h4iku/coconut_java2006 · Datasets at Hugging Face

SettingsManager.saveSettings();

public void commit() { getData(); }

52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/65023340f7287fee8d2f1535446bf62c3ed50749/LocalPreference.java/buggy/src/java/org/jivesoftware/sparkimpl/settings/local/LocalPreference.java

return Res.getString("title.login.settings");

public String getTooltip() { return Res.getString("title.login.settings"); }

52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/65023340f7287fee8d2f1535446bf62c3ed50749/LocalPreference.java/buggy/src/java/org/jivesoftware/sparkimpl/settings/local/LocalPreference.java

getRuby().getIter().push( getRuby().isBlockGiven() ? RubyIter.ITER_PRE : RubyIter.ITER_NOT); RubyObject result = getReceiverClass().call0( getReceiver(), getMethodId(), new RubyPointer(args), getBodyNode(), false); getRuby().getIter().pop();

public RubyObject call(RubyObject[] args) { getRuby().getIter().push( getRuby().isBlockGiven() ? RubyIter.ITER_PRE : RubyIter.ITER_NOT); RubyObject result = getReceiverClass().call0( getReceiver(), getMethodId(), new RubyPointer(args), getBodyNode(), false); getRuby().getIter().pop(); return result; }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/0a7181933af700ea8025a4197f3a5ebcc08333c3/RubyMethod.java/buggy/org/jruby/RubyMethod.java

return result; }

public RubyObject call(RubyObject[] args) { getRuby().getIter().push( getRuby().isBlockGiven() ? RubyIter.ITER_PRE : RubyIter.ITER_NOT); RubyObject result = getReceiverClass().call0( getReceiver(), getMethodId(), new RubyPointer(args), getBodyNode(), false); getRuby().getIter().pop(); return result; }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/0a7181933af700ea8025a4197f3a5ebcc08333c3/RubyMethod.java/buggy/org/jruby/RubyMethod.java

_broker = broker;

this(broker,"wm");

protected WMTemplate(Broker broker) { _broker = broker; }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/78a66b349748346624878ff04bb72f314bdac97c/WMTemplate.java/buggy/webmacro/src/org/webmacro/engine/WMTemplate.java

return (Filter) myFilters.get(name);

return (Filter) _filters.get(name);

public Filter getFilter(String name) { return (Filter) myFilters.get(name); }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/78a66b349748346624878ff04bb72f314bdac97c/WMTemplate.java/buggy/webmacro/src/org/webmacro/engine/WMTemplate.java

return myParameters.get(key);

return _parameters.get(key);

public Object getParam(String key) throws IOException, TemplateException { // perform double checked lock in case template has not yet // been parsed. try { return myParameters.get(key); } catch (NullPointerException e) { synchronized(this) { parse(); return myParameters.get(key); } } }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/78a66b349748346624878ff04bb72f314bdac97c/WMTemplate.java/buggy/webmacro/src/org/webmacro/engine/WMTemplate.java

return myParameters.get(key);

return _parameters.get(key);

public Object getParam(String key) throws IOException, TemplateException { // perform double checked lock in case template has not yet // been parsed. try { return myParameters.get(key); } catch (NullPointerException e) { synchronized(this) { parse(); return myParameters.get(key); } } }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/78a66b349748346624878ff04bb72f314bdac97c/WMTemplate.java/buggy/webmacro/src/org/webmacro/engine/WMTemplate.java

return myParameters;

return _parameters;

public HashMap getParameters() { return myParameters; }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/78a66b349748346624878ff04bb72f314bdac97c/WMTemplate.java/buggy/webmacro/src/org/webmacro/engine/WMTemplate.java

public final void parse() throws IOException, TemplateException { // thread policy: // // unsynchronized code elsewhere will access myContent. We must // ensure that any data copied into myContent is ready for public // use--which means dealing with two subtle issues. First, the Block // created by this method must be written back to main memory BEFORE // being referenced by myContent. Second, once we add it to myContent, // our copy of myContent has to be copied back to main memory as well. // // Therefore we synchronize around the access to myContent so as to // accomplish both these things. newContent will be written to main // memory at the start of the synchronized block, and myContent will // be written to main memory at the close. Block newContent = null; HashMap newParameters = null; Reader source = null; Hashtable newFilters = null; try { Parser parser; try { parser = (Parser) _broker.getValue("parser","wm"); } catch (Exception e) { Engine.log.exception(e); throw new TemplateException("Could not load \"wm\" parser:" + e); } Reader in = getReader(); BlockBuilder bb = parser.parseBlock(toString(),in); in.close(); BuildContext bc = new BuildContext(_broker); newParameters = bc.getLocalVariables(); newFilters = bc.getFilters(); newContent = (Block) bb.build(bc); } catch (BuildException be) { newContent = null; _log.error("Template contained invalid data: " + be); throw be; } catch (IOException e) { newContent = null; // don't let the old one survive _log.error("Template: Could not read template: " + this); throw e; } finally { try { source.close(); } catch (Exception e) { } synchronized(this) { myParameters = newParameters; myFilters = newFilters; myContent = newContent; } } }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/78a66b349748346624878ff04bb72f314bdac97c/WMTemplate.java/buggy/webmacro/src/org/webmacro/engine/WMTemplate.java

public final void parse() throws IOException, TemplateException { // thread policy: // // unsynchronized code elsewhere will access myContent. We must // ensure that any data copied into myContent is ready for public // use--which means dealing with two subtle issues. First, the Block // created by this method must be written back to main memory BEFORE // being referenced by myContent. Second, once we add it to myContent, // our copy of myContent has to be copied back to main memory as well. // // Therefore we synchronize around the access to myContent so as to // accomplish both these things. newContent will be written to main // memory at the start of the synchronized block, and myContent will // be written to main memory at the close. Block newContent = null; HashMap newParameters = null; Reader source = null; Hashtable newFilters = null; try { Parser parser; try { parser = (Parser) _broker.getValue("parser","wm"); } catch (Exception e) { Engine.log.exception(e); throw new TemplateException("Could not load \"wm\" parser:" + e); } Reader in = getReader(); BlockBuilder bb = parser.parseBlock(toString(),in); in.close(); BuildContext bc = new BuildContext(_broker); newParameters = bc.getLocalVariables(); newFilters = bc.getFilters(); newContent = (Block) bb.build(bc); } catch (BuildException be) { newContent = null; _log.error("Template contained invalid data: " + be); throw be; } catch (IOException e) { newContent = null; // don't let the old one survive _log.error("Template: Could not read template: " + this); throw e; } finally { try { source.close(); } catch (Exception e) { } synchronized(this) { myParameters = newParameters; myFilters = newFilters; myContent = newContent; } } }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/78a66b349748346624878ff04bb72f314bdac97c/WMTemplate.java/buggy/webmacro/src/org/webmacro/engine/WMTemplate.java

public final void parse() throws IOException, TemplateException { // thread policy: // // unsynchronized code elsewhere will access myContent. We must // ensure that any data copied into myContent is ready for public // use--which means dealing with two subtle issues. First, the Block // created by this method must be written back to main memory BEFORE // being referenced by myContent. Second, once we add it to myContent, // our copy of myContent has to be copied back to main memory as well. // // Therefore we synchronize around the access to myContent so as to // accomplish both these things. newContent will be written to main // memory at the start of the synchronized block, and myContent will // be written to main memory at the close. Block newContent = null; HashMap newParameters = null; Reader source = null; Hashtable newFilters = null; try { Parser parser; try { parser = (Parser) _broker.getValue("parser","wm"); } catch (Exception e) { Engine.log.exception(e); throw new TemplateException("Could not load \"wm\" parser:" + e); } Reader in = getReader(); BlockBuilder bb = parser.parseBlock(toString(),in); in.close(); BuildContext bc = new BuildContext(_broker); newParameters = bc.getLocalVariables(); newFilters = bc.getFilters(); newContent = (Block) bb.build(bc); } catch (BuildException be) { newContent = null; _log.error("Template contained invalid data: " + be); throw be; } catch (IOException e) { newContent = null; // don't let the old one survive _log.error("Template: Could not read template: " + this); throw e; } finally { try { source.close(); } catch (Exception e) { } synchronized(this) { myParameters = newParameters; myFilters = newFilters; myContent = newContent; } } }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/78a66b349748346624878ff04bb72f314bdac97c/WMTemplate.java/buggy/webmacro/src/org/webmacro/engine/WMTemplate.java

public final void parse() throws IOException, TemplateException { // thread policy: // // unsynchronized code elsewhere will access myContent. We must // ensure that any data copied into myContent is ready for public // use--which means dealing with two subtle issues. First, the Block // created by this method must be written back to main memory BEFORE // being referenced by myContent. Second, once we add it to myContent, // our copy of myContent has to be copied back to main memory as well. // // Therefore we synchronize around the access to myContent so as to // accomplish both these things. newContent will be written to main // memory at the start of the synchronized block, and myContent will // be written to main memory at the close. Block newContent = null; HashMap newParameters = null; Reader source = null; Hashtable newFilters = null; try { Parser parser; try { parser = (Parser) _broker.getValue("parser","wm"); } catch (Exception e) { Engine.log.exception(e); throw new TemplateException("Could not load \"wm\" parser:" + e); } Reader in = getReader(); BlockBuilder bb = parser.parseBlock(toString(),in); in.close(); BuildContext bc = new BuildContext(_broker); newParameters = bc.getLocalVariables(); newFilters = bc.getFilters(); newContent = (Block) bb.build(bc); } catch (BuildException be) { newContent = null; _log.error("Template contained invalid data: " + be); throw be; } catch (IOException e) { newContent = null; // don't let the old one survive _log.error("Template: Could not read template: " + this); throw e; } finally { try { source.close(); } catch (Exception e) { } synchronized(this) { myParameters = newParameters; myFilters = newFilters; myContent = newContent; } } }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/78a66b349748346624878ff04bb72f314bdac97c/WMTemplate.java/buggy/webmacro/src/org/webmacro/engine/WMTemplate.java

Parser parser; try { parser = (Parser) _broker.getValue("parser","wm"); } catch (Exception e) { Engine.log.exception(e); throw new TemplateException("Could not load \"wm\" parser:" + