneMap.put(geneId,vo); } // add the expression experiment ExpressionExperimentValueObject eeVo = new ExpressionExperimentValueObject(); eeVo.setId( scroll.getLong( 3 ).toString() ); eeVo.setShortName( scroll.getString( 4 ) ); eeVo.setName( scroll.getString( 5 ) ); vo.addExpressionExperimentValueObject( eeVo ); } // do query joining coexpressed genes through the secondVector to the firstVector queryObject = super.getSession( false ).createQuery( queryStringSecondVector ); queryObject.setLong( "id", id ); // this is to make the query faster by narrowing down the gene join queryObject.setLong( "taxonId", gene.getTaxon().getId() ); if (ees.size() > 0) { queryObject.setParameterList( "ees", eeIds ); } // put genes in the geneSet scroll = queryObject.scroll(ScrollMode.FORWARD_ONLY); while (scroll.next()) { CoexpressionValueObject vo; Long geneId = scroll.getLong( 0 ); // check to see if geneId is already in the geneMap if (geneMap.containsKey( geneId )) { vo = geneMap.get( geneId ); } else { vo = new CoexpressionValueObject(); vo.setGeneId( geneId ); vo.setGeneName( scroll.getString( 1 ) ); vo.setGeneOfficialName( scroll.getString( 2 ) ); geneMap.put(geneId,vo); } // add the expression experiment ExpressionExperimentValueObject eeVo = new ExpressionExperimentValueObject(); eeVo.setId( scroll.getLong( 3 ).toString() ); eeVo.setShortName( scroll.getString( 4 ) ); eeVo.setName( scroll.getString( 5 ) ); vo.addExpressionExperimentValueObject( eeVo ); } // add count of original matches to coexpression data coexpressions.setLinkCount( geneMap.size() ); // parse out stringency failures Set keys = geneMap.keySet(); for ( Object object : keys ) { Long key = (Long) object; if (geneMap.get( key ).getExpressionExperimentValueObjects().size() >= stringency) { // add in coexpressions that match stringency coexpressions.getCoexpressionData().add( geneMap.get( key ) ); // add in expression experiments that match stringency Collection eeVos = geneMap.get( key ).getExpressionExperimentValueObjects(); for ( Object o : eeVos ) { ExpressionExperimentValueObject ee = (ExpressionExperimentValueObject) o; eeMap.put( Long.parseLong(ee.getId()), ee ); } } } // add count of pruned matches to coexpression data coexpressions.setStringencyLinkCount( coexpressions.getCoexpressionData().size() ); // add the distinct set of expression experiments involved // in the query to coexpression data coexpressions.setExpressionExperiments( eeMap.values() ); } catch ( org.hibernate.HibernateException ex ) { throw super.convertHibernateAccessException( ex ); } return coexpressions; }

4335 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/4335/71d023ff940a83104d33a0ec7a241d4b25474a37/GeneDaoImpl.java/clean/gemma-mda/src/main/java/ubic/gemma/model/genome/GeneDaoImpl.java

table.getCell( 4, 1 ).getContent( ).add( data );

table.getCell( GroupHandle.FOOTER_SLOT, 1, 1, 1 ).getContent( ).add( data );

public void testBoundColumnWithGroup( ) throws Exception { createDesign( ); TableHandle table = designHandle.getElementFactory( ).newTableItem( "table1", 3 ); //$NON-NLS-1$ designHandle.getBody( ).add( table ); TableGroupHandle group = designHandle.getElementFactory( ) .newTableGroup( ); group.getFooter( ).add( designHandle.getElementFactory( ).newTableRow( 3 ) ); table.getGroups( ).add( group ); group = designHandle.getElementFactory( ).newTableGroup( ); group.getFooter( ).add( designHandle.getElementFactory( ).newTableRow( 3 ) ); table.getGroups( ).add( group ); DataItemHandle data = designHandle.getElementFactory( ).newDataItem( "data1" ); //$NON-NLS-1$ data.setValueExpr( "row[\"valueData\"]" ); //$NON-NLS-1$ table.getCell( 3, 1 ).getContent( ).add( data ); data = designHandle.getElementFactory( ).newDataItem( "data1" ); //$NON-NLS-1$ data.setValueExpr( "row[\"valueData\"]" ); //$NON-NLS-1$ table.getCell( 4, 1 ).getContent( ).add( data ); saveAs( "CompatibleExpression_out_2.xml" ); //$NON-NLS-1$ assertTrue( compareTextFile( "CompatibleExpression_golden_2.xml", //$NON-NLS-1$ "CompatibleExpression_out_2.xml" ) ); //$NON-NLS-1$ }

5230 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/5230/de4e32d64d24337e8801521456bb895f21408aa9/APICompatibleTest.java/clean/model/org.eclipse.birt.report.model.tests/test/org/eclipse/birt/report/model/api/APICompatibleTest.java

public static Object getProperty(Map props, Object key, Object defaultValue) {

public static Object getProperty(Map props, Object key, Object defaultValue) {

public static Object getProperty(Map props, Object key, Object defaultValue) { if (props == null) { return defaultValue; } Object temp = props.get(key); if (temp == null) { temp = defaultValue; } return temp; }

28323 /local/tlutelli/issta_data/temp/all_java2context/java/2006_temp/2006/28323/5c7badd7924d8f30223c81136f63117d913be921/PropertiesHelper.java/clean/src/java/org/mule/util/PropertiesHelper.java

public void finish() { }

public void finish() { }

public void finish() { }

10715 /local/tlutelli/issta_data/temp/all_java1context/java/2006_temp/2006/10715/1d541964940eaa91b52b21469dc5b763fef1d8d1/AnalysisRun.java/clean/findbugs/src/java/edu/umd/cs/findbugs/gui/AnalysisRun.java

if ( ( sNewSubType.equalsIgnoreCase( "Stacked" ) || sNewSubType.equalsIgnoreCase( "Percent Stacked" ) ) )

if ( ( sNewSubType.equalsIgnoreCase( STACKED_SUBTYPE_LITERAL) || sNewSubType.equalsIgnoreCase( PERCENTSTACKED_SUBTYPE_LITERAL ) ) )

private Chart getConvertedChart( Chart currentChart, String sNewSubType, Orientation newOrientation, String sNewDimension ) { Chart helperModel = (Chart) EcoreUtil.copy( currentChart ); ChartDimension oldDimension = currentChart.getDimension( ); if ( ( currentChart instanceof ChartWithAxes ) ) { if ( currentChart.getType( ).equals( TYPE_LITERAL ) ) // Original // chart is // of this type // (LineChart) { if ( !currentChart.getSubType( ).equals( sNewSubType ) ) // Original // chart // is // of // the // required // subtype { currentChart.setSubType( sNewSubType ); EList axes = ( (Axis) ( (ChartWithAxes) currentChart ).getAxes( ) .get( 0 ) ).getAssociatedAxes( ); for ( int i = 0; i < axes.size( ); i++ ) { if ( sNewSubType.equalsIgnoreCase( "Percent Stacked" ) ) //$NON-NLS-1$ { ( (Axis) axes.get( i ) ).setPercent( true ); } else { ( (Axis) axes.get( i ) ).setPercent( false ); } EList seriesdefinitions = ( (Axis) axes.get( i ) ).getSeriesDefinitions( ); for ( int j = 0; j < seriesdefinitions.size( ); j++ ) { Series series = ( (SeriesDefinition) seriesdefinitions.get( j ) ).getDesignTimeSeries( ); if ( ( sNewSubType.equalsIgnoreCase( "Stacked" ) || sNewSubType //$NON-NLS-1$ .equalsIgnoreCase( "Percent Stacked" ) ) ) //$NON-NLS-1$ { series.setStacked( true ); } else { series.setStacked( false ); } } } } } else if ( currentChart.getType( ).equals( BarChart.TYPE_LITERAL ) || currentChart.getType( ).equals( AreaChart.TYPE_LITERAL ) || currentChart.getType( ).equals( StockChart.TYPE_LITERAL ) || currentChart.getType( ) .equals( ScatterChart.TYPE_LITERAL ) ) { if ( !currentChart.getType( ).equals( BarChart.TYPE_LITERAL ) ) //$NON-NLS-1$ { currentChart.setSampleData( getConvertedSampleData( currentChart.getSampleData( ) ) ); ( (Axis) ( (ChartWithAxes) currentChart ).getAxes( ) .get( 0 ) ).setType( AxisType.TEXT_LITERAL ); } currentChart.setType( TYPE_LITERAL ); currentChart.setSubType( sNewSubType ); currentChart.getTitle( ).getLabel( ).getCaption( ).setValue( CHART_TITLE ); EList axes = ( (Axis) ( (ChartWithAxes) currentChart ).getAxes( ) .get( 0 ) ).getAssociatedAxes( ); for ( int i = 0; i < axes.size( ); i++ ) { if ( sNewSubType.equalsIgnoreCase( "Percent Stacked" ) ) //$NON-NLS-1$ { ( (Axis) axes.get( i ) ).setPercent( true ); } else { ( (Axis) axes.get( i ) ).setPercent( false ); } EList seriesdefinitions = ( (Axis) axes.get( i ) ).getSeriesDefinitions( ); for ( int j = 0; j < seriesdefinitions.size( ); j++ ) { Series series = ( (SeriesDefinition) seriesdefinitions.get( j ) ).getDesignTimeSeries( ); series = getConvertedSeries( series ); if ( ( sNewSubType.equalsIgnoreCase( "Stacked" ) || sNewSubType.equalsIgnoreCase( "Percent Stacked" ) ) ) //$NON-NLS-1$ //$NON-NLS-2$ { series.setStacked( true ); } else { series.setStacked( false ); } ( (SeriesDefinition) seriesdefinitions.get( j ) ).getSeries( ) .clear( ); ( (SeriesDefinition) seriesdefinitions.get( j ) ).getSeries( ) .add( series ); } } } else { return null; } ( (Axis) ( (ChartWithAxes) currentChart ).getAxes( ).get( 0 ) ).setCategoryAxis( true ); } else { // Create a new instance of the correct type and set initial // properties currentChart = ChartWithAxesImpl.create( ); currentChart.setType( TYPE_LITERAL ); currentChart.setSubType( sNewSubType ); ( (ChartWithAxes) currentChart ).setOrientation( newOrientation ); currentChart.setDimension( getDimensionFor( sNewDimension ) ); ( (Axis) ( (ChartWithAxes) currentChart ).getAxes( ).get( 0 ) ).setOrientation( Orientation.HORIZONTAL_LITERAL ); ( (Axis) ( (ChartWithAxes) currentChart ).getAxes( ).get( 0 ) ).setType( AxisType.TEXT_LITERAL ); ( (Axis) ( (ChartWithAxes) currentChart ).getAxes( ).get( 0 ) ).setCategoryAxis( true ); ( (Axis) ( (Axis) ( (ChartWithAxes) currentChart ).getAxes( ) .get( 0 ) ).getAssociatedAxes( ).get( 0 ) ).setOrientation( Orientation.VERTICAL_LITERAL ); ( (Axis) ( (Axis) ( (ChartWithAxes) currentChart ).getAxes( ) .get( 0 ) ).getAssociatedAxes( ).get( 0 ) ).setType( AxisType.LINEAR_LITERAL ); // Copy generic chart properties from the old chart currentChart.setBlock( helperModel.getBlock( ) ); currentChart.setDescription( helperModel.getDescription( ) ); currentChart.setGridColumnCount( helperModel.getGridColumnCount( ) ); currentChart.setSampleData( helperModel.getSampleData( ) ); currentChart.setScript( helperModel.getScript( ) ); currentChart.setSeriesThickness( helperModel.getSeriesThickness( ) ); currentChart.setUnits( helperModel.getUnits( ) ); if ( helperModel.getType( ).equals( PieChart.TYPE_LITERAL ) || helperModel.getType( ).equals( MeterChart.TYPE_LITERAL ) ) { // Clear existing series definitions ( (Axis) ( (ChartWithAxes) currentChart ).getAxes( ).get( 0 ) ).getSeriesDefinitions( ) .clear( ); // Copy base series definitions ( (Axis) ( (ChartWithAxes) currentChart ).getAxes( ).get( 0 ) ).getSeriesDefinitions( ) .add( ( (ChartWithoutAxes) helperModel ).getSeriesDefinitions( ) .get( 0 ) ); // Clear existing series definitions ( (Axis) ( (Axis) ( (ChartWithAxes) currentChart ).getAxes( ) .get( 0 ) ).getAssociatedAxes( ).get( 0 ) ).getSeriesDefinitions( ) .clear( ); // Copy orthogonal series definitions ( (Axis) ( (Axis) ( (ChartWithAxes) currentChart ).getAxes( ) .get( 0 ) ).getAssociatedAxes( ).get( 0 ) ).getSeriesDefinitions( ) .addAll( ( (SeriesDefinition) ( (Axis) ( (ChartWithAxes) currentChart ).getAxes( ) .get( 0 ) ).getSeriesDefinitions( ).get( 0 ) ).getSeriesDefinitions( ) ); // Update the base series Series series = ( (SeriesDefinition) ( (Axis) ( (ChartWithAxes) currentChart ).getAxes( ) .get( 0 ) ).getSeriesDefinitions( ).get( 0 ) ).getDesignTimeSeries( ); series = getConvertedSeries( series ); // Clear existing series ( (SeriesDefinition) ( (Axis) ( (ChartWithAxes) currentChart ).getAxes( ) .get( 0 ) ).getSeriesDefinitions( ).get( 0 ) ).getSeries( ) .clear( ); // Add converted series ( (SeriesDefinition) ( (Axis) ( (ChartWithAxes) currentChart ).getAxes( ) .get( 0 ) ).getSeriesDefinitions( ).get( 0 ) ).getSeries( ) .add( series ); // Update the orthogonal series EList seriesdefinitions = ( (Axis) ( (Axis) ( (ChartWithAxes) currentChart ).getAxes( ) .get( 0 ) ).getAssociatedAxes( ).get( 0 ) ).getSeriesDefinitions( ); for ( int j = 0; j < seriesdefinitions.size( ); j++ ) { series = ( (SeriesDefinition) seriesdefinitions.get( j ) ).getDesignTimeSeries( ); series = getConvertedSeries( series ); if ( ( sNewSubType.equalsIgnoreCase( "Stacked" ) || sNewSubType.equalsIgnoreCase( "Percent Stacked" ) ) ) //$NON-NLS-1$ //$NON-NLS-2$ { series.setStacked( true ); } else { series.setStacked( false ); } // Clear any existing series ( (SeriesDefinition) seriesdefinitions.get( j ) ).getSeries( ) .clear( ); // Add the new series ( (SeriesDefinition) seriesdefinitions.get( j ) ).getSeries( ) .add( series ); } } else { return null; } currentChart.getLegend( ).setItemType( LegendItemType.SERIES_LITERAL ); currentChart.getTitle( ).getLabel( ).getCaption( ).setValue( CHART_TITLE ); } if ( currentChart instanceof ChartWithAxes && !( (ChartWithAxes) currentChart ).getOrientation( ) .equals( newOrientation ) ) { ( (ChartWithAxes) currentChart ).setOrientation( newOrientation ); } if ( !currentChart.getDimension( ) .equals( getDimensionFor( sNewDimension ) ) ) { currentChart.setDimension( getDimensionFor( sNewDimension ) ); } if ( sNewDimension.equals( THREE_DIMENSION_TYPE ) && getDimensionFor( sNewDimension ) != oldDimension ) { ( (ChartWithAxes) currentChart ).setRotation( Rotation3DImpl.create( new Angle3D[]{ Angle3DImpl.create( -20, 45, 0 ) } ) ); ( (ChartWithAxes) currentChart ).setUnitSpacing( 50 ); ( (ChartWithAxes) currentChart ).getPrimaryBaseAxes( )[0].getAncillaryAxes( ) .clear( ); Axis zAxisAncillary = AxisImpl.create( Axis.ANCILLARY_BASE ); zAxisAncillary.setTitlePosition( Position.BELOW_LITERAL ); zAxisAncillary.getTitle( ) .getCaption( ) .setValue( Messages.getString( "ChartWithAxesImpl.Z_Axis.title" ) ); //$NON-NLS-1$ zAxisAncillary.getTitle( ).setVisible( true ); zAxisAncillary.setPrimaryAxis( true ); zAxisAncillary.setLabelPosition( Position.BELOW_LITERAL ); zAxisAncillary.setOrientation( Orientation.HORIZONTAL_LITERAL ); zAxisAncillary.getOrigin( ).setType( IntersectionType.MIN_LITERAL ); zAxisAncillary.getOrigin( ) .setValue( NumberDataElementImpl.create( 0 ) ); zAxisAncillary.getTitle( ).setVisible( false ); zAxisAncillary.setType( AxisType.TEXT_LITERAL ); ( (ChartWithAxes) currentChart ).getPrimaryBaseAxes( )[0].getAncillaryAxes( ) .add( zAxisAncillary ); SeriesDefinition sdZ = SeriesDefinitionImpl.create( ); sdZ.getSeriesPalette( ).update( 0 ); sdZ.getSeries( ).add( SeriesImpl.create( ) ); zAxisAncillary.getSeriesDefinitions( ).add( sdZ ); if ( currentChart.getSampleData( ) .getAncillarySampleData( ) .isEmpty( ) ) { BaseSampleData sdAncillary = DataFactory.eINSTANCE.createBaseSampleData( ); sdAncillary.setDataSetRepresentation( "Series 1" ); //$NON-NLS-1$ currentChart.getSampleData( ) .getAncillarySampleData( ) .add( sdAncillary ); } } return currentChart; }

5230 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/5230/ae5c99c975d28a2277f3b75baa2207ddf1c0d0ae/LineChart.java/clean/chart/org.eclipse.birt.chart.ui.extension/src/org/eclipse/birt/chart/ui/swt/type/LineChart.java

public Context createSubcontext( Name name ) throws NamingException

public Context createSubcontext( String name ) throws NamingException

public Context createSubcontext( Name name ) throws NamingException { /* * Start building the server side attributes to be added directly to * the backend. * * The RDN from name can be a multivalued RDN based on more than one * attribute using the '+' AVA concatenator in a name component. Right * now this code will bomb out because we presume single valued RDNs. * * TODO Add multivalued RDN handling code */ Attributes attributes = new LockableAttributesImpl(); LdapName target = buildTarget( name ); String rdn = name.get( name.size() - 1 ); String rdnAttribute = NamespaceTools.getRdnAttribute( rdn ); String rdnValue = NamespaceTools.getRdnValue( rdn ); /* * TODO Add code within the interceptor service managing operational * attributes the ability to add the target user provided DN to the * attributes before normalization. The result should have ths same * affect as the following line within the interceptor. * * attributes.put( BootstrapSchema.DN_ATTR, target.toString() ); */ attributes.put( rdnAttribute, rdnValue ); attributes.put( JavaLdapSupport.OBJECTCLASS_ATTR, JavaLdapSupport.JCONTAINER_ATTR ); attributes.put( JavaLdapSupport.OBJECTCLASS_ATTR, JavaLdapSupport.TOP_ATTR ); /* * Add the new context to the server which as a side effect adds * operational attributes to the attributes refering instance which * can them be used to initialize a new EveLdapContext. Remember * we need to copy over the controls as well to propagate the complete * environment besides whats in the hashtable for env. */ nexusProxy.add( target.toString(), target, attributes ); EveLdapContext ctx = new EveLdapContext( principal, nexusProxy, env, target ); Control [] controls = ( Control [] ) ( ( EveLdapContext ) this ).getRequestControls().clone(); ctx.setRequestControls( controls ); return ctx; }

17035 /local/tlutelli/issta_data/temp/all_java1context/java/2006_temp/2006/17035/0132d1f6fc999a40038ffa4e9d000e622b4e44d4/EveContext.java/buggy/jndi-provider/src/java/org/apache/eve/jndi/EveContext.java

otherMock.stubs().method("hello").id(priorCall); mock.stubs().method("goodbye").after(otherMock, priorCall);

otherMock.stubs().method("hello").id(priorCall); mock.stubs().method("goodbye").after(otherMock, priorCall);

public void testDetectsUnexpectedOrderOverDifferentMocks() { String otherMockName = "otherMock"; String priorCall = "HELLO-CALL-ID"; Mock otherMock = mock(ExampleInterface.class, otherMockName); otherMock.stubs().method("hello").id(priorCall); mock.stubs().method("goodbye").after(otherMock, priorCall); try { proxy.goodbye(); fail("expected DynamicMockError"); } catch (DynamicMockError ex) { assertTrue("error message should contain id of prior call", ex.getMessage().indexOf(priorCall) >= 0); assertTrue("error message should contain name of mock receiving prior call", ex.getMessage().indexOf(otherMockName) >= 0); } }

57371 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57371/c26c57f3ac4851e6bc9c5df8515ac73f4045eebf/OrderedInvocationsAcceptanceTest.java/buggy/jmock/core/acceptance-tests/atest/jmock/OrderedInvocationsAcceptanceTest.java

return RubyFixnum.zero(runtime);

return RubyFixnum.zero(getRuntime());

public RubyFixnum op_cmp(IRubyObject other) { long millis = getTimeInMillis(); if (other instanceof RubyFloat || other instanceof RubyBignum) { double time = millis / 1000.0; double time_other = ((RubyNumeric) other).getDoubleValue(); if (time > time_other) { return RubyFixnum.one(runtime); } else if (time < time_other) { return RubyFixnum.minus_one(runtime); } else { return RubyFixnum.zero(runtime); } } long millis_other = (other instanceof RubyTime) ? ((RubyTime) other).getTimeInMillis() : RubyNumeric.num2long(other) * 1000; if (millis > millis_other) { return RubyFixnum.one(runtime); } else if (millis < millis_other) { return RubyFixnum.minus_one(runtime); } else { return RubyFixnum.zero(runtime); } }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/870e1da9b41bfdbae259e1fc5f18fc8b76686998/RubyTime.java/clean/src/org/jruby/RubyTime.java

public boolean performFinish() { queryPage.getQueryDialog().okPressed(); final BugzillaRepositoryQuery queryCategory = new BugzillaRepositoryQuery( repository.getUrl(), queryPage.getQueryDialog().getUrl(), queryPage.getQueryDialog().getName(), queryPage.getQueryDialog().getMaxHits(), MylarTaskListPlugin.getTaskListManager().getTaskList()); if (queryPage.getQueryDialog().isCustom()) { queryCategory.setCustomQuery(true); } // else {// queryCategory = new BugzillaCustomRepositoryQuery(// repository.getUrl().toExternalForm(), // queryPage.getQueryDialog().getName(), // queryPage.getQueryDialog().getUrl(), // queryPage.getQueryDialog().getMaxHits());// } MylarTaskListPlugin.getTaskListManager().getTaskList().addQuery(queryCategory); boolean offline = MylarTaskListPlugin.getMylarCorePrefs().getBoolean(TaskListPreferenceConstants.WORK_OFFLINE); if (!offline) { WorkspaceModifyOperation op = new WorkspaceModifyOperation() { protected void execute(IProgressMonitor monitor) throws CoreException { monitor.beginTask("Executing query", 50); try { AbstractRepositoryConnector client = MylarTaskListPlugin.getRepositoryManager().getRepositoryConnector(BugzillaPlugin.REPOSITORY_KIND); client.synchronize(queryCategory, null);// if (TaskListView.getDefault() != null) {// TaskListView.getDefault().getViewer().refresh();// }// queryCategory.refreshBugs(new SubProgressMonitor(monitor, 50)); } finally { monitor.done(); } } }; try { getContainer().run(true, false, op); } catch (Exception e) { MylarStatusHandler.log(e, "There was a problem executing the query refresh"); } }// if (TaskListView.getDefault() != null) {// TaskListView.getDefault().getViewer().refresh();// } return true; }

51989 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/51989/36f9c08d02fadb543a4958543b208eb8fbe9398f/NewBugzillaQueryWizard.java/clean/org.eclipse.mylyn.bugzilla.ui/src/org/eclipse/mylyn/internal/bugzilla/ui/tasklist/NewBugzillaQueryWizard.java

System.err.println("DOM: status URL load - " +

System.err.println(prefix + " :status URL load - " +

public void statusURLLoad(String url, String message, Document doc) { if (debug) System.err.println("DOM: status URL load - " + url.toString() + " (" + message + ")"); }

12376 /local/tlutelli/issta_data/temp/all_java1context/java/2006_temp/2006/12376/d5d632bf9df2e7c37640ec01b53cc4d876888be9/TestDocLoadListener.java/clean/java/dom/tests/src/TestDocLoadListener.java

log(aBrace.getLineNo(), aBrace.getColumnNo(), "'{' should be on a new line.");

log(aBrace.getLineNo(), aBrace.getColumnNo(), "line.new", "{");

private void checkLCurly(int aStartLine, MyCommonAST aBrace, LeftCurlyOption aOption) { verifyWSAroundBegin(aBrace.getLineNo(), aBrace.getColumnNo() + 1, aBrace.getText()); final String braceLine = mLines[aBrace.getLineNo() - 1]; // calculate the previous line length without trailing whitespace. Need // to handle the case where there is no previous line, cause the line // being check is the first line in the file. final int prevLineLen = (aBrace.getLineNo() == 1) ? mConfig.getMaxLineLength() : Utils.lengthMinusTrailingWhitespace( mLines[aBrace.getLineNo() - 2]); // Check for being told to ignore, or have '{}' which is a special case if ((aOption == LeftCurlyOption.IGNORE) || ((braceLine.length() > (aBrace.getColumnNo() + 1)) && (braceLine.charAt(aBrace.getColumnNo() + 1) == '}'))) { // ignore } else if (aOption == LeftCurlyOption.NL) { if (!Utils.whitespaceBefore(aBrace.getColumnNo(), braceLine)) { log(aBrace.getLineNo(), aBrace.getColumnNo(), "'{' should be on a new line."); } } else if (aOption == LeftCurlyOption.EOL) { if (Utils.whitespaceBefore(aBrace.getColumnNo(), braceLine) && ((prevLineLen + 2) <= mConfig.getMaxLineLength())) { log(aBrace.getLineNo(), aBrace.getColumnNo(), "'{' should be on the previous line."); } } else if (aOption == LeftCurlyOption.NLOW) { if (aStartLine == aBrace.getLineNo()) { // all ok as on the same line } else if ((aStartLine + 1) == aBrace.getLineNo()) { if (!Utils.whitespaceBefore(aBrace.getColumnNo(), braceLine)) { log(aBrace.getLineNo(), aBrace.getColumnNo(), "'{' should be on a new line."); } else if ((prevLineLen + 2) <= mConfig.getMaxLineLength()) { log(aBrace.getLineNo(), aBrace.getColumnNo(), "'{' should be on the previous line."); } } else if (!Utils.whitespaceBefore(aBrace.getColumnNo(), braceLine)) { log(aBrace.getLineNo(), aBrace.getColumnNo(), "'{' should be on a new line."); } } }

50482 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50482/513205d86a53fb1b65da8613563fa177bd5f4882/Verifier.java/clean/src/checkstyle/com/puppycrawl/tools/checkstyle/Verifier.java

public void writeUTF(String str) throws IOException { throw new IOException("not required"); }

public void writeUTF(String str) throws IOException { throw new IOException("not required"); }

public void writeUTF(String str) throws IOException { throw new IOException("not required");}

13625 /local/tlutelli/issta_data/temp/all_java1context/java/2006_temp/2006/13625/84d120cc49d42a79bfbc68fe36429395bdef90fd/UnicastRemoteCall.java/buggy/libjava/gnu/java/rmi/server/UnicastRemoteCall.java

return getPresentation().getControl().getBounds();

Rectangle bounds = getClientArea(); if (site.getState() == IStackPresentationSite.STATE_MAXIMIZED) { return bounds; } boolean horizontal = Geometry.isHorizontal(side); int available = Geometry.getDimension(bounds, !horizontal); return Geometry.getExtrudedEdge(bounds, Math.min(FastViewPane.this.size, available), side);

private Rectangle getBounds() { return getPresentation().getControl().getBounds(); }

58148 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/58148/1334a76d3033f5c80020f1a0c5c45fe244eebfad/FastViewPane.java/buggy/bundles/org.eclipse.ui.workbench/Eclipse UI/org/eclipse/ui/internal/FastViewPane.java

ResultSet result = ExecSQL("select typname from pg_type where oid = " + oid); if (((AbstractJdbc1ResultSet)result).getColumnCount() != 1 || ((AbstractJdbc1ResultSet)result).getTupleCount() != 1) throw new PSQLException("postgresql.unexpected"); result.next(); String pgType = result.getString(1);

String pgType; if (oid == 0) { pgType = "opaque"; } else { String sql; if (haveMinimumServerVersion("7.3")) { sql = "SELECT typname FROM pg_catalog.pg_type WHERE oid = " +oid; } else { sql = "SELECT typname FROM pg_type WHERE oid = " +oid; } ResultSet result = ExecSQL(sql); if (((AbstractJdbc1ResultSet)result).getColumnCount() != 1 || ((AbstractJdbc1ResultSet)result).getTupleCount() != 1) { throw new PSQLException("postgresql.unexpected"); } result.next(); pgType = result.getString(1); result.close(); }

public int getSQLType(int oid) throws SQLException { Integer sqlType = (Integer)sqlTypeCache.get(new Integer(oid)); // it's not in the cache, so perform a query, and add the result to the cache if (sqlType == null) { ResultSet result = ExecSQL("select typname from pg_type where oid = " + oid); if (((AbstractJdbc1ResultSet)result).getColumnCount() != 1 || ((AbstractJdbc1ResultSet)result).getTupleCount() != 1) throw new PSQLException("postgresql.unexpected"); result.next(); String pgType = result.getString(1); Integer iOid = new Integer(oid); sqlType = new Integer(getSQLType(result.getString(1))); sqlTypeCache.put(iOid, sqlType); pgTypeCache.put(iOid, pgType); result.close(); } return sqlType.intValue(); }

47293 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/47293/7c553901d7ab010ad1cb5bf44f9ca2fdae83909a/AbstractJdbc1Connection.java/buggy/src/interfaces/jdbc/org/postgresql/jdbc1/AbstractJdbc1Connection.java

e.printStackTrace();

ImViewerAgent.getRegistry().getLogger().error(this, e.getMessage());

private void writeImage(BufferedImage image, String n) { UserNotifier un = ImViewerAgent.getRegistry().getUserNotifier(); n += "."+format; File f = new File(n); try { if (format.equals(TIFFFilter.TIF)) { Encoder encoder = new TIFFEncoder(Factory.createImage(image), new DataOutputStream(new FileOutputStream(f))); WriterImage.saveImage(encoder); } else WriterImage.saveImage(f, image, format); un.notifyInfo("Image Saved", saveMessage); setClosed(true); } catch (Exception e) { e.printStackTrace(); f.delete(); un.notifyError("Save image failure", "Unable to save the image", e); } }

13273 /local/tlutelli/issta_data/temp/all_java1context/java/2006_temp/2006/13273/5aacd98a1cfb2219e218c87eed17b5a0f0e9738a/ImgSaver.java/clean/SRC/org/openmicroscopy/shoola/agents/imviewer/util/saver/ImgSaver.java

depth);}

depth); }

public void parse(boolean NS) throws EncodingException, EOFException, EntityException, ParseException { // define internal variables ns = NS; int temp_offset = 0, length1 = 0, length2 = 0, increment = 1; int depth = -1, attr_count = 0, ch = 0, ch_temp = 0; int prev_ch = 0, prev2_ch = 0, parser_state = STATE_DOC_START; //boolean has_amp = false; boolean is_ns = false; encoding = FORMAT_UTF8; boolean main_loop = true, hasDTD = false, hasDecl = false, docEnd = false, firstLT = true; char char_temp; //holds the ' or " indicating start of attr val boolean must_utf_8 = false; boolean BOM_detected = false; //long[] tag_stack = new long[256]; //long[] attr_name_array = new long[512]; // 512 attributes limit //ASCII UTF-8 UTF-16 UTF-16BE UTF-16LE ISO-8859-1 // //int[] scratch_buffer = new int[10]; // first check first several bytes BOM to determine if encoding is UTF16 if (XMLDoc[offset] == -2) { increment = 2; if (XMLDoc[offset + 1] == -1) { offset += 2; encoding = FORMAT_UTF_16BE; BOM_detected = true; r = new UTF16BEReader(); //increment = 2; } else throw new EncodingException("Unknown Character encoding: not UTF-16LE"); } else if (XMLDoc[offset] == -1) { increment = 2; if (XMLDoc[offset + 1] == -2) { offset += 2; //increment = 2; encoding = FORMAT_UTF_16LE; BOM_detected = true; r = new UTF16LEReader(); } else throw new EncodingException("Unknown Character encoding: not UTF-16LE"); } else if (XMLDoc[offset] == -17){ if (XMLDoc[offset+1] == -69 && XMLDoc[offset+2]==-65){ offset +=3; must_utf_8= true; } else throw new EncodingException("Unknown Character encoding: not UTF-8"); } else if (XMLDoc[offset]==0){ if (XMLDoc[offset+1] == 0x3c && XMLDoc[offset+2] == 0 && XMLDoc[offset+3] == 0x3f){ encoding = FORMAT_UTF_16BE; increment = 2; r = new UTF16BEReader(); } else throw new EncodingException("Unknown Character encoding: not UTF-16BE"); } else if (XMLDoc[offset]==0x3c){ if (XMLDoc[offset+1] == 0 && XMLDoc[offset+2] == 0x3f && XMLDoc[offset+3] == 0){ increment = 2; encoding = FORMAT_UTF_16LE; r = new UTF16LEReader(); } } // check for max file size exception if (encoding < FORMAT_UTF_16BE) { if ((offset + docLen) >= 1L << 30) throw new ParseException("Other error: file size too large "); } else { if ((offset - 2 + docLen) >= 1L << 31) throw new ParseException("Other error: file size too large "); } // enter the main finite state machine try { while (main_loop) { switch (parser_state) { case STATE_DOC_START : if (r.getChar() == '<') { temp_offset = offset; // xml decl has to be right after the start of the document if (r.skipChar('?') && (r.skipChar('x') || r.skipChar('X')) && (r.skipChar('m') || r.skipChar('M')) && (r.skipChar('l') || r.skipChar('L'))) { if (r.skipChar(' ') || r.skipChar('\t') || r.skipChar('\n') || r.skipChar('\r')) { ch = getCharAfterS(); temp_offset = offset; parser_state = STATE_DEC_ATTR_NAME; break; } else if (r.skipChar('?')) throw new ParseException( "Error in XML decl: premature ending" + formatLineNumber()); } offset = temp_offset; parser_state = STATE_LT_SEEN; break; } throw new ParseException( "Other Error: XML not starting properly" + formatLineNumber()); case STATE_DOC_END : docEnd = true; ch = getCharAfterS(); // eof exception should be thrown here for premature ending if (ch == '<') { if (r.skipChar('?')) { // processing instruction after end tag of root element temp_offset = offset; parser_state = STATE_END_PI; break; } else if ( r.skipChar('!') && r.skipChar('-') && r.skipChar('-')) { // comments allowed after the end tag of the root element temp_offset = offset; parser_state = STATE_END_COMMENT; break; } } throw new ParseException( "Other Error: XML not terminated properly" + formatLineNumber()); case STATE_LT_SEEN : //if (depth < -1) // throw new ParseException("Other Errors: Invalid depth"); temp_offset = offset; ch = r.getChar(); if (XMLChar.isNameStartChar(ch)) { //temp_offset = offset; //length1++; depth++; //if (ch == ':') // length2 = 0; parser_state = STATE_START_TAG; } else { switch (ch) { case '/' : parser_state = STATE_END_TAG; break; case '?' : temp_offset = offset; ch = r.getChar(); if (XMLChar.isNameStartChar(ch)) { //temp_offset = offset; if ((ch == 'x' || ch == 'X') && (r.skipChar('m') || r.skipChar('M')) && (r.skipChar('l') || r.skipChar('L'))) { ch = r.getChar(); if (ch == '?' || XMLChar.isSpaceChar(ch)) throw new ParseException( "Error in PI: [xX][mM][lL] not a valid PI targetname" + formatLineNumber()); offset = getPrevOffset(); } parser_state = STATE_PI_TAG; break; } throw new ParseException( "Other Error: First char after <? invalid" + formatLineNumber()); case '!' : // three possibility (comment, CDATA, DOCTYPE) ch = r.getChar(); switch (ch) { case '-' : if (r.skipChar('-')) { temp_offset = offset; parser_state = STATE_COMMENT; break; } else throw new ParseException( "Error in comment: Invalid char sequence to start a comment" + formatLineNumber()); case '[' : if (r.skipChar('C') && r.skipChar('D') && r.skipChar('A') && r.skipChar('T') && r.skipChar('A') && r.skipChar('[') && (depth != -1)) { temp_offset = offset; parser_state = STATE_CDATA; break; } else { if (depth == -1) throw new ParseException( "Error in CDATA: Wrong place for CDATA" + formatLineNumber()); throw new ParseException( "Error in CDATA: Invalid char sequence for CDATA" + formatLineNumber()); } case 'D' : if (r.skipChar('O') && r.skipChar('C') && r.skipChar('T') && r.skipChar('Y') && r.skipChar('P') && r.skipChar('E') && (depth == -1) && !hasDTD) { hasDTD = true; temp_offset = offset; parser_state = STATE_DOCTYPE; break; } else { if (hasDTD == true) throw new ParseException( "Error for DOCTYPE: Only DOCTYPE allowed" + formatLineNumber()); if (depth != -1) throw new ParseException( "Error for DOCTYPE: DTD at wrong place" + formatLineNumber()); throw new ParseException( "Error for DOCTYPE: Invalid char sequence for DOCTYPE" + formatLineNumber()); } default : throw new ParseException( "Other Error: Unrecognized char after <!" + formatLineNumber()); } break; default : throw new ParseException( "Other Error: Invalid char after <" + formatLineNumber()); } } break; case STATE_START_TAG : //name space is handled by while (true) { ch = r.getChar(); if (XMLChar.isNameChar(ch)) { if (ch == ':') { length2 = offset - temp_offset - increment; } } else break; } length1 = offset - temp_offset - increment; if (depth > MAX_DEPTH) { throw new ParseException( "Other Error: Depth exceeds MAX_DEPTH" + formatLineNumber()); } //writeVTD(offset, TOKEN_STARTING_TAG, length2:length1, depth) long x = ((long) length1 << 32) + temp_offset; tag_stack[depth] = x; // System.out.println( // " " + (temp_offset) + " " + length2 + ":" + length1 + " startingTag " + depth); if (depth > VTDDepth) VTDDepth = depth; if (encoding < FORMAT_UTF_16BE){ if (length2>MAX_PREFIX_LENGTH || length1 > MAX_QNAME_LENGTH) throw new ParseException( "Token Length Error: Starting tag prefix or qname length too long" + formatLineNumber()); writeVTD( (temp_offset), (length2 << 11) | length1, TOKEN_STARTING_TAG, depth);} else{ if (length2>(MAX_PREFIX_LENGTH<<1) || (length1 > MAX_QNAME_LENGTH<<1)) throw new ParseException( "Token Length Error: Starting tag prefix or qname length too long" + formatLineNumber()); writeVTD( (temp_offset) >> 1, (length2 << 10) | (length1 >> 1), TOKEN_STARTING_TAG, depth); } //offset += length1; length2 = 0; if (XMLChar.isSpaceChar(ch)) { ch = getCharAfterS(); if (XMLChar.isNameStartChar(ch)) { // seen an attribute here temp_offset = getPrevOffset(); parser_state = STATE_ATTR_NAME; break; } } if (ch == '/') { depth--; ch = r.getChar(); } if (ch == '>') { if (depth != -1) { temp_offset = offset; ch = getCharAfterSe(); // consume WSs if (ch == '<') { parser_state = STATE_LT_SEEN; if (r.skipChar('/')) { length1 = offset - temp_offset - 2 * increment; if (length1 > 0) { if (encoding < FORMAT_UTF_16BE) writeVTD( (temp_offset), length1, TOKEN_CHARACTER_DATA, depth); else writeVTD( (temp_offset) >> 1, (length1 >> 1), TOKEN_CHARACTER_DATA, depth); //offset += length1; } parser_state = STATE_END_TAG; break; } } else if (XMLChar.isContentChar(ch)) { //temp_offset = offset; parser_state = STATE_TEXT; } else if (ch == '&') { //has_amp = true; //temp_offset = offset; entityIdentifier(); parser_state = STATE_TEXT; } else throw new ParseException( "Error in text content: Invalid char" + formatLineNumber()); } else { parser_state = STATE_DOC_END; } break; } throw new ParseException( "Starting tag Error: Invalid char in starting tag" + formatLineNumber()); case STATE_END_TAG : temp_offset = offset; while (true) { ch = r.getChar(); if (!XMLChar.isNameChar(ch)) { break; } } length1 = offset - temp_offset - increment; int sos = (int) tag_stack[depth]; int sl = (int) (tag_stack[depth] >> 32); if (sl == length1) { for (int i = 0; i < length1; i++) { if (XMLDoc[sos + i] != XMLDoc[temp_offset + i]) throw new ParseException( "Ending tag error: Start/ending tag mismatch" + formatLineNumber()); // System.out.println( // " " + (char) XMLDoc[sos + i] + "<==> " + (char) XMLDoc[temp_offset + i]); } } else throw new ParseException( "Ending tag error: Start/ending tag mismatch, length different" + formatLineNumber()); //System.out.println(" " + temp_offset + " " + length1 + " ending tag " + depth); //writeVTD(temp_offset, length1, TOKEN_ENDING_TAG, depth); depth--; if (XMLChar.isSpaceChar(ch)) { ch = getCharAfterS(); } if (ch == '>') { if (depth != -1) { temp_offset = offset; ch = getCharAfterS(); if (ch == '<') parser_state = STATE_LT_SEEN; else if (XMLChar.isContentChar(ch)) { parser_state = STATE_TEXT; } else if (ch == '&') { //has_amp = true; entityIdentifier(); parser_state = STATE_TEXT; } else throw new ParseException( "Other Error: Invalid char in xml" + formatLineNumber()); } else parser_state = STATE_DOC_END; break; } else throw new ParseException( "Other Error: Invalid char in ending tag" + formatLineNumber()); case STATE_UNRECORDED_TEXT : break; case STATE_PI_TAG : while (true) { ch = r.getChar(); if (!XMLChar.isNameChar(ch)) break; } length1 = offset - temp_offset - increment; /*System.out.println( ((char) XMLDoc[temp_offset]) + " " + (temp_offset) + " " + length1 + " PI Target " + depth); */ if (encoding < FORMAT_UTF_16BE){ if (length1 > MAX_TOKEN_LENGTH) throw new ParseException("Token Length Error:" +" PI name too long (>0xfffff)" + formatLineNumber()); writeVTD( (temp_offset), length1, TOKEN_PI_NAME, depth); } else{ if (length1 > (MAX_TOKEN_LENGTH<<1)) throw new ParseException("Token Length Error:" +" PI name too long (>0xfffff)" + formatLineNumber()); writeVTD( (temp_offset) >> 1, (length1 >> 1), TOKEN_PI_NAME, depth); } //length1 = 0; temp_offset = offset; if (XMLChar.isSpaceChar(ch)) { ch = r.getChar(); } if (ch == '?') { if (r.skipChar('>')) { temp_offset = offset; ch = getCharAfterSe(); if (ch == '<') { parser_state = STATE_LT_SEEN; } else if (XMLChar.isContentChar(ch)) { parser_state = STATE_TEXT; } else if (ch == '&') { //has_amp = true; entityIdentifier(); parser_state = STATE_TEXT; } else throw new ParseException( "Error in text content: Invalid char" + formatLineNumber()); break; } else throw new ParseException( "Error in PI: invalid termination sequence" + formatLineNumber()); } parser_state = STATE_PI_VAL; break; //throw new ParseException("Error in PI: Invalid char"); case STATE_PI_VAL : //temp_offset = offset; while (true) { if (XMLChar.isValidChar(ch)) { //System.out.println(""+(char)ch); if (ch == '?') if (r.skipChar('>')) { break; } else throw new ParseException( "Error in PI: invalid termination sequence for PI" + formatLineNumber()); } else throw new ParseException( "Errors in PI: Invalid char in PI val" + formatLineNumber()); ch = r.getChar(); } length1 = offset - temp_offset - 2 * increment; /*System.out.println( ((char) XMLDoc[temp_offset]) + " " + (temp_offset) + " " + length1 + " PI val " + depth);*/ if (encoding < FORMAT_UTF_16BE){ if (length1 > MAX_TOKEN_LENGTH) throw new ParseException("Token Length Error:" +" PI val too long (>0xfffff)" + formatLineNumber()); writeVTD(temp_offset, length1, TOKEN_PI_VAL, depth); } else{ if (length1 > (MAX_TOKEN_LENGTH<<1)) throw new ParseException("Token Length Error:" +" PI val too long (>0xfffff)" + formatLineNumber()); writeVTD( temp_offset >> 1, length1 >> 1, TOKEN_PI_VAL, depth); } //length1 = 0; temp_offset = offset; ch = getCharAfterSe(); if (ch == '<') { parser_state = STATE_LT_SEEN; } else if (XMLChar.isContentChar(ch)) { //temp_offset = offset; parser_state = STATE_TEXT; } else if (ch == '&') { //has_amp = true; //temp_offset = offset; entityIdentifier(); parser_state = STATE_TEXT; } else throw new ParseException( "Error in text content: Invalid char" + formatLineNumber()); break; case STATE_DEC_ATTR_NAME : if (ch == 'v' && r.skipChar('e') && r.skipChar('r') && r.skipChar('s') && r.skipChar('i') && r.skipChar('o') && r.skipChar('n')) { ch = getCharAfterS(); if (ch == '=') { /*System.out.println( " " + (temp_offset - 1) + " " + 7 + " dec attr name version " + depth);*/ if (encoding < FORMAT_UTF_16BE) writeVTD( temp_offset - 1, 7, TOKEN_DEC_ATTR_NAME, depth); else writeVTD( (temp_offset - 2) >> 1, 7, TOKEN_DEC_ATTR_NAME, depth); } else throw new ParseException( "XML decl error: Invalid char" + formatLineNumber()); } else throw new ParseException( "XML decl error: should be version" + formatLineNumber()); ch_temp = getCharAfterS(); if (ch_temp != '\'' && ch_temp != '"') throw new ParseException( "XML decl error: Invalid char to start attr name" + formatLineNumber()); temp_offset = offset; // support 1.0 or 1.1 if (r.skipChar('1') && r.skipChar('.') && (r.skipChar('0') || r.skipChar('1'))) { /*System.out.println( " " + temp_offset + " " + 3 + " dec attr val (version)" + depth);*/ if (encoding < FORMAT_UTF_16BE) writeVTD( temp_offset, 3, TOKEN_DEC_ATTR_VAL, depth); else writeVTD( temp_offset >> 1, 3, TOKEN_DEC_ATTR_VAL, depth); } else throw new ParseException( "XML decl error: Invalid version(other than 1.0 or 1.1) detected" + formatLineNumber()); if (!r.skipChar(ch_temp)) throw new ParseException( "XML decl error: version not terminated properly" + formatLineNumber()); ch = r.getChar(); //? space or e if (XMLChar.isSpaceChar(ch)) { ch = getCharAfterS(); temp_offset = offset - increment; if (ch == 'e') { if (r.skipChar('n') && r.skipChar('c') && r.skipChar('o') && r.skipChar('d') && r.skipChar('i') && r.skipChar('n') && r.skipChar('g')) { ch = r.getChar(); if (XMLChar.isSpaceChar(ch)) ch = getCharAfterS(); if (ch == '=') { /*System.out.println( " " + (temp_offset) + " " + 8 + " dec attr name (encoding) " + depth);*/ if (encoding < FORMAT_UTF_16BE) writeVTD( temp_offset, 8, TOKEN_DEC_ATTR_NAME, depth); else writeVTD( temp_offset >> 1, 8, TOKEN_DEC_ATTR_NAME, depth); } else throw new ParseException( "XML decl error: Invalid char" + formatLineNumber()); ch_temp = getCharAfterS(); if (ch_temp != '"' && ch_temp != '\'') throw new ParseException( "XML decl error: Invalid char to start attr name" + formatLineNumber()); temp_offset = offset; ch = r.getChar(); switch (ch) { case 'a' : case 'A' : if ((r.skipChar('s') || r.skipChar('S')) && (r.skipChar('c') || r.skipChar('C')) && (r.skipChar('i') || r.skipChar('I')) && (r.skipChar('i') || r.skipChar('I')) && r.skipChar(ch_temp)) { if (encoding != FORMAT_UTF_16LE && encoding != FORMAT_UTF_16BE) { if (must_utf_8) throw new EncodingException("Can't switch from UTF-8" + formatLineNumber()); encoding = FORMAT_ASCII; r = new ASCIIReader(); /*System.out.println( " " + (temp_offset) + " " + 5 + " dec attr val (encoding) " + depth);*/ if (encoding < FORMAT_UTF_16BE) writeVTD( temp_offset, 5, TOKEN_DEC_ATTR_VAL, depth); else writeVTD( temp_offset >> 1, 5, TOKEN_DEC_ATTR_VAL, depth); break; } else throw new ParseException( "XML decl error: Can't switch encoding to ASCII" + formatLineNumber()); } throw new ParseException( "XML decl error: Invalid Encoding" + formatLineNumber()); case 'i' : case 'I' : if ((r.skipChar('s') || r.skipChar('S')) && (r.skipChar('o') || r.skipChar('O')) && r.skipChar('-') && r.skipChar('8') && r.skipChar('8') && r.skipChar('5') && r.skipChar('9') && r.skipChar('-') && r.skipChar('1') && r.skipChar(ch_temp)) { if (encoding != FORMAT_UTF_16LE && encoding != FORMAT_UTF_16BE) { if (must_utf_8) throw new EncodingException("Can't switch from UTF-8" + formatLineNumber()); encoding = FORMAT_ISO_8859; r = new ISO8859Reader(); /*System.out.println( " " + (temp_offset) + " " + 10 + " dec attr val (encoding) " + depth);*/ if (encoding < FORMAT_UTF_16BE) writeVTD( temp_offset, 10, TOKEN_DEC_ATTR_VAL, depth); else writeVTD( temp_offset >> 1, 10, TOKEN_DEC_ATTR_VAL, depth); break; } else throw new ParseException( "XML decl error: Can't switch encoding to ISO-8859" + formatLineNumber()); } throw new ParseException( "XML decl error: Invalid Encoding" + formatLineNumber()); case 'u' : case 'U' : if ((r.skipChar('s') || r.skipChar('S'))) if (r.skipChar('-') && (r.skipChar('a') || r.skipChar('A')) && (r.skipChar('s') || r.skipChar('S')) && (r.skipChar('c') || r.skipChar('C')) && (r.skipChar('i') || r.skipChar('I')) && (r.skipChar('i') || r.skipChar('I')) && r.skipChar(ch_temp)) { if (encoding != FORMAT_UTF_16LE && encoding != FORMAT_UTF_16BE) { if (must_utf_8) throw new EncodingException("Can't switch from UTF-8" + formatLineNumber()); encoding = FORMAT_ASCII; r = new ASCIIReader(); //System.out.println( // " " + (temp_offset) + " " + 5 + " dec attr val (encoding) " + depth); if (encoding < FORMAT_UTF_16BE) writeVTD( temp_offset, 5, TOKEN_DEC_ATTR_VAL, depth); else writeVTD( temp_offset >> 1, 5, TOKEN_DEC_ATTR_VAL, depth); break; } else throw new ParseException( "XML decl error: Can't switch encoding to US-ASCII" + formatLineNumber()); } else throw new ParseException( "XML decl error: Invalid Encoding" + formatLineNumber()); if ((r.skipChar('t') || r.skipChar('T')) && (r.skipChar('f') || r.skipChar('F')) && r.skipChar('-')) { if (r.skipChar('8') && r.skipChar(ch_temp)) { if (encoding != FORMAT_UTF_16LE && encoding != FORMAT_UTF_16BE) { //encoding = FORMAT_UTF8; /*System.out.println( " " + (temp_offset) + " " + 5 + " dec attr val (encoding) " + depth);*/ if (encoding < FORMAT_UTF_16BE) writeVTD( temp_offset, 5, TOKEN_DEC_ATTR_VAL, depth); else writeVTD( temp_offset >> 1, 5, TOKEN_DEC_ATTR_VAL, depth); break; } else throw new ParseException( "XML decl error: Can't switch encoding to UTF-8" + formatLineNumber()); } if (r.skipChar('1') && r.skipChar('6')) { if (r.skipChar(ch_temp)) { if (encoding == FORMAT_UTF_16LE || encoding == FORMAT_UTF_16BE) { if (!BOM_detected) throw new EncodingException("BOM not detected for UTF-16" + formatLineNumber()); /*System.out.println( " " + (temp_offset) + " " + 6 + " dec attr val (encoding) " + depth);*/ if (encoding < FORMAT_UTF_16BE) writeVTD( temp_offset, 6, TOKEN_DEC_ATTR_VAL, depth); else writeVTD( temp_offset >> 1, 6, TOKEN_DEC_ATTR_VAL, depth); break; } throw new ParseException( "XML decl error: Can't switch encoding to UTF-16" + formatLineNumber()); } else if ( (r.skipChar('l') || r.skipChar('L')) && (r.skipChar('e') || r.skipChar( 'E')) && r.skipChar( ch_temp)) { if (encoding == FORMAT_UTF_16LE) { /*System.out.println( " " + (temp_offset) + " " + 7 + " dec attr val (encoding) " + depth);*/ if (encoding < FORMAT_UTF_16BE) writeVTD( temp_offset, 7, TOKEN_DEC_ATTR_VAL, depth); else writeVTD( temp_offset >> 1, 7, TOKEN_DEC_ATTR_VAL, depth); break; } throw new ParseException( "XML del error: Can't switch encoding to UTF-16LE" + formatLineNumber()); } else if ( (r.skipChar('b') || r.skipChar('B')) && (r.skipChar('e') || r.skipChar( 'E')) && r.skipChar( ch_temp)) { if (encoding == FORMAT_UTF_16BE) { /*System.out.println( " " + (temp_offset) + " " + 7 + " dec attr val (encoding) " + depth);*/ if (encoding < FORMAT_UTF_16BE) writeVTD( temp_offset, 7, TOKEN_DEC_ATTR_VAL, depth); else writeVTD( temp_offset >> 1, 7, TOKEN_DEC_ATTR_VAL, depth); break; } throw new ParseException( "XML del error: Can't swtich encoding to UTF-16BE" + formatLineNumber()); } throw new ParseException( "XML decl error: Invalid encoding" + formatLineNumber()); } } default : throw new ParseException( "XML decl Error: invalid encoding" + formatLineNumber()); } ch = r.getChar(); if (XMLChar.isSpaceChar(ch)) ch = getCharAfterS(); temp_offset = offset - increment; } else throw new ParseException( "XML decl Error: Invalid char" + formatLineNumber()); } if (ch == 's') { if (r.skipChar('t') && r.skipChar('a') && r.skipChar('n') && r.skipChar('d') && r.skipChar('a') && r.skipChar('l') && r.skipChar('o') && r.skipChar('n') && r.skipChar('e')) { ch = getCharAfterS(); if (ch != '=') throw new ParseException( "XML decl error: Invalid char" + formatLineNumber()); /*System.out.println( " " + temp_offset + " " + 3 + " dec attr name (standalone) " + depth);*/ if (encoding < FORMAT_UTF_16BE) writeVTD( temp_offset, 10, TOKEN_DEC_ATTR_NAME, depth); else writeVTD( temp_offset >> 1, 10, TOKEN_DEC_ATTR_NAME, depth); ch_temp = getCharAfterS(); temp_offset = offset; if (ch_temp != '"' && ch_temp != '\'') throw new ParseException( "XML decl error: Invalid char to start attr name" + formatLineNumber()); ch = r.getChar(); if (ch == 'y') { if (r.skipChar('e') && r.skipChar('s') && r.skipChar(ch_temp)) { /*System.out.println( " " + (temp_offset) + " " + 3 + " dec attr val (standalone) " + depth);*/ if (encoding < FORMAT_UTF_16BE) writeVTD( temp_offset, 3, TOKEN_DEC_ATTR_VAL, depth); else writeVTD( temp_offset >> 1, 3, TOKEN_DEC_ATTR_VAL, depth); } else throw new ParseException( "XML decl error: invalid val for standalone" + formatLineNumber()); } else if (ch == 'n') { if (r.skipChar('o') && r.skipChar(ch_temp)) { /*System.out.println( " " + (temp_offset) + " " + 2 + " dec attr val (standalone)" + depth);*/ if (encoding < FORMAT_UTF_16BE) writeVTD( temp_offset, 2, TOKEN_DEC_ATTR_VAL, depth); else writeVTD( temp_offset >> 1, 2, TOKEN_DEC_ATTR_VAL, depth); } else throw new ParseException( "XML decl error: invalid val for standalone" + formatLineNumber()); } else throw new ParseException( "XML decl error: invalid val for standalone" + formatLineNumber()); } else throw new ParseException( "XML decl error" + formatLineNumber()); ch = r.getChar(); if (XMLChar.isSpaceChar(ch)) ch = getCharAfterS(); } } if (ch == '?' && r.skipChar('>')) { temp_offset = offset; ch = getCharAfterS(); if (ch == '<') { parser_state = STATE_LT_SEEN; } else throw new ParseException( "Other Error: Invalid Char in XML" + formatLineNumber()); } else throw new ParseException( "XML decl Error: Invalid termination sequence" + formatLineNumber()); break; case STATE_COMMENT : while (true) { ch = r.getChar(); if (XMLChar.isValidChar(ch)) { if (ch == '-' && r.skipChar('-')) { length1 = offset - temp_offset - 2 * increment; break; } } else throw new ParseException( "Error in comment: Invalid Char" + formatLineNumber()); } if (r.getChar() == '>') { //System.out.println(" " + (temp_offset) + " " + length1 + " comment " + depth); if (encoding < FORMAT_UTF_16BE) writeVTD( temp_offset, length1, TOKEN_COMMENT, depth); else writeVTD( temp_offset >> 1, length1 >> 1, TOKEN_COMMENT, depth); //length1 = 0; temp_offset = offset; ch = getCharAfterSe(); if (ch == '<') { parser_state = STATE_LT_SEEN; } else if (XMLChar.isContentChar(ch)) { //temp_offset = offset; parser_state = STATE_TEXT; } else if (ch == '&') { //has_amp = true; //temp_offset = offset; entityIdentifier(); parser_state = STATE_TEXT; } else throw new ParseException( "Error in text content: Invalid char" + formatLineNumber()); break; } else throw new ParseException( "Error in comment: Invalid terminating sequence" + formatLineNumber()); case STATE_CDATA : while (true) { ch = r.getChar(); if (XMLChar.isValidChar(ch)) { if (ch == ']' && r.skipChar(']')) { while (r.skipChar(']')); if (r.skipChar('>')) { break; } else throw new ParseException( "Error in CDATA: Invalid termination sequence" + formatLineNumber()); } } else throw new ParseException( "Error in CDATA: Invalid Char" + formatLineNumber()); } length1 = offset - temp_offset - 3 * increment; if (encoding < FORMAT_UTF_16BE){ writeVTD( temp_offset, length1, TOKEN_CDATA_VAL, depth); } else { writeVTD( temp_offset >> 1, length1 >> 1, TOKEN_CDATA_VAL, depth); } //System.out.println(" " + (temp_offset) + " " + length1 + " CDATA " + depth); ch = getCharAfterSe(); if (ch == '<') { parser_state = STATE_LT_SEEN; } else if (XMLChar.isContentChar(ch)) { temp_offset = offset; parser_state = STATE_TEXT; } else if (ch == '&') { //has_amp = true; temp_offset = offset; entityIdentifier(); parser_state = STATE_TEXT; //temp_offset = offset; } else throw new ParseException("Other Error: Invalid char in xml"); break; case STATE_DOCTYPE : int z = 1; while (true) { ch = r.getChar(); if (XMLChar.isValidChar(ch)) { if (ch == '>') z--; else if (ch == '<') z++; if (z == 0) break; } else throw new ParseException( "Error in DOCTYPE: Invalid char" + formatLineNumber()); } length1 = offset - temp_offset - increment; /*System.out.println( " " + (temp_offset) + " " + length1 + " DOCTYPE val " + depth);*/ if (encoding < FORMAT_UTF_16BE){ if (length1 > MAX_TOKEN_LENGTH) throw new ParseException("Token Length Error:" +" DTD val too long (>0xfffff)" + formatLineNumber()); writeVTD( temp_offset, length1, TOKEN_DTD_VAL, depth); } else{ if (length1 > (MAX_TOKEN_LENGTH<<1)) throw new ParseException("Token Length Error:" +" DTD val too long (>0xfffff)" + formatLineNumber()); writeVTD( temp_offset >> 1, length1 >> 1, TOKEN_DTD_VAL, depth); } ch = getCharAfterS(); if (ch == '<') { parser_state = STATE_LT_SEEN; } else throw new ParseException( "Other Error: Invalid char in xml" + formatLineNumber()); break; case STATE_TEXT : if (depth == -1) throw new ParseException( "Error in text content: Char data at the wrong place" + formatLineNumber()); while (true) { ch = r.getChar(); if (XMLChar.isContentChar(ch)) { } else if (ch == '&') { //has_amp = true; if (!XMLChar.isValidChar(entityIdentifier())) throw new ParseException( "Error in text content: Invalid char in text content " + formatLineNumber()); //parser_state = STATE_TEXT; } else if (ch == '<') { break; } else if (ch == ']') { if (r.skipChar(']')) { while (r.skipChar(']')) { } if (r.skipChar('>')) throw new ParseException( "Error in text content: ]]> in text content" + formatLineNumber()); } } else throw new ParseException( "Error in text content: Invalid char in text content " + formatLineNumber()); } length1 = offset - increment - temp_offset; if (encoding < FORMAT_UTF_16BE) writeVTD( temp_offset, length1, TOKEN_CHARACTER_DATA, depth); else writeVTD( temp_offset >> 1, length1 >> 1, TOKEN_CHARACTER_DATA, depth); //has_amp = true; parser_state = STATE_LT_SEEN; break; case STATE_ATTR_NAME : if (ch == 'x') { if (r.skipChar('m') && r.skipChar('l') && r.skipChar('n') && r.skipChar('s')) { ch = r.getChar(); if (ch == '=' || XMLChar.isSpaceChar(ch) || ch == ':') { is_ns = true; //break; } } } while (true) { if (XMLChar.isNameChar(ch)) { if (ch == ':') { length2 = offset - temp_offset - increment; } ch = r.getChar(); } else break; } length1 = getPrevOffset() - temp_offset; // check for uniqueness here boolean unique = true; boolean unequal; for (int i = 0; i < attr_count; i++) { unequal = false; int prevLen = (int) attr_name_array[i]; if (length1 == prevLen) { int prevOffset = (int) (attr_name_array[i] >> 32); for (int j = 0; j < prevLen; j++) { if (XMLDoc[prevOffset + j] != XMLDoc[temp_offset + j]) { unequal = true; break; } } } else unequal = true; unique = unique && unequal; } if (!unique && attr_count != 0) throw new ParseException( "Error in attr: Attr name not unique" + formatLineNumber()); unique = true; if (attr_count < attr_name_array.length) { //System.out.println("attr_count is "+ attr_count); //System.out.println("attr_name_array.length is " +attr_name_array.length); attr_name_array[attr_count] = ((long) (temp_offset) << 32) + length1; attr_count++; } else // grow the attr_name_array by 16 { long[] temp_array = attr_name_array; System.out.println( "size increase from " + temp_array.length + " to " + (attr_count + 16)); attr_name_array = new long[attr_count + ATTR_NAME_ARRAY_SIZE]; for (int i = 0; i < attr_count; i++) { attr_name_array[i] = temp_array[i]; } attr_name_array[attr_count] = ((long) (temp_offset) << 32) + length1; attr_count++; } // after checking, write VTD if (is_ns) { if (encoding < FORMAT_UTF_16BE){ if (length2>MAX_PREFIX_LENGTH || length1 > MAX_QNAME_LENGTH) throw new ParseException( "Token Length Error: Attr ns prefix or qname length too long" + formatLineNumber()); writeVTD( temp_offset, (length2 << 11) | length1, TOKEN_ATTR_NS, depth); } else{ if (length2>(MAX_PREFIX_LENGTH << 1) || length1 > (MAX_QNAME_LENGTH <<1)) throw new ParseException( "Token Length Error: Attr ns prefix or qname length too long" + formatLineNumber()); writeVTD( temp_offset >> 1, (length2 << 10) | (length1 >> 1), TOKEN_ATTR_NS, depth); } is_ns = false; } else { if (encoding < FORMAT_UTF_16BE){ if (length2>MAX_PREFIX_LENGTH || length1 > MAX_QNAME_LENGTH) throw new ParseException( "Token Length Error: attr name prefix or qname length too long" + formatLineNumber()); writeVTD( temp_offset, (length2 << 11) | length1, TOKEN_ATTR_NAME, depth); } else{ if (length2>(MAX_PREFIX_LENGTH<<1) || length1 > (MAX_QNAME_LENGTH<<1)) throw new ParseException( "Token Length Error: Attr name prefix or qname length too long" + formatLineNumber()); writeVTD( temp_offset >> 1, (length2 << 10) | (length1 >> 1), TOKEN_ATTR_NAME, depth); } } /*System.out.println( " " + temp_offset + " " + length2 + ":" + length1 + " attr name " + depth);*/ length2 = 0; if (XMLChar.isSpaceChar(ch)) { ch = getCharAfterS(); } if (ch != '=') throw new ParseException( "Error in attr: invalid char" + formatLineNumber()); ch_temp = getCharAfterS(); if (ch_temp != '"' && ch_temp != '\'') throw new ParseException( "Error in attr: invalid char (should be ' or \" )" + formatLineNumber()); temp_offset = offset; parser_state = STATE_ATTR_VAL; break; case STATE_ATTR_VAL : while (true) { ch = r.getChar(); if (XMLChar.isValidChar(ch) && ch != '<') { if (ch == ch_temp) break; if (ch == '&') { // as in vtd spec, we mark attr val with entities if (!XMLChar .isValidChar(entityIdentifier())) { throw new ParseException( "Error in attr: Invalid XML char" + formatLineNumber()); } } } else throw new ParseException( "Error in attr: Invalid XML char" + formatLineNumber()); } length1 = offset - temp_offset - increment; if (encoding < FORMAT_UTF_16BE){ if (length1 > MAX_TOKEN_LENGTH) throw new ParseException("Token Length Error:" +" Attr val too long (>0xfffff)" + formatLineNumber()); writeVTD( temp_offset, length1, TOKEN_ATTR_VAL, depth); } else{ if (length1 > MAX_TOKEN_LENGTH <<1) throw new ParseException("Token Length Error:" +" Attr val too long (>0xfffff)" + formatLineNumber()); writeVTD( temp_offset >> 1, length1 >> 1, TOKEN_ATTR_VAL, depth); } //System.out.println(" " + temp_offset + " " + length1 + " attr val " + depth); //has_amp = false; //length1 = 0; ch = r.getChar(); if (XMLChar.isSpaceChar(ch)) { ch = getCharAfterS(); if (XMLChar.isNameStartChar(ch)) { temp_offset = offset - increment; parser_state = STATE_ATTR_NAME; break; } } if (ch == '/') { depth--; ch = r.getChar(); } if (ch == '>') { attr_count = 0; if (depth != -1) { temp_offset = offset; ch = getCharAfterSe(); if (ch == '<') { parser_state = STATE_LT_SEEN; } else if (XMLChar.isContentChar(ch)) { //temp_offset = offset; parser_state = STATE_TEXT; } else if (ch == '&') { //has_amp = true; //temp_offset = offset; entityIdentifier(); parser_state = STATE_TEXT; } else throw new ParseException( "Error in text content: Invalid char" + formatLineNumber()); } else { parser_state = STATE_DOC_END; } break; } throw new ParseException( "Starting tag Error: Invalid char in starting tag" + formatLineNumber()); case STATE_END_PI : ch = r.getChar(); if (XMLChar.isNameStartChar(ch)) { if ((ch == 'x' || ch == 'X') && (r.skipChar('m') || r.skipChar('M')) && (r.skipChar('l') && r.skipChar('L'))) { //temp_offset = offset; ch = r.getChar(); if (XMLChar.isSpaceChar(ch) || ch == '?') throw new ParseException( "Error in PI: [xX][mM][lL] not a valid PI target" + formatLineNumber()); //offset = temp_offset; } while (true) { //ch = getChar(); if (!XMLChar.isNameChar(ch)) { break; } ch = r.getChar(); } length1 = offset - temp_offset - increment; /*System.out.println( "" + (char) XMLDoc[temp_offset] + " " + (temp_offset) + " " + length1 + " PI Target " + depth);*/ if (encoding < FORMAT_UTF_16BE){ if (length1 > MAX_TOKEN_LENGTH) throw new ParseException("Token Length Error:" +"PI name too long (>0xfffff)" + formatLineNumber()); writeVTD( temp_offset, length1, TOKEN_PI_NAME, depth); } else{ if (length1 > (MAX_TOKEN_LENGTH<<1)) throw new ParseException("Token Length Error:" +"PI name too long (>0xfffff)" + formatLineNumber()); writeVTD( temp_offset >> 1, length1 >> 1, TOKEN_PI_NAME, depth); } //length1 = 0; temp_offset = offset; if (XMLChar.isSpaceChar(ch)) { ch = getCharAfterS(); while (true) { if (XMLChar.isValidChar(ch)) { if (ch == '?') if (r.skipChar('>')) { parser_state = STATE_DOC_END; break; } else throw new ParseException( "Error in PI: invalid termination sequence" + formatLineNumber()); } else throw new ParseException( "Error in PI: Invalid char in PI val" + formatLineNumber()); ch = r.getChar(); } length1 = offset - temp_offset - 2 * increment; if (encoding < FORMAT_UTF_16BE){ if (length1 > MAX_TOKEN_LENGTH) throw new ParseException("Token Length Error:" +"PI val too long (>0xfffff)" + formatLineNumber()); writeVTD( temp_offset, length1, TOKEN_PI_VAL, depth); } else{ if (length1 > (MAX_TOKEN_LENGTH<<1)) throw new ParseException("Token Length Error:" +"PI val too long (>0xfffff)" + formatLineNumber()); writeVTD( temp_offset >> 1, length1 >> 1, TOKEN_PI_VAL, depth); } //System.out.println(" " + temp_offset + " " + length1 + " PI val " + depth); } else { if ((ch == '?') && r.skipChar('>')) { parser_state = STATE_DOC_END; } else throw new ParseException( "Error in PI: invalid termination sequence" + formatLineNumber()); } //parser_state = STATE_DOC_END; } else throw new ParseException("Error in PI: invalid char in PI target" +formatLineNumber()); break; case STATE_END_COMMENT : while (true) { ch = r.getChar(); if (XMLChar.isValidChar(ch)) { if (ch == '-' && r.skipChar('-')) { length1 = offset - temp_offset - 2 * increment; break; } } else throw new ParseException( "Error in comment: Invalid Char" + formatLineNumber()); } if (r.getChar() == '>') { //System.out.println(" " + temp_offset + " " + length1 + " comment " + depth); if (encoding < FORMAT_UTF_16BE) writeVTD( temp_offset, length1, TOKEN_COMMENT, depth); else writeVTD( temp_offset >> 1, length1 >> 1, TOKEN_COMMENT, depth); //length1 = 0; parser_state = STATE_DOC_END; break; } throw new ParseException( "Error in comment: '-->' expected" + formatLineNumber()); default : throw new ParseException( "Other error: invalid parser state" +formatLineNumber()); } } } catch (EOFException e) { if (parser_state != STATE_DOC_END) throw e; } }

3680 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/3680/b398d55c30402df8a8de6650255b1399d4c8067b/VTDGen1.java/clean/com/ximpleware/VTDGen1.java

public static Object getNamedPlugin(Class intfc, String name) throws PluginInstantiationException { try { String iname = intfc.getName(); configureNamedPlugin(iname); String key = iname + SEP + name; String cname = (String)namedPluginClasses.get(key); if (cname == null) log.warn("Cannot find named plugin for interface="+iname+", name=\""+name+"\""); else { Class pluginClass = Class.forName(cname); if (cacheMe(pluginClass)) { String nkey = pluginClass.getName() + SEP + name; Object cached = namedInstanceCache.get(nkey); if (cached == null) { cached = pluginClass.newInstance(); if (cached instanceof SelfNamedPlugin) ((SelfNamedPlugin)cached).setPluginInstanceName(name); namedInstanceCache.put(nkey, cached); } return cached; } else { Object result = pluginClass.newInstance(); if (result instanceof SelfNamedPlugin) ((SelfNamedPlugin)result).setPluginInstanceName(name); } } } catch (ClassNotFoundException e) { throw new PluginInstantiationException("Cannot load plugin class!",e); } catch (InstantiationException e) { throw new PluginInstantiationException(e); } catch (IllegalAccessException e) { throw new PluginInstantiationException(e); } return null; }

47292 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/47292/8cf0447063158ac73720ac9b14bede8703c61f25/PluginManager.java/buggy/dspace/src/org/dspace/core/PluginManager.java

jjmatchedKind = 18; return jjMoveStringLiteralDfa1_6(0x28000L);

jjmatchedKind = 15; return jjMoveStringLiteralDfa1_6(0x5000L);

private final int jjMoveStringLiteralDfa0_6(){ switch(curChar) { case 35: jjmatchedKind = 18; return jjMoveStringLiteralDfa1_6(0x28000L); case 42: return jjMoveStringLiteralDfa1_6(0x1000000L); default : return jjMoveNfa_6(3, 0); }}

9291 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/9291/89173502837b4d67a69cd30d0b93cf47ed84c8cc/ParserTokenManager.java/clean/src/java/org/apache/velocity/runtime/parser/ParserTokenManager.java

String organism = null;

public boolean readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) throws IllegalSymbolException, IOException, ParseException { String line; boolean hasAnotherSequence = true; //boolean hasInternalWhitespace = false; rlistener.startSequence(); if (ns==null) ns=RichObjectFactory.getDefaultNamespace(); rlistener.setNamespace(ns); // Get an ordered list of key->value pairs in array-tuples String sectionKey = null; NCBITaxon tax = null; String organism = null; String accession = null; int xrefCount = 0; do { List section = this.readSection(reader); sectionKey = ((String[])section.get(0))[0]; if(sectionKey == null){ throw new ParseException("Section key was null. Accession:"+ accession == null ? "Not set" : accession); } // process section-by-section if (sectionKey.equals(LOCUS_TAG)) { // entryname dataclass; moltype; sequencelength AA. String loc = ((String[])section.get(0))[1]; Matcher m = lp.matcher(loc); if (m.matches()) { rlistener.setName(m.group(2)); rlistener.setDivision(m.group(3)); rlistener.addSequenceProperty(Terms.getDataClassTerm(),m.group(4)); rlistener.addSequenceProperty(Terms.getMolTypeTerm(),m.group(5)); } else { throw new ParseException("Bad ID line found: "+loc); } } else if (sectionKey.equals(DEFINITION_TAG)) { String val = ((String[])section.get(0))[1]; if (val.endsWith(".")) val = val.substring(0, val.length()-1); // chomp dot rlistener.setDescription(val); } else if (sectionKey.equals(SOURCE_TAG)) { // use SOURCE_TAG and TAXON_TAG values String sciname = null; String comname = null; List synonym = new ArrayList(); int taxid = 0; for (int i = 0; i < section.size(); i++) { String tag = ((String[])section.get(i))[0]; String value = ((String[])section.get(i))[1].trim(); if (tag.equals(SOURCE_TAG)) { if (value.endsWith(".")) value = value.substring(0,value.length()-1); // chomp trailing dot String[] parts = value.split("\\("); sciname = parts[0].trim(); if (parts.length>1) { comname = parts[1].trim(); if (comname.endsWith(")")) comname = comname.substring(0,comname.length()-1); // chomp trailing bracket if (parts.length>2) { // synonyms for (int j = 2 ; j < parts.length; j++) { String syn = parts[j].trim(); if (syn.endsWith(")")) syn = syn.substring(0,syn.length()-1); // chomp trailing bracket synonym.add(syn); } } } } else if (tag.equals(TAXON_TAG)) { String[] parts = value.split(";"); for (int j = 0; j < parts.length; j++) { String[] bits = parts[j].split("="); if (bits[0].equals("NCBI_TaxID")) { String[] morebits = bits[1].split(","); taxid = Integer.parseInt(morebits[0].trim()); } } } else if (tag.equals(ORGANELLE_TAG)) { if (value.endsWith(".")) value = value.substring(0,value.length()-1); // chomp trailing dot String[] parts = value.split(";"); for (int j = 0; j < parts.length; j++) { parts[j]=parts[j].trim(); rlistener.addSequenceProperty(Terms.getOrganelleTerm(),parts[j]); } } } // Set the Taxon tax = (NCBITaxon)RichObjectFactory.getObject(SimpleNCBITaxon.class, new Object[]{new Integer(taxid)}); rlistener.setTaxon(tax); try { if (sciname!=null) tax.addName(NCBITaxon.SCIENTIFIC,sciname); if (comname!=null) tax.addName(NCBITaxon.COMMON,comname); for (Iterator j = synonym.iterator(); j.hasNext(); ) tax.addName(NCBITaxon.SYNONYM, (String)j.next()); } catch (ChangeVetoException e) { throw new ParseException(e); } } else if (sectionKey.equals(DATE_TAG)) { String chunk = ((String[])section.get(0))[1]; Matcher dm = dp.matcher(chunk); if (dm.matches()) { String date = dm.group(1).trim(); String type = dm.group(2).trim(); String rel = dm.group(3); if (rel!=null) rel = rel.trim(); if (type.startsWith("integrated into UniProtKB")) { String dbname = type.split("/")[1]; rlistener.addSequenceProperty(Terms.getDateCreatedTerm(), date); rlistener.addSequenceProperty(Terms.getUniProtDBNameTerm(), dbname); } else if (type.equalsIgnoreCase("sequence version")) { if (rel==null) throw new ParseException("Version missing for "+type); rlistener.addSequenceProperty(Terms.getDateUpdatedTerm(), date); rlistener.addSequenceProperty(Terms.getRelUpdatedTerm(), rel); } else if (type.equalsIgnoreCase("entry version")) { if (rel==null) throw new ParseException("Version missing for "+type); rlistener.addSequenceProperty(Terms.getDateAnnotatedTerm(), date); rlistener.addSequenceProperty(Terms.getRelAnnotatedTerm(), rel); } else throw new ParseException("Bad date type found: "+type); } else throw new ParseException("Bad date line found: "+chunk); } else if (sectionKey.equals(ACCESSION_TAG)) { // if multiple accessions, store only first as accession, // and store rest in annotation String[] accs = ((String[])section.get(0))[1].split(";"); accession = accs[0].trim(); rlistener.setAccession(accession); for (int i = 1; i < accs.length; i++) { rlistener.addSequenceProperty(Terms.getAdditionalAccessionTerm(),accs[i].trim()); } } else if (sectionKey.equals(KEYWORDS_TAG)) { String val = ((String[])section.get(0))[1]; if (val.endsWith(".")) val = val.substring(0, val.length()-1); // chomp dot String[] kws = val.split(";"); for (int i = 0; i < kws.length; i++) { String kw = kws[i].trim(); if (kw.length()==0) continue; rlistener.addSequenceProperty(Terms.getKeywordTerm(), kw); } } else if (sectionKey.equals(GENE_TAG)) { String[] genes = ((String[])section.get(0))[1].split("\\s+(or|and)\\s+"); for (int geneID = 0; geneID < genes.length; geneID++) { String[] parts = genes[geneID].split(";"); for (int j = 0; j < parts.length; j++) { String[] moreparts = parts[j].split("="); String[] values = moreparts[1].split(","); // nasty hack - we really should have notes on the gene object itself... if such a thing existed... if (moreparts[0].trim().equals(Terms.GENENAME_KEY)) rlistener.addSequenceProperty(Terms.getGeneNameTerm(),geneID+":"+values[0].trim()); else if (moreparts[0].trim().equals(Terms.GENESYNONYM_KEY)) { for (int k = 0; k < values.length; k++) rlistener.addSequenceProperty(Terms.getGeneSynonymTerm(),geneID+":"+values[k].trim()); } else if (moreparts[0].trim().equals(Terms.ORDLOCNAME_KEY)) { for (int k = 0; k < values.length; k++) rlistener.addSequenceProperty(Terms.getOrderedLocusNameTerm(),geneID+":"+values[k].trim()); } else if (moreparts[0].trim().equals(Terms.ORFNAME_KEY)) { for (int k = 0; k < values.length; k++) rlistener.addSequenceProperty(Terms.getORFNameTerm(),geneID+":"+values[k].trim()); } } } } else if (sectionKey.equals(DATABASE_XREF_TAG)) { // database_identifier; primary_identifier; secondary_identifier.... String val = ((String[])section.get(0))[1]; if (val.endsWith(".")) val = val.substring(0, val.length()-1); // chomp dot String[] parts = val.split(";"); // construct a DBXREF out of the dbname part[0] and accession part[1] String dbname = parts[0].trim(); String acc = parts[1].trim(); CrossRef crossRef = (CrossRef)RichObjectFactory.getObject(SimpleCrossRef.class,new Object[]{dbname,acc,new Integer(0)}); // assign remaining bits of info as additional accession annotations for (int j = 2; j < parts.length; j++) { ComparableTerm t = (ComparableTerm)Terms.getAdditionalAccessionTerm(); Note note = new SimpleNote(t,parts[j].trim(),j); try { ((RichAnnotation)crossRef.getAnnotation()).addNote(note); } catch (ChangeVetoException ce) { ParseException pe = new ParseException("Could not annotate additional accession terms"); pe.initCause(ce); throw pe; } } RankedCrossRef rcrossRef = new SimpleRankedCrossRef(crossRef, ++xrefCount); rlistener.setRankedCrossRef(rcrossRef); } else if (sectionKey.equals(REFERENCE_TAG) && !this.getElideReferences()) { // first line of section has rank and location String refrank = ((String[])section.get(0))[1]; int ref_rank = Integer.parseInt(refrank.substring(1,refrank.length()-1)); // rest can be in any order String authors = null; String consortium = null; String title = null; String locator = null; String pubmed = null; String medline = null; String doi = null; String remark = null; Integer rstart = null; Integer rend = null; for (int i = 1; i < section.size(); i++) { String key = ((String[])section.get(i))[0]; String val = ((String[])section.get(i))[1]; //System.err.println(key+": "+val); if (key.equals(AUTHORS_TAG)) { if (val.endsWith(";")) val = val.trim().substring(0, val.length()-1); // chomp semicolon authors = val; } if (key.equals(CONSORTIUM_TAG)) { if (val.endsWith(";")) val = val.trim().substring(0, val.length()-1); // chomp semicolon consortium = val; } if (key.equals(TITLE_TAG)) { if (val.endsWith(";")) val = val.trim().substring(0, val.length()-1); // chomp semicolon if (val.endsWith("\"")) val = val.trim().substring(1, val.length()-2); // chomp quotes title = val; } if (key.equals(LOCATION_TAG)) { if (val.endsWith(".")) val = val.trim().substring(0, val.length()-1); // chomp dot locator = val; } if (key.equals(REFERENCE_XREF_TAG)) { // database_identifier=primary_identifier; String[] refs = val.split(";"); for (int j = 0 ; j < refs.length; j++) { if (refs[j].trim().length()==0) continue; String[] parts = refs[j].split("="); String db = parts[0]; String ref = parts[1]; if (db.equalsIgnoreCase(Terms.PUBMED_KEY)) pubmed = ref; else if (db.equalsIgnoreCase(Terms.MEDLINE_KEY)) medline = ref; else if (db.equalsIgnoreCase(Terms.DOI_KEY)) doi = ref; } } if (key.equals(RP_LINE_TAG)) { remark = val; if (val.endsWith(".")) val = val.substring(0, val.length()-1); // chomp dot // Try to use it to find the location of the reference, if we have one. Matcher m = rppat.matcher(val); if (m.matches()) { rstart = Integer.valueOf(m.group(1)); rend = Integer.valueOf(m.group(2)); } } if (key.equals(RC_LINE_TAG)) { // Split into key=value pairs separated by semicolons and terminated with semicolon. String[] parts = val.split(";"); for (int j = 0; j < parts.length; j++) { String[] subparts = parts[j].split("="); // get term for first section String termName = subparts[0].trim(); Term t; if (termName.equalsIgnoreCase(Terms.SPECIES_KEY)) t = Terms.getSpeciesTerm(); else if (termName.equalsIgnoreCase(Terms.STRAIN_KEY)) t = Terms.getStrainTerm(); else if (termName.equalsIgnoreCase(Terms.TISSUE_KEY)) t = Terms.getTissueTerm(); else if (termName.equalsIgnoreCase(Terms.TRANSPOSON_KEY)) t = Terms.getTransposonTerm(); else if (termName.equalsIgnoreCase(Terms.PLASMID_KEY)) t = Terms.getPlasmidTerm(); else throw new ParseException("Invalid RC term found: "+termName); // assign notes using term and rank:second section as value // nasty hack - we really should have notes on the reference itself. rlistener.addSequenceProperty(t, ref_rank+":"+subparts[1].trim()); } } } // create the pubmed crossref and assign to the bioentry CrossRef pcr = null; if (pubmed!=null) { pcr = (CrossRef)RichObjectFactory.getObject(SimpleCrossRef.class,new Object[]{Terms.PUBMED_KEY, pubmed, new Integer(0)}); RankedCrossRef rpcr = new SimpleRankedCrossRef(pcr, 0); rlistener.setRankedCrossRef(rpcr); } // create the medline crossref and assign to the bioentry CrossRef mcr = null; if (medline!=null) { mcr = (CrossRef)RichObjectFactory.getObject(SimpleCrossRef.class,new Object[]{Terms.MEDLINE_KEY, medline, new Integer(0)}); RankedCrossRef rmcr = new SimpleRankedCrossRef(mcr, 0); rlistener.setRankedCrossRef(rmcr); } // create the doi crossref and assign to the bioentry CrossRef dcr = null; if (doi!=null) { dcr = (CrossRef)RichObjectFactory.getObject(SimpleCrossRef.class,new Object[]{Terms.DOI_KEY, doi, new Integer(0)}); RankedCrossRef rdcr = new SimpleRankedCrossRef(dcr, 0); rlistener.setRankedCrossRef(rdcr); } // create the docref object try { List auths = null; if(authors != null) auths = DocRefAuthor.Tools.parseAuthorString(authors); if (consortium!=null){ if(auths == null) auths = new ArrayList(); auths.add(new SimpleDocRefAuthor(consortium,true,false)); } DocRef dr = (DocRef)RichObjectFactory.getObject(SimpleDocRef.class,new Object[]{auths,locator}); if (title!=null) dr.setTitle(title); // assign either the pubmed or medline to the docref - medline gets priority, then pubmed, then doi if (mcr!=null) dr.setCrossref(mcr); else if (pcr!=null) dr.setCrossref(pcr); else if (dcr!=null) dr.setCrossref(dcr); // assign the remarks if (!this.getElideComments()) dr.setRemark(remark); // assign the docref to the bioentry RankedDocRef rdr = new SimpleRankedDocRef(dr,rstart,rend,ref_rank); rlistener.setRankedDocRef(rdr); } catch (ChangeVetoException e) { throw new ParseException(e); } } else if (sectionKey.equals(COMMENT_TAG) && !this.getElideComments()) { // Set up some comments String val = ((String[])section.get(0))[1]; if (UniProtCommentParser.isParseable(val)) rlistener.setComment(val); else { // copyright message rlistener.addSequenceProperty(Terms.getCopyrightTerm(), val); } } else if (sectionKey.equals(FEATURE_TAG) && !this.getElideFeatures()) { // starting from second line of input, start a new feature whenever we come across // a key that does not start with / boolean seenAFeature = false; for (int i = 1 ; i < section.size(); i++) { String key = ((String[])section.get(i))[0]; String val = ((String[])section.get(i))[1]; val = val.trim(); if (val.endsWith(".")) val = val.substring(0,val.length()-1); // chomp dot if (key.startsWith("/")) { key = key.substring(1); // strip leading slash if (key.equals("FTId")) rlistener.addFeatureProperty(Terms.getFTIdTerm(),val); else { // should never happen - but here just in case rlistener.addFeatureProperty(RichObjectFactory.getDefaultOntology().getOrCreateTerm(key),val); } } else { // new feature! // end previous feature if (seenAFeature) rlistener.endFeature(); // start next one, with lots of lovely info in it RichFeature.Template templ = new RichFeature.Template(); templ.annotation = new SimpleRichAnnotation(); templ.sourceTerm = Terms.getUniProtTerm(); templ.typeTerm = RichObjectFactory.getDefaultOntology().getOrCreateTerm(key); templ.featureRelationshipSet = new TreeSet(); templ.rankedCrossRefs = new TreeSet(); String desc = null; String status = null; val = val.replaceAll("\n", " "); // Nasty hack but we have to do this, sadly. Matcher m = fp.matcher(val); if (m.matches()) { String loc = m.group(1); desc = m.group(3); templ.location = UniProtLocationParser.parseLocation(loc); } else { System.err.println("XX"+val+"XX"); throw new ParseException("Bad feature value: "+val); } rlistener.startFeature(templ); if (desc!=null) rlistener.addFeatureProperty(Terms.getFeatureDescTerm(),desc); seenAFeature = true; } } if (seenAFeature) rlistener.endFeature(); } else if (sectionKey.equals(START_SEQUENCE_TAG) && !this.getElideSymbols()) { StringBuffer seq = new StringBuffer(); for (int i = 0 ; i < section.size(); i++) seq.append(((String[])section.get(i))[1]); try { SymbolList sl = new SimpleSymbolList(symParser, seq.toString().replaceAll("\\s+","").replaceAll("[\\.|~]","-")); rlistener.addSymbols(symParser.getAlphabet(), (Symbol[])(sl.toList().toArray(new Symbol[0])), 0, sl.length()); } catch (Exception e) { throw new ParseException(e); } } } while (!sectionKey.equals(END_SEQUENCE_TAG)); // Allows us to tolerate trailing whitespace without // thinking that there is another Sequence to follow while (true) { reader.mark(1); int c = reader.read(); if (c == -1) { hasAnotherSequence = false; break; } if (Character.isWhitespace((char) c)) { //hasInternalWhitespace = true; continue; } //if (hasInternalWhitespace) //System.err.println("Warning: whitespace found between sequence entries"); reader.reset(); break; } // Finish up. rlistener.endSequence(); return hasAnotherSequence; }

50397 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50397/05b36241610b2e40a85168dccc182f8d5f51e4de/UniProtFormat.java/clean/src/org/biojavax/bio/seq/io/UniProtFormat.java

iterateNodeSet(documentWrapper, xpathEvaluator, modelBind, new NodeHandler() {

final XPathEvaluator xpathEvaluator = new XPathEvaluator(documentWrapper); StandaloneContext context = (StandaloneContext) xpathEvaluator.getStaticContext(); for (Iterator j = modelBind.getNamespaceMap().keySet().iterator(); j.hasNext();) { String prefix = (String) j.next(); context.declareNamespace(prefix, (String) modelBind.getNamespaceMap().get(prefix)); } iterateNodeSet(documentWrapper, modelBind, new NodeHandler() {

public void applyInputOutputBinds(Document instance) { for (Iterator i = binds.iterator(); i.hasNext();) { final ModelBind modelBind = (ModelBind) i.next(); try { // Create XPath evaluator for this bind DocumentWrapper documentWrapper = new DocumentWrapper(instance, null); final XPathEvaluator xpathEvaluator = new XPathEvaluator(documentWrapper); StandaloneContext context = (StandaloneContext) xpathEvaluator.getStaticContext(); for (Iterator j = modelBind.getNamespaceMap().keySet().iterator(); j.hasNext();) { String prefix = (String) j.next(); context.declareNamespace(prefix, (String) modelBind.getNamespaceMap().get(prefix)); } // Handle relevant if (modelBind.getRelevant() != null) { iterateNodeSet(documentWrapper, xpathEvaluator, modelBind, new NodeHandler() { public void handleNode(Node node) { // Evaluate "relevant" XPath expression on this node boolean relevant = ((Boolean) XPathUtils.evaluateSingle (xpathEvaluator, "boolean(" + modelBind.getRelevant() + ")", modelBind.getLocationData())).booleanValue(); // Mark node InstanceData instanceData = XFormsUtils.getInstanceData((Node) node); instanceData.getRelevant().set(relevant); } }); } // Handle calculate if (modelBind.getCalculate() != null) { iterateNodeSet(documentWrapper, xpathEvaluator, modelBind, new NodeHandler() { public void handleNode(Node node) { if (node instanceof Element) { // Compute calculated value List result = XPathUtils.evaluate(xpathEvaluator, modelBind.getCalculate(), modelBind.getLocationData()); // Place in element Element elementNode = (Element) node; elementNode.clearContent(); for (Iterator k = result.iterator(); k.hasNext();) { Object resultItem = k.next(); if (resultItem instanceof Node) { elementNode.add(((Node) elementNode.clone())); } else { elementNode.add(DocumentFactory.getInstance().createText(resultItem.toString())); } } } else { // Compute calculated value and place in attribute XFormsUtils.fillNode(node, (String) XPathUtils.evaluateSingle(xpathEvaluator, "string(" + modelBind.getCalculate() + ")", modelBind.getLocationData())); } } }); } // Handle type constraint if (modelBind.getType() != null) { iterateNodeSet(documentWrapper, xpathEvaluator, modelBind, new NodeHandler() { public void handleNode(Node node) { if (XFormsUtils.getInstanceData(node).getValid().get()) { // Get type information int requiredType = -1; boolean foundType = false; { String type = modelBind.getType(); int prefixPosition = type.indexOf(':'); if (prefixPosition > 0) { String prefix = type.substring(0, prefixPosition); String namespace = (String) modelBind.getNamespaceMap().get(prefix); if (namespace == null) throw new ValidationException("Namespace not declared for prefix '" + prefix + "'", modelBind.getLocationData()); ItemType itemType = Type.getBuiltInItemType((String) modelBind.getNamespaceMap().get(prefix), type.substring(prefixPosition + 1)); if (itemType != null) { requiredType = itemType.getPrimitiveType(); foundType = true; } } } if (!foundType) throw new ValidationException("Invalid type '" + modelBind.getType() + "'", modelBind.getLocationData()); // Try to perform casting String nodeStringValue = node.getStringValue(); if (XFormsUtils.getInstanceData(node).getRequired().get() || nodeStringValue.length() != 0) { try { StringValue stringValue = new StringValue(nodeStringValue); XPathContext xpContext = new XPathContextMajor(stringValue, xpathEvaluator.getStaticContext().getConfiguration()); stringValue.convert(requiredType, xpContext); markValidity(true, node, modelBind.getId()); } catch (XPathException e) { markValidity(false, node, modelBind.getId()); } } } } }); } // Handle XPath constraint if (modelBind.getConstraint() != null) { iterateNodeSet(documentWrapper, xpathEvaluator, modelBind, new NodeHandler() { public void handleNode(Node node) { if (XFormsUtils.getInstanceData(node).getValid().get()) { // Evaluate constraint Boolean valid = (Boolean) XPathUtils.evaluateSingle(xpathEvaluator, "boolean(" + modelBind.getConstraint() + ")", modelBind.getLocationData()); markValidity(valid.booleanValue(), node, modelBind.getId()); } } }); } // Handle required if (modelBind.getRequired() != null) { iterateNodeSet(documentWrapper, xpathEvaluator, modelBind, new NodeHandler() { public void handleNode(Node node) { // Evaluate "required" XPath expression on this node boolean required = ((Boolean) (XPathUtils.evaluateSingle (xpathEvaluator, "boolean(" + modelBind.getRequired() + ")", modelBind.getLocationData()))).booleanValue(); // Mark node InstanceData instanceData = XFormsUtils.getInstanceData((Node) node); instanceData.getRequired().set(required); // If required, check the string value is not empty markValidity(!required || node.getStringValue().length() > 0, node, modelBind.getId()); } }); } // Handle read only if (modelBind.getReadonly() != null) { iterateNodeSet(documentWrapper, xpathEvaluator, modelBind, new NodeHandler() { public void handleNode(Node node) { // Evaluate "readonly" XPath expression on this node boolean readonly = ((Boolean) (XPathUtils.evaluateSingle (xpathEvaluator, "boolean(" + modelBind.getReadonly() + ")", modelBind.getLocationData()))).booleanValue(); // Mark node InstanceData instanceData = XFormsUtils.getInstanceData((Node) node); instanceData.getReadonly().set(readonly); } }); } } catch (Exception e) { throw new ValidationException(e, modelBind.getLocationData()); } } reconciliate(instance.getRootElement()); }

57229 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57229/5996bad8ae7a5e6bde143d457470ccb6e7d8a675/Model.java/buggy/src/java/org/orbeon/oxf/processor/xforms/Model.java

String codeBase = getCodeBase().toExternalForm().substring(7);

String extForm = getCodeBase().toExternalForm(); String codeBase = extForm.substring(extForm.indexOf(":") + 3);

public void init() { this.subAppletClassName = getParameter("subapplet.classname"); if (subAppletClassName == null){ displayError("Init failed : Missing subapplet.classname argument"); return; } this.subAppletDisplayName = getParameter("subapplet.displayname"); if (subAppletDisplayName == null){ subAppletDisplayName = "Applet"; } this.subAppletImageName = getParameter("subapplet.image"); initLoaderLayout(); validate(); String codeBase = getCodeBase().toExternalForm().substring(7); // minus http:// this.installDirectory = codeBase.replace(':', '_') .replace('.', '_').replace('/', '_').replace('~','_'); // clean up the name String osName = System.getProperty("os.name"); String osArch = System.getProperty("os.arch"); if (checkOSAndArch(osName, osArch)) { this.isInitOk = true; } else { displayError("Init failed : Unsupported os / arch ( " + osName + " / " + osArch + " )"); } }

47282 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/47282/1f4c024d5dd562a5c2b1e1c1257648b732a105a9/JOGLAppletLauncher.java/clean/src/classes/com/sun/opengl/util/JOGLAppletLauncher.java

private void synchBugInstance() { // Get current bug instance BugInstance selected = getCurrentBugInstance(); if (selected == null) return; // If the details window is minimized, then the user can't see // it and there is no point in updating it. if (!viewBugDetailsItem.isSelected()) return; // Get the current source line annotation. // If the current leaf selected is not a source line annotation, // use the default source line annotation from the current bug instance // (if any). JTree bugTree = getCurrentBugTree(); SourceLineAnnotation srcLine = null; TreePath selPath = bugTree.getSelectionPath(); if (selPath != null) { Object leaf = ((DefaultMutableTreeNode)selPath.getLastPathComponent()).getUserObject(); if (leaf instanceof SourceLineAnnotation) srcLine = (SourceLineAnnotation) leaf; else srcLine = selected.getPrimarySourceLineAnnotation(); } // Show source code. if (srcLine != currentSourceLineAnnotation) { Project project = getCurrentProject(); AnalysisRun analysisRun = getCurrentAnalysisRun(); if (project == null) throw new IllegalStateException("null project!"); if (analysisRun == null) throw new IllegalStateException("null analysis run!"); viewSource(project, analysisRun, srcLine); currentSourceLineAnnotation = srcLine; } // Show bug info. showBugInfo(selected); // Now the bug details are up to date. currentBugInstance = selected; }

10715 /local/tlutelli/issta_data/temp/all_java1context/java/2006_temp/2006/10715/a6faccf1f33035b730d9878d13d0da9fa199f1f8/FindBugsFrame.java/clean/findbugs/src/java/edu/umd/cs/findbugs/gui/FindBugsFrame.java

if (jj_3R_478()) return true;

if (jj_scan_token(100)) return true;

final private boolean jj_3R_475() { Token xsp; xsp = jj_scanpos; if (jj_3_32()) { jj_scanpos = xsp; if (jj_3R_478()) return true; } return false; }

11192 /local/tlutelli/issta_data/temp/all_java1context/java/2006_temp/2006/11192/9aa0c6bec51662a685ea4b86bc02a52c9e593d8a/Parser.java/clean/dynamicjava/src/koala/dynamicjava/parser/Parser.java

public org.quickfix.field.OrdType getOrdType() throws FieldNotFound { org.quickfix.field.OrdType value = new org.quickfix.field.OrdType();

public quickfix.field.OrdType getOrdType() throws FieldNotFound { quickfix.field.OrdType value = new quickfix.field.OrdType();

public org.quickfix.field.OrdType getOrdType() throws FieldNotFound { org.quickfix.field.OrdType value = new org.quickfix.field.OrdType(); getField(value); return value; }

5926 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/5926/fecc27f98261270772ff182a1d4dfd94b5daa73d/QuoteResponse.java/clean/src/java/src/quickfix/fix44/QuoteResponse.java

XSDocumentInfo (Document schemaDoc) {

XSDocumentInfo (Document schemaDoc, XSAttributeChecker attrChecker) {

XSDocumentInfo (Document schemaDoc) { fSchemaDoc = schemaDoc; if(schemaDoc != null) { Element root = DOMUtil.getRoot(schemaDoc); // assign attributes appropriately according to // generalAttrCheck as applied to root. } }

4434 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/4434/6f04e9c6fc78d4e3eda5026b14b51f3b636479ac/XSDocumentInfo.java/clean/src/org/apache/xerces/impl/v2/XSDocumentInfo.java

final Register tmpr = requestRegister(JvmType.INT, false);

final Register tmpr = L1AHelper.requestRegister(eContext, JvmType.INT, false);

public final void visit_checkcast(VmConstClass classRef) { // Pre-claim ECX requestRegister(ECX); requestRegister(EAX); // check that top item is a reference final RefItem ref = vstack.popRef(); // Load the ref ref.load(eContext); final Register refr = ref.getRegister(); final Register classr = EAX; final Register tmpr = requestRegister(JvmType.INT, false); // Resolve the class writeResolveAndLoadClassToReg(classRef, classr); final Label okLabel = new Label(this.curInstrLabel + "cc-ok"); /* Is objectref null? */ os.writeTEST(refr, refr); os.writeJCC(okLabel, X86Constants.JZ); /* Is instanceof? */ instanceOf(refr, classr, tmpr, okLabel, true); /* Not instanceof */ // Release temp registers here, so invokeJavaMethod can use it releaseRegister(ECX); releaseRegister(classr); releaseRegister(tmpr); // Call SoftByteCodes.systemException os.writePUSH(SoftByteCodes.EX_CLASSCAST); os.writePUSH(0); invokeJavaMethod(context.getSystemExceptionMethod()); final RefItem exi = vstack.popRef(); assertCondition(exi.uses(EAX), "item must be in eax"); exi.release(eContext); /* Exception in EAX, throw it */ helper.writeJumpTableCALL(X86JumpTable.VM_ATHROW_OFS); /* Normal exit */ os.setObjectRef(okLabel); // Leave ref on stack vstack.push(ref); }

50763 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50763/7f3f443c80552e30cb144c1a1ce760d89fa35f2b/X86BytecodeVisitor.java/clean/core/src/core/org/jnode/vm/x86/compiler/l1a/X86BytecodeVisitor.java

label_17: while (true) { if (jj_2_67(2)) { ; } else { break label_17; } ptr_operator(); } qualified_id(); jj_consume_token(LPARENTHESIS);

label_17: while (true) { if (jj_2_67(2)) { ; } else { break label_17; } ptr_operator();

static final public void function_declarator_lookahead() throws ParseException { label_17: while (true) { if (jj_2_67(2)) { ; } else { break label_17; } ptr_operator(); } qualified_id(); jj_consume_token(LPARENTHESIS); }

41673 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/41673/23e69d576250f417c265d779703b8da08a67aaed/CPPParser.java/clean/pmd/src/net/sourceforge/pmd/cpd/cppast/CPPParser.java

setProperty((String) evalAttr("property", getProperty(),

setProperty((String) evalAttr("property", getPropertyExpr(),

private void evaluateExpressions() throws JspException { try { setAccesskey((String) evalAttr("accessKey", getAccesskey(), String.class)); } catch (NullAttributeException ex) { setAccesskey(null); } try { setAlt((String) evalAttr("alt", getAlt(), String.class)); } catch (NullAttributeException ex) { setAlt(null); } try { setAltKey((String) evalAttr("altKey", getAltKey(), String.class)); } catch (NullAttributeException ex) { setAltKey(null); } try { setDisabled(((Boolean) evalAttr("disabled", getDisabledExpr(), Boolean.class)). booleanValue()); } catch (NullAttributeException ex) { setDisabled(false); } try { setName((String) evalAttr("name", getName(), String.class)); } catch (NullAttributeException ex) { setName(null); } try { setOnblur((String) evalAttr("onblur", getOnblur(), String.class)); } catch (NullAttributeException ex) { setOnblur(null); } try { setOnchange((String) evalAttr("onchange", getOnchange(), String.class)); } catch (NullAttributeException ex) { setOnchange(null); } try { setOnclick((String) evalAttr("onclick", getOnclick(), String.class)); } catch (NullAttributeException ex) { setOnclick(null); } try { setOndblclick((String) evalAttr("ondblclick", getOndblclick(), String.class)); } catch (NullAttributeException ex) { setOndblclick(null); } try { setOnfocus((String) evalAttr("onfocus", getOnfocus(), String.class)); } catch (NullAttributeException ex) { setOnfocus(null); } try { setOnkeydown((String) evalAttr("onkeydown", getOnkeydown(), String.class)); } catch (NullAttributeException ex) { setOnkeydown(null); } try { setOnkeypress((String) evalAttr("onkeypress", getOnkeypress(), String.class)); } catch (NullAttributeException ex) { setOnkeypress(null); } try { setOnkeyup((String) evalAttr("onkeyup", getOnkeyup(), String.class)); } catch (NullAttributeException ex) { setOnkeyup(null); } try { setOnmousedown((String) evalAttr("onmousedown", getOnmousedown(), String.class)); } catch (NullAttributeException ex) { setOnmousedown(null); } try { setOnmousemove((String) evalAttr("onmousemove", getOnmousemove(), String.class)); } catch (NullAttributeException ex) { setOnmousemove(null); } try { setOnmouseout((String) evalAttr("onmouseout", getOnmouseout(), String.class)); } catch (NullAttributeException ex) { setOnmouseout(null); } try { setOnmouseover((String) evalAttr("onmouseover", getOnmouseover(), String.class)); } catch (NullAttributeException ex) { setOnmouseover(null); } try { setOnmouseup((String) evalAttr("onmouseup", getOnmouseup(), String.class)); } catch (NullAttributeException ex) { setOnmouseup(null); } try { setProperty((String) evalAttr("property", getProperty(), String.class)); } catch (NullAttributeException ex) { setProperty(null); } try { setStyle((String) evalAttr("style", getStyle(), String.class)); } catch (NullAttributeException ex) { setStyle(null); } try { setStyleClass((String) evalAttr("styleClass", getStyleClass(), String.class)); } catch (NullAttributeException ex) { setStyleClass(null); } try { setStyleId((String) evalAttr("styleId", getStyleId(), String.class)); } catch (NullAttributeException ex) { setStyleId(null); } try { setTabindex((String) evalAttr("tabindex", getTabindex(), String.class)); } catch (NullAttributeException ex) { setTabindex(null); } try { setTitle((String) evalAttr("title", getTitle(), String.class)); } catch (NullAttributeException ex) { setTitle(null); } try { setTitleKey((String) evalAttr("titleKey", getTitleKey(), String.class)); } catch (NullAttributeException ex) { setTitleKey(null); } try { setValue((String) evalAttr("value", getValue(), String.class)); } catch (NullAttributeException ex) { setValue(null); } }

48068 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/48068/db064e19656421b94aaf753550935d95f44bd5f9/ELMultiboxTag.java/clean/contrib/struts-el/src/share/org/apache/strutsel/taglib/html/ELMultiboxTag.java

target.translate(-1.0 * getFloatOption(Option.FROM_TRACE_SAMPLE), 1.0);

target.translate(-1.0 * getFloatOption(Option.FROM_TRACE_SAMPLE), 0.0);

public void getTransformAndConcat(AffineTransform target) { target.scale(horizScale, vertScale); // the y translation is a continuation of the rescale behavior found in // generatePaths target.translate(-1.0 * getFloatOption(Option.FROM_TRACE_SAMPLE), 1.0); }

50115 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50115/fd43d3699b4d4360c98e57cc3e1aff45c90dfbc8/ChromatogramGraphic.java/buggy/src/org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.java

try { setAnchor((String) evalAttr("anchor", getAnchorExpr(), String.class)); } catch (NullAttributeException ex) { }

String string = null; Boolean bool = null;

private void evaluateExpressions() throws JspException { try { setAnchor((String) evalAttr("anchor", getAnchorExpr(), String.class)); } catch (NullAttributeException ex) { } try { setForward((String) evalAttr("forward", getForwardExpr(), String.class)); } catch (NullAttributeException ex) { } try { setHref((String) evalAttr("href", getHrefExpr(), String.class)); } catch (NullAttributeException ex) { } try { setName((String) evalAttr("name", getNameExpr(), String.class)); } catch (NullAttributeException ex) { } try { setPage((String) evalAttr("page", getPageExpr(), String.class)); } catch (NullAttributeException ex) { } try { setParamId((String) evalAttr("paramId", getParamIdExpr(), String.class)); } catch (NullAttributeException ex) { } try { setParamName((String) evalAttr("paramName", getParamNameExpr(), String.class)); } catch (NullAttributeException ex) { } try { setParamProperty((String) evalAttr("paramProperty", getParamPropertyExpr(), String.class)); } catch (NullAttributeException ex) { } try { setParamScope((String) evalAttr("paramScope", getParamScopeExpr(), String.class)); } catch (NullAttributeException ex) { } try { setProperty((String) evalAttr("property", getPropertyExpr(), String.class)); } catch (NullAttributeException ex) { } try { setScope((String) evalAttr("scope", getScopeExpr(), String.class)); } catch (NullAttributeException ex) { } try { setTransaction(((Boolean) evalAttr("transaction", getTransactionExpr(), Boolean.class)). booleanValue()); } catch (NullAttributeException ex) { } }

48068 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/48068/022bd23c954cf673e53731849d562b3c295473f1/ELRedirectTag.java/clean/contrib/struts-el/src/share/org/apache/strutsel/taglib/logic/ELRedirectTag.java

if (sym.isSynthetic()) return type.widen(); return type; case CompoundType(Type[] parts, Scope members): if (global.debug) return type;

if (sym.isSynthetic()) return type.widen(); return type; case CompoundType(Type[] parts, Scope members): if (global.debug) return type;

public Type getTypeToPrintForType0(Type type) { switch (type) { case ThisType(_): if (global.debug) return type; return type.expandModuleThis(); case SingleType(_, Symbol sym): if (global.debug) return type; if (sym.isSynthetic()) return type.widen(); return type; case CompoundType(Type[] parts, Scope members): if (global.debug) return type; if (type.isFunctionType()) return parts[1]; return type; case TypeVar(Type origin, Constraint constr): if (constr.inst != Type.NoType) return constr.inst; return type; default: return type; } }

48012 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/48012/51a5386fa3225c117633ea7171760590d01bf6f3/SymbolTablePrinter.java/buggy/sources/scalac/symtab/SymbolTablePrinter.java

super.setPersonOrder(result.getResultParticipationsCount()); super.setResultParticipationRole(role);

super.setPersonOrder(order); super.setRole(role);

private void fillAllAttributes(Result result, Person participator, ResultParticipationRole role) { super.setResult(result); super.setPerson(participator); super.setPersonOrder(result.getResultParticipationsCount()); super.setResultParticipationRole(role); }

2645 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/2645/f7abe00b5548b12caf61a615516273677cbc5915/ResultParticipation.java/clean/src/net/sourceforge/fenixedu/domain/research/result/ResultParticipation.java

System.out.println("...running "+descr+" via "+testCase.getFile()); out = openFile(outputDir, testCase.getFile(), ".out");

String testName = testCase.getFile(); System.out.println("...running "+descr+" via "+testName); String logFileName = testName.substring(0, testName.lastIndexOf('.')); out = openFile(outputDir, logFileName + ".out");

private static void seqRunCases(Vector cases, String descr, String inputDir, String outputDir) throws FileNotFoundException, IOException, ijFatalException { LocalizedOutput out; BufferedInputStream in; mtTestCase testCase; if (cases == null) { System.out.println("...no "+descr+" being performed"); return; } Enumeration e = cases.elements(); while (e.hasMoreElements()) { testCase = (mtTestCase)e.nextElement(); System.out.println("...running "+descr+" via "+testCase.getFile()); out = openFile(outputDir, testCase.getFile(), ".out"); in = testCase.initialize(inputDir); testCase.runMe(log, out, in); } }

56322 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/56322/ece3ee6502c4a8c75d31ee4c66c7dcb6d8db45e4/MultiTest.java/buggy/java/testing/org/apache/derbyTesting/functionTests/harness/MultiTest.java

return; }

return; }

public void endElement(String name) { //System.err.println("End: " + name); if (((HtmlTagMap)myTags).isHead(name)) { // we do nothing return; } if (((HtmlTagMap)myTags).isTitle(name)) { if (currentChunk != null) { bodyAttributes.put(ElementTags.TITLE, currentChunk.content()); } return; } if (((HtmlTagMap)myTags).isMeta(name)) { // we do nothing return; } if (((HtmlTagMap)myTags).isLink(name)) { // we do nothing return; } if (((HtmlTagMap)myTags).isBody(name)) { // we do nothing return; } if (myTags.containsKey(name)) { XmlPeer peer = (XmlPeer) myTags.get(name); super.handleEndingTags(peer.getTag()); return; } super.handleEndingTags(name); }

4174 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/4174/1f2223c2de935f818616fc1991f79ce136873350/SAXmyHtmlHandler.java/clean/src/com/lowagie/text/html/SAXmyHtmlHandler.java

private Interpreter createCompiler() {

private Interpreter createCompiler() {

private Interpreter createCompiler() { Interpreter result = null; if (optimizationLevel >= 0 && codegenClass != null) { result = (Interpreter)Kit.newInstanceOrNull(codegenClass); } if (result == null) { result = new Interpreter(); } return result; }

19042 /local/tlutelli/issta_data/temp/all_java1context/java/2006_temp/2006/19042/767031d59e433c96cbc46c5e9fa8adb631f14074/Context.java/buggy/src/org/mozilla/javascript/Context.java

Node.Target catchTarget = new Node.Target();

Node catchTarget = Node.newTarget();

Node createTryCatchFinally(Node tryBlock, Node catchBlocks, Node finallyBlock, int lineno) { boolean hasFinally = (finallyBlock != null) && (finallyBlock.getType() != Token.BLOCK || finallyBlock.hasChildren()); // short circuit if (tryBlock.getType() == Token.BLOCK && !tryBlock.hasChildren() && !hasFinally) { return tryBlock; } boolean hasCatch = catchBlocks.hasChildren(); // short circuit if (!hasFinally && !hasCatch) { // bc finally might be an empty block... return tryBlock; } Node handlerBlock = new Node(Token.LOCAL_BLOCK); Node.Jump pn = new Node.Jump(Token.TRY, tryBlock, lineno); pn.putProp(Node.LOCAL_BLOCK_PROP, handlerBlock); if (hasCatch) { // jump around catch code Node.Target endCatch = new Node.Target(); pn.addChildToBack(makeJump(Token.GOTO, endCatch)); // make a TARGET for the catch that the tcf node knows about Node.Target catchTarget = new Node.Target(); pn.target = catchTarget; // mark it pn.addChildToBack(catchTarget); // // Given // // try { // tryBlock; // } catch (e if condition1) { // something1; // ... // // } catch (e if conditionN) { // somethingN; // } catch (e) { // somethingDefault; // } // // rewrite as // // try { // tryBlock; // goto after_catch: // } catch (x) { // with (newCatchScope(e, x)) { // if (condition1) { // something1; // goto after_catch; // } // } // ... // with (newCatchScope(e, x)) { // if (conditionN) { // somethingN; // goto after_catch; // } // } // with (newCatchScope(e, x)) { // somethingDefault; // goto after_catch; // } // } // after_catch: // // If there is no default catch, then the last with block // arround "somethingDefault;" is replaced by "rethrow;" // It is assumed that catch handler generation will store // exeception object in handlerBlock register // Block with local for exception scope objects Node catchScopeBlock = new Node(Token.LOCAL_BLOCK); // expects catchblocks children to be (cond block) pairs. Node cb = catchBlocks.getFirstChild(); boolean hasDefault = false; int scopeIndex = 0; while (cb != null) { int catchLineNo = cb.getLineno(); Node name = cb.getFirstChild(); Node cond = name.getNext(); Node catchStatement = cond.getNext(); cb.removeChild(name); cb.removeChild(cond); cb.removeChild(catchStatement); // Add goto to the catch statement to jump out of catch // but prefix it with LEAVEWITH since try..catch produces // "with"code in order to limit the scope of the exception // object. catchStatement.addChildToBack(new Node(Token.LEAVEWITH)); catchStatement.addChildToBack(makeJump(Token.GOTO, endCatch)); // Create condition "if" when present Node condStmt; if (cond.getType() == Token.EMPTY) { condStmt = catchStatement; hasDefault = true; } else { condStmt = createIf(cond, catchStatement, null, catchLineNo); } // Generate code to create the scope object and store // it in catchScopeBlock register Node catchScope = new Node(Token.CATCH_SCOPE, name, createUseLocal(handlerBlock)); catchScope.putProp(Node.LOCAL_BLOCK_PROP, catchScopeBlock); catchScope.putIntProp(Node.CATCH_SCOPE_PROP, scopeIndex); catchScopeBlock.addChildToBack(catchScope); // Add with statement based on catch scope object catchScopeBlock.addChildToBack( createWith(createUseLocal(catchScopeBlock), condStmt, catchLineNo)); // move to next cb cb = cb.getNext(); ++scopeIndex; } pn.addChildToBack(catchScopeBlock); if (!hasDefault) { // Generate code to rethrow if no catch clause was executed Node rethrow = new Node(Token.RETHROW); rethrow.putProp(Node.LOCAL_BLOCK_PROP, handlerBlock); pn.addChildToBack(rethrow); } pn.addChildToBack(endCatch); } if (hasFinally) { Node.Target finallyTarget = new Node.Target(); pn.setFinally(finallyTarget); // add jsr finally to the try block pn.addChildToBack(makeJump(Token.JSR, finallyTarget)); // jump around finally code Node.Target finallyEnd = new Node.Target(); pn.addChildToBack(makeJump(Token.GOTO, finallyEnd)); pn.addChildToBack(finallyTarget); Node fBlock = new Node(Token.FINALLY, finallyBlock); fBlock.putProp(Node.LOCAL_BLOCK_PROP, handlerBlock); pn.addChildToBack(fBlock); pn.addChildToBack(finallyEnd); } handlerBlock.addChildToBack(pn); return handlerBlock; }

19042 /local/tlutelli/issta_data/temp/all_java1context/java/2006_temp/2006/19042/00c3a706bf401545154202d57d1edaa0e2f9b8b8/IRFactory.java/buggy/src/org/mozilla/javascript/IRFactory.java

throw Debug.abort("illegal case", location);

throw Debug.abort("unknown case", location);

public ATreePrinter printLocation(ALocation location) { switch (location) { case Module(Symbol module): return printSymbol(module); case Field(Void, Symbol field, true): return printSymbol(field.owner()).print('.').printSymbol(field); case Field(ACode object, Symbol field, boolean isStatic): printCode(object).print('.'); if (isStatic) print("<static>").space(); return printSymbol(field); case Local(Symbol local, _): return printSymbol(local); case ArrayItem(ACode array, ACode index): return printCode(array).print('(').printCode(index).print(')'); default: throw Debug.abort("illegal case", location); } }

9617 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/9617/eb5ca252d44bafe0848494c5be6c9fbfd0260eee/ATreePrinter.java/buggy/sources/scalac/atree/ATreePrinter.java

+" &doubleBracket;> and &doubleBracket&gt;"

+" &doubleBracket;> and &doubleBracket;&gt;"

public void testQuotedCDataEndMarker() throws XMLStreamException { try { // First, using pre-defined/char entities String XML = "<root>" +"Ok the usual one: ]]&gt;" +" and then alternatives: &#93;]>" +", &#93;&#93;&gt;" +"</root>"; XMLStreamReader sr = getReader(XML, true, false, true); streamThrough(sr); } catch (Exception e) { fail("Didn't except problems with pre-def/char entity quoted ']]>'; got: "+e); } try { // Then using general entities: String XML = "<!DOCTYPE root [\n" +"<!ENTITY doubleBracket ']]'>\n" +"]\n" +"<root>" +" &doubleBracket;> and &doubleBracket&gt;" +"</root>"; XMLStreamReader sr = getReader(XML, true, false, true); streamThrough(sr); } catch (Exception e) { fail("Didn't except problems with general entity quoted ']]>'; got: "+e); } }

2047 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/2047/37838724c0ce94182ddd5f78a55ad091a8974edb/TestEntityRead.java/clean/dev/src/org/codehaus/stax/test/stream/TestEntityRead.java

0, -1, -1, -1, -1, -1, 124, 125, -1, -1, 10, -1, -1, -1, -1, -1, -1, -1, -1, 318,

-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,

private static final short[] yyCheck2() { return new short[] { 126, -1, -1, -1, -1, -1, -1, -1, 94, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 257, 258, 259, 124, 261, 262, 263, 264, 265, 266, -1, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, -1, 280, -1, -1, 283, 284, 285, 286, 287, 288, 289, 290, 291, -1, 293, 294, 295, 296, 297, -1, 299, -1, -1, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, -1, 313, 314, -1, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, -1, -1, 333, 334, 335, 336, -1, -1, 339, 340, 341, 342, -1, 344, 345, 346, 347, 348, 349, 350, 351, -1, 257, 258, 259, 356, 261, 262, 263, 264, 265, 266, -1, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, -1, 280, -1, -1, 283, 284, 285, 286, 287, 288, 289, 290, 291, -1, 293, 294, 295, 296, 297, -1, 299, -1, -1, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, -1, 313, 314, -1, 316, 317, 318, 319, 320, 321, 322, 323, 324, 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267, 268, 269, -1, 271, -1, -1, -1, -1, 124, -1, -1, 37, 38, 281, 282, 41, 42, 43, 44, 45, -1, 47, 290, 291, -1, 293, 294, 295, 296, 297, -1, -1, 58, 59, 60, -1, 62, 63, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 0, -1, 333, 334, 93, 94, -1, 338, }; }

46454 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/46454/f5c9a1ebd775712f2dc086acfce1a14a123ec632/YyTables.java/clean/src/org/jruby/parser/YyTables.java

public void testIsCompletedToday() { ITask task = new Task("1", "task-1", true); task.setCompleted(true); task.setCompletionDate(new Date()); assertTrue(manager.isCompletedToday(task)); MockRepositoryTask mockTask = new MockRepositoryTask(MOCK_REPOSITORY_URL+"-1"); manager.getTaskList().addTask(mockTask); mockTask.setCompleted(true); mockTask.setCompletionDate(new Date()); assertFalse(manager.isCompletedToday(mockTask)); mockTask = new MockRepositoryTask(MOCK_REPOSITORY_URL+"-2"); manager.getTaskList().addTask(mockTask); mockTask.setCompleted(true); mockTask.setCompletionDate(new Date()); repository.setAuthenticationCredentials("testUser", "testPassword"); mockTask.setOwner("testUser"); assertTrue(manager.isCompletedToday(mockTask)); }

51989 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/51989/a5afacf1ca03ddad22ebd22b524fac207d9216ab/TaskListManagerTest.java/clean/org.eclipse.mylyn.tasks.tests/src/org/eclipse/mylyn/tasks/tests/TaskListManagerTest.java

recoverOriginalLibrary( "LibraryToReload_backup.xml", "LibraryToReload.xml" );

String libFilePath = (String) filePaths.get( 1 );

public void testReloadLibraryWithException( ) throws Exception { openDesign( "DesignToReloadLibrary.xml" ); //$NON-NLS-1$ // make modification on its library. openLibrary( "Library_1.xml" );//$NON-NLS-1$ try { designHandle.reloadLibrary( libraryHandle ); fail( ); } catch ( SemanticException e ) { assertEquals( LibraryException.DESIGN_EXCEPTION_LIBRARY_NOT_FOUND, e.getErrorCode( ) ); } recoverOriginalLibrary( "LibraryToReload_backup.xml", //$NON-NLS-1$ "LibraryToReload.xml" ); //$NON-NLS-1$ openLibrary( "LibraryToReload.xml" ); //$NON-NLS-1$ File f = new File( getClassFolder( ) + INPUT_FOLDER + "LibraryToReload.xml" ); //$NON-NLS-1$ if ( f.exists( ) ) f.delete( ); designHandle.reloadLibrary( libraryHandle ); assertNull( designHandle.findElement( "table1" ).getExtends( ) ); //$NON-NLS-1$ assertNotNull( designHandle .findElement( "table1" ).getStringProperty( DesignElementHandle.EXTENDS_PROP ) ); //$NON-NLS-1$ File f1 = new File( getClassFolder( ) + INPUT_FOLDER + "LibraryToReload_errors.xml" ); //$NON-NLS-1$ FileInputStream fis = new FileInputStream( f1 ); FileOutputStream fos = new FileOutputStream( f ); byte[] data = new byte[10000]; fis.read( data ); fos.write( data ); fis.close( ); fos.close( ); try { designHandle.reloadLibrary( libraryHandle ); fail( ); } catch ( LibraryException e ) { save( ); } recoverOriginalLibrary( "LibraryToReload_backup.xml", //$NON-NLS-1$ "LibraryToReload.xml" ); //$NON-NLS-1$ compareTextFile( "DesignToReloadLibrary_golden_1.xml"); //$NON-NLS-1$ }

5230 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/5230/14f7f5097c347fb97b4edd5251bb64dc3c62527b/ReloadLibraryTest.java/buggy/model/org.eclipse.birt.report.model.tests/test/org/eclipse/birt/report/model/library/ReloadLibraryTest.java

HttpServletResponse response) throws IOException, ServletException {

HttpServletResponse response) throws IOException, ServletException {

public void doPost(HttpServletRequest request, HttpServletResponse response) throws IOException, ServletException { process(request, response); }

48068 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/48068/893cf1f05ff2aed2f868307f45763b5b3bc5a257/ActionServlet.java/buggy/src/share/org/apache/struts/action/ActionServlet.java

String getColorizedContent(final String content, final String fileExtension) throws IOException;

String getColorizedContent(final String content, final String fileExtension, final String encoding) throws IOException;

String getColorizedContent(final String content, final String fileExtension) throws IOException;

50734 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50734/fbfc226d156d9aabfa62e069392e1ed246b2985c/Colorer.java/buggy/sventon/dev/java/src/de/berlios/sventon/colorer/Colorer.java

try { position++; bCodeStream[classFileOffset++] = OPC_iconst_0; } catch (IndexOutOfBoundsException e) { resizeByteArray(OPC_iconst_0);

if (classFileOffset >= bCodeStream.length) { resizeByteArray();

final public void iconst_0() { if (DEBUG) System.out.println(position + "\t\ticonst_0"); //$NON-NLS-1$ countLabels = 0; stackDepth++; if (stackDepth > stackMax) stackMax = stackDepth; try { position++; bCodeStream[classFileOffset++] = OPC_iconst_0; } catch (IndexOutOfBoundsException e) { resizeByteArray(OPC_iconst_0); }}

10698 /local/tlutelli/issta_data/temp/all_java1context/java/2006_temp/2006/10698/3a562aaf09f9f323b583086b80b4683378886606/CodeStream.java/buggy/org.eclipse.jdt.core/compiler/org/eclipse/jdt/internal/compiler/codegen/CodeStream.java

public void visitLocalVariableInstruction(LocalVariableInstruction obj) { }

public void visitLocalVariableInstruction(LocalVariableInstruction obj) { }

public void visitLocalVariableInstruction(LocalVariableInstruction obj) { }

7352 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/7352/4748a5a9b76f3dd763ee6bc7755c932a711bd6a6/AbstractFrameModelingVisitor.java/clean/findbugs/src/java/edu/umd/cs/findbugs/ba/AbstractFrameModelingVisitor.java

if (log.isInfoEnabled())

if (log.isDebugEnabled())

public void doTest(String jspName) throws Exception { WebRequest request = new GetMethodWebRequest(jspName); WebResponse response = runner.getResponse(request); if (log.isInfoEnabled()) { log.info(response.getText()); } WebTable[] tables = response.getTables(); assertEquals("Expected one table in result.", 1, tables.length); WebLink[] links = response.getLinks(); assertEquals("Wrong number of links in result.", 1, links.length); assertEquals("Parameter in link should be encoded.", "/context/dynlink?param=1%2B1", links[0].getURLString()); }

7284 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/7284/69ec962b1ef555522adf327d671a25f9f991f896/EncodedParametersTest.java/buggy/displaytag/src/test/java/org/displaytag/tags/EncodedParametersTest.java

Symbol alias = staticsClass.newTypeAlias(Position.NOPOS, translateAttributes(ntype), aliasname, make.classType(nclazz)); statics.enterNoHide(alias);

protected String doComplete(Symbol root) { clazz = root; clazz.owner().initialize(); //??? if (make == null) make = new JavaTypeCreator(global.definitions); clazz.flags = translateAttributes(type); Type[] ifaces = type.getInterfaces(); scalac.symtab.Type[] baseTypes = new scalac.symtab.Type[ifaces.length+1]; baseTypes[0] = type.BaseType() != null ? getCLRType(type.BaseType()) : (type.IsInterface() ? make.objectType() : make.anyType()); for (int i = 0; i < ifaces.length; i++) baseTypes[i + 1] = getCLRType(ifaces[i]); members = new Scope(); statics = new Scope(); scalac.symtab.Type clazzInfo = scalac.symtab.Type.compoundType(baseTypes, members, clazz); clazz.setInfo(clazzInfo); Symbol staticsModule = clazz.linkedModule(); staticsClass = staticsModule.moduleClass(); assert staticsClass.isModuleClass(): Debug.show(staticsClass); scalac.symtab.Type staticsInfo = scalac.symtab.Type.compoundType (scalac.symtab.Type.EMPTY_ARRAY, statics, staticsClass); staticsClass.setInfo(staticsInfo); staticsModule.setInfo(make.classType(staticsClass)); clazzType = make.classType(clazz); // import nested types Type[] nestedTypes = type.getNestedTypes(); for (int i = 0; i < nestedTypes.length; i++) { Type ntype = nestedTypes[i]; if (ntype.IsNestedPrivate() || ntype.IsNestedAssembly() || ntype.IsNestedFamANDAssem()) continue; int j = ntype.FullName.lastIndexOf('.'); String n = (j < 0 ? ntype.FullName : ntype.FullName.substring(j + 1)) .replace('+', '#'); Name classname = Name.fromString(n).toTypeName(); Name aliasname = Name.fromString(ntype.Name).toTypeName(); // put the class at the level of its outermost class // the owner of a class is always its most specific package CLRClassParser loader = new CLRClassParser(global, ntype); SymbolOrigin origin = SymbolOrigin.CLRAssembly(ntype.Assembly()); Symbol nclazz = clazz.owner().newLoadedClass (JAVA, classname, loader, null, origin); clrTypes.map(nclazz, ntype); // create an alias in the module of the outer class Symbol alias = staticsClass.newTypeAlias(Position.NOPOS, translateAttributes(ntype), aliasname, make.classType(nclazz)); statics.enterNoHide(alias); } FieldInfo[] fields = type.getFields(); for (int i = 0; i < fields.length; i++) { if (fields[i].IsPrivate() || fields[i].IsAssembly() || fields[i].IsFamilyAndAssembly()) continue; int mods = translateAttributes(fields[i]); Name name = Name.fromString(fields[i].Name); scalac.symtab.Type fieldType = getCLRType(fields[i].FieldType); if (fields[i].IsLiteral() && !fields[i].FieldType.IsEnum()) fieldType = make.constantType( getConstant(fieldType.symbol(), fields[i].getValue())); Symbol owner = fields[i].IsStatic() ? staticsClass : clazz; Symbol field = owner.newField(Position.NOPOS, mods, name); parseMeta(field, fields[i], fieldType); (fields[i].IsStatic() ? statics : members).enterOrOverload(field); clrTypes.map(field, fields[i]); } Set methodsSet = new HashSet(Arrays.asList(type.getMethods())); PropertyInfo[] props = type.getProperties(); for (int i = 0; i < props.length; i++) { scalac.symtab.Type proptype = getCLSType(props[i].PropertyType); if (proptype == null) continue; MethodInfo getter = props[i].GetGetMethod(true); MethodInfo setter = props[i].GetSetMethod(true); if (getter == null || getter.IsPrivate() || getter.IsAssembly() || getter.IsFamilyAndAssembly()) continue; assert props[i].PropertyType == getter.ReturnType; Name n; Symbol method; scalac.symtab.Type mtype; ParameterInfo[] gparams = getter.GetParameters(); if (gparams.length == 0) { n = Name.fromString(props[i].Name); mtype = scalac.symtab.Type.PolyType(Symbol.EMPTY_ARRAY, proptype); } else { n = Names.apply; mtype = methodType(getter, getter.ReturnType); } Symbol owner = getter.IsStatic() ? staticsClass : clazz; int mods = translateAttributes(getter); method = owner.newMethod(Position.NOPOS, mods, n); setParamOwners(mtype, method); method.setInfo(mtype); (getter.IsStatic() ? statics : members).enterOrOverload(method); clrTypes.map(method, getter); assert methodsSet.contains(getter) : "" + getter; methodsSet.remove(getter); if (setter == null || setter.IsPrivate() || setter.IsAssembly() || setter.IsFamilyAndAssembly()) continue; ParameterInfo[] sparams = setter.GetParameters(); assert getter.IsStatic() == setter.IsStatic(); assert setter.ReturnType == clrTypes.VOID; assert sparams.length == gparams.length + 1 : "" + getter + "; " + setter; if (gparams.length == 0) n = Name.fromString(n.toString() + Names._EQ); else n = Names.update; mods = translateAttributes(setter); method = owner.newMethod(Position.NOPOS, mods, n); mtype = methodType(setter, global.definitions.UNIT_TYPE()); setParamOwners(mtype, method); method.setInfo(mtype); (setter.IsStatic() ? statics : members).enterOrOverload(method); clrTypes.map(method, setter); assert methodsSet.contains(setter) : "" + setter; methodsSet.remove(setter); } for (Iterator i = methodsSet.iterator(); i.hasNext(); ) { MethodInfo method = (MethodInfo)i.next(); if ((clrTypes.getSymbol(method) != null) || method.IsPrivate() || method.IsAssembly() || method.IsFamilyAndAssembly()) continue; createMethod(method); } // for enumerations introduce comparison and bitwise logical operations; // the backend should recognize and replace them with comparison or // bitwise logical operations on the primitive underlying type if (type.IsEnum()) { scalac.symtab.Type[] argTypes = new scalac.symtab.Type[] {clazzType}; int mods = Modifiers.JAVA | Modifiers.FINAL; for (int i = 0; i < ENUM_CMP_NAMES.length; i++) { scalac.symtab.Type enumCmpType = make.methodType(argTypes, global.definitions.boolean_TYPE(), scalac.symtab.Type.EMPTY_ARRAY); Symbol enumCmp = clazz.newMethod (Position.NOPOS, mods, ENUM_CMP_NAMES[i]); setParamOwners(enumCmpType, enumCmp); enumCmp.setInfo(enumCmpType); members.enterOrOverload(enumCmp); } for (int i = 0; i < ENUM_BIT_LOG_NAMES.length; i++) { scalac.symtab.Type enumBitLogType = make.methodType (argTypes, clazzType, scalac.symtab.Type.EMPTY_ARRAY); Symbol enumBitLog = clazz.newMethod (Position.NOPOS, mods, ENUM_BIT_LOG_NAMES[i]); setParamOwners(enumBitLogType, enumBitLog); enumBitLog.setInfo(enumBitLogType); members.enterOrOverload(enumBitLog); } } ConstructorInfo[] constrs = type.getConstructors(); for (int i = 0; i < constrs.length; i++) { if (constrs[i].IsStatic() || constrs[i].IsPrivate() || constrs[i].IsAssembly() || constrs[i].IsFamilyAndAssembly()) continue; createConstructor(constrs[i]); } Symbol constr = clazz.primaryConstructor(); if (!constr.isInitialized()) { constr.setInfo(scalac.symtab.Type.MethodType (Symbol.EMPTY_ARRAY, clazzType)); if ((clazz.flags & Modifiers.INTERFACE) == 0) constr.flags |= Modifiers.PRIVATE; } parseMeta(clazz, type, clazzInfo); return type + " from assembly " + type.Assembly(); }

32355 /local/tlutelli/issta_data/temp/all_java3context/java/2006_temp/2006/32355/061a14c274eca558d490241b994ca3b780794eab/CLRClassParser.java/clean/sources/scalac/symtab/classfile/CLRClassParser.java

nodeList.add(listNode2);

nodeList.add(listNode3);

ArrayList new26() { ArrayList nodeList = new ArrayList(); ArrayList nodeArrayList1 = (ArrayList) pop(); TypedLinkedList listNode2 = new TypedLinkedList(); { PStringEntry pstringentryNode1; pstringentryNode1 = (PStringEntry)nodeArrayList1.get(0); if(pstringentryNode1 != null) { listNode2.add(pstringentryNode1); } } nodeList.add(listNode2); return nodeList; }

48893 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/48893/9ba080b0c901d335db2cb543a5bc7d76ff474439/Parser.java/buggy/source/net/sourceforge/texlipse/bibparser/parser/Parser.java

public void setConf(NutchConf conf) {

public void setConf(Configuration conf) {

public void setConf(NutchConf conf) { super.setConf(conf); // the default constructor was called if (this.rules == null) { String filename = getConf().get("urlnormalizer.regex.file"); URL url = getConf().getResource(filename); try { this.rules = readConfigurationFile(url.toString()); } catch (IOException e) { // TODO mb@media-style.com: throw Exception? Because broken api. throw new RuntimeException(e.getMessage(), e); } catch (MalformedPatternException e) { // TODO mb@media-style.com: throw Exception? Because broken api. throw new RuntimeException(e.getMessage(), e); } } }

1316 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/1316/25437bc825d50715dcc9a289a1b4c8fbbc6aced1/RegexUrlNormalizer.java/buggy/src/java/org/apache/nutch/net/RegexUrlNormalizer.java

return i != null ? i.intValue() : 0;

return i != null ? i.intValue() : -1;

public synchronized int getContentLength() { Integer i = (Integer)propertiesMap.get(FILE_SIZE); return i != null ? i.intValue() : 0; }

5134 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/5134/fff57b4b651bc4003027538bf5191349456c108b/ManagedDownloader.java/clean/components/gnutella-core/src/main/java/com/limegroup/gnutella/downloader/ManagedDownloader.java

{"Minimal_Days",new java.lang.Integer(1),},

{"Minimal_Days",java.lang.Integer.valueOf(1),},

protected Object[][] getContents() { Object[][] contents = { {"Minimal_Days",new java.lang.Integer(1),}, {"Date_SHORT","d/MM/yy",}, {"Time_FULL","H.mm' u. 'z",}, {"CurrencySymbol","\u20ac",}, {"IntCurrencySymbol","EUR",}, {"Currency","#,##0.00 \u00a4",}, };return contents;}

54769 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54769/4cd556f6bcafbcc4bb2142e05523342b18bd2dda/Locale_nl_BE.java/clean/modules/luni/src/main/java/org/apache/harmony/luni/internal/locale/Locale_nl_BE.java

if ( oc.contains( COLLECTIVE_SUBENTRY_OC ) )

if ( oc.contains( COLLECTIVE_AREA ) )

private int getSubentryTypes( Attributes subentry ) throws NamingException { int types = 0; Attribute oc = subentry.get( "objectClass" ); if ( oc == null ) { throw new LdapSchemaViolationException( "A subentry must have an objectClass attribute", ResultCodeEnum.OBJECTCLASSVIOLATION ); } if ( oc.contains( AUTONOUMOUS_AREA_SUBENTRY_OC ) ) { types |= Subentry.AUTONOMOUS_AREA_SUBENTRY; } if ( oc.contains( AC_SUBENTRY_OC ) ) { types |= Subentry.ACCESS_CONTROL_SUBENTRY; } if ( oc.contains( SCHEMA_SUBENTRY_OC ) ) { types |= Subentry.SCHEMA_SUBENTRY; } if ( oc.contains( COLLECTIVE_SUBENTRY_OC ) ) { types |= Subentry.COLLECTIVE_SUBENTRY; } return types; }

17035 /local/tlutelli/issta_data/temp/all_java1context/java/2006_temp/2006/17035/7a89d588ce906f19fa641170e9721907534af40e/SubentryService.java/clean/core/src/main/java/org/apache/directory/server/core/subtree/SubentryService.java

return 3;

return 4;

public int getColumnCount() { return 3; } //}}}

6564 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/6564/a06d5bdd990bb0b2b070235682983982a0dce844/ManagePanel.java/buggy/org/gjt/sp/jedit/pluginmgr/ManagePanel.java

BufferedReader br = new BufferedReader(new FileReader(settings.getReleaseNotes()));

br = new BufferedReader(new FileReader(settings.getReleaseNotes()));

public ECUEditor() { // get settings from xml try { InputSource src = new InputSource(new FileInputStream(new File("./settings.xml"))); DOMSettingsUnmarshaller domUms = new DOMSettingsUnmarshaller(); DOMParser parser = new DOMParser(); parser.parse(src); Document doc = parser.getDocument(); settings = domUms.unmarshallSettings(doc.getDocumentElement()); if (!settings.getRecentVersion().equalsIgnoreCase(version)) { // new version being used, display release notes JTextArea releaseNotes = new JTextArea(); releaseNotes.setEditable(false); releaseNotes.setWrapStyleWord(true); releaseNotes.setLineWrap(true); releaseNotes.setFont(new Font("Tahoma", Font.PLAIN, 12)); JScrollPane scroller = new JScrollPane(releaseNotes, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); scroller.setPreferredSize(new Dimension(600,500)); BufferedReader br = new BufferedReader(new FileReader(settings.getReleaseNotes())); StringBuffer sb = new StringBuffer(); while (br.ready()) { sb.append(br.readLine() + "\n"); } releaseNotes.setText(sb+""); JOptionPane.showMessageDialog(this, scroller, "Enginuity " + version + " Release Notes", JOptionPane.INFORMATION_MESSAGE); } } catch (Exception ex) { JOptionPane.showMessageDialog(this, "Settings file not found.\n" + "A new file will be created.", "Error Loading Settings", JOptionPane.INFORMATION_MESSAGE); } setSize(getSettings().getWindowSize()); setLocation(getSettings().getWindowLocation()); if (getSettings().isWindowMaximized() == true) setExtendedState(JFrame.MAXIMIZED_BOTH); JScrollPane rightScrollPane = new JScrollPane(rightPanel, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED); JScrollPane leftScrollPane = new JScrollPane(imageList, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED); splitPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, leftScrollPane, rightScrollPane); splitPane.setDividerSize(2); splitPane.setDividerLocation(getSettings().getSplitPaneLocation()); splitPane.addPropertyChangeListener(this); getContentPane().add(splitPane); rightPanel.setBackground(Color.BLACK); imageList.setScrollsOnExpand(true); imageList.setContainer(this); //create menubar and toolbar menuBar = new ECUEditorMenuBar(this); this.setJMenuBar(menuBar); toolBar = new ECUEditorToolBar(this); this.add(toolBar, BorderLayout.NORTH); //set remaining window properties setIconImage(new ImageIcon("./graphics/enginuity-ico.gif").getImage()); setDefaultCloseOperation(EXIT_ON_CLOSE); addWindowListener(this); setTitle(titleText); setVisible(true); }

48870 /local/tlutelli/issta_data/temp/all_java4context/java/2006_temp/2006/48870/d28857129c457538d854eb19124ccddf5695887d/ECUEditor.java/clean/src/enginuity/ECUEditor.java

value = new String(Base64.base64ToByteArray(new StringBuffer(cdata.toString().trim()), null), "UTF-8");

value = new String(SVNBase64.base64ToByteArray(new StringBuffer(cdata.toString().trim()), null), "UTF-8");

protected void endElement(DAVElement parent, DAVElement element, StringBuffer cdata) throws SVNException { if (element == OPEN_DIRECTORY || element == ADD_DIRECTORY) { myEditor.closeDir(); if ("".equals(myPath)) { myEditor.closeEdit(); } myChecksum = null; myPath = SVNPathUtil.removeTail(myPath); } else if (element == OPEN_FILE || element == ADD_FILE) { myEditor.closeFile(myPath, myChecksum); myChecksum = null; myPath = SVNPathUtil.removeTail(myPath); } else if (element == DAVElement.MD5_CHECKSUM) { myChecksum = cdata.toString(); } else if (element == DAVElement.CREATOR_DISPLAY_NAME || element == DAVElement.VERSION_NAME || element == DAVElement.CREATION_DATE || element == SET_PROP || element == DAVElement.HREF) { if (myPropertyName == null) { myPropertyName = computeWCPropertyName(element); } String value = cdata.toString(); if ("base64".equals(myEncoding)) { try { value = new String(Base64.base64ToByteArray(new StringBuffer(cdata.toString().trim()), null), "UTF-8"); } catch (UnsupportedEncodingException e) { value = new String(Base64.base64ToByteArray(new StringBuffer(cdata.toString().trim()), null)); } } if (myIsDirectory) { myEditor.changeDirProperty(myPropertyName, value); } else { myEditor.changeFileProperty(myPath, myPropertyName, value); } myPropertyName = null; myEncoding = null; } else if (element == TX_DELTA && myIsFetchContent) { setDeltaProcessing(false); } }

5695 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/5695/7d9e268d6a37ea439479b898087708ee528aa904/DAVEditorHandler.java/clean/javasvn/src/org/tmatesoft/svn/core/internal/io/dav/handlers/DAVEditorHandler.java

public void actionPerformed(ActionEvent e) { try { String lsid = (String) JOptionPane.showInputDialog(null, "LSID to open?", "LSID Required", JOptionPane.QUESTION_MESSAGE, null, null, "URN:LSID:"); if (lsid != null && store != null) {

public void actionPerformed(ActionEvent e) { try { String lsid = (String) JOptionPane.showInputDialog(null, "LSID to open?", "LSID Required", JOptionPane.QUESTION_MESSAGE, null, null, "URN:LSID:"); if (lsid != null && store != null) {

public void actionPerformed(ActionEvent e) { try { String lsid = (String) JOptionPane.showInputDialog(null, "LSID to open?", "LSID Required", JOptionPane.QUESTION_MESSAGE, null, null, "URN:LSID:"); if (lsid != null && store != null) { DataThing thing = store.fetchDataThing(lsid); addDataThing(thing); } } catch (Exception ex) { JOptionPane.showMessageDialog(null, "Problem opening content from web : \n" + ex.getMessage(), "Exception!", JOptionPane.ERROR_MESSAGE); } }

7616 /local/tlutelli/issta_data/temp/all_java0context/java/2006_temp/2006/7616/6001f3303b9becce97c03f7b0fae6a5972cb3bdf/DataThingConstructionPanel.java/buggy/trunk/taverna1.0/src/org/embl/ebi/escience/scuflui/DataThingConstructionPanel.java

" should be opened in a try block, and closed in a finally block #loc";

" should be opened in a try block, and closed in a finally block #loc";

public String buildErrorString(PsiElement location){ final PsiExpression expression = (PsiExpression) location; final PsiType type = expression.getType(); final String text = type.getPresentableText(); return "JDBC " + text + " should be opened in a try block, and closed in a finally block #loc"; }

17306 /local/tlutelli/issta_data/temp/all_java1context/java/2006_temp/2006/17306/bd57f07c33c419f20715b114b71a7e93425b34c9/JDBCResourceInspection.java/buggy/plugins/InspectionGadgets/src/com/siyeh/ig/resources/JDBCResourceInspection.java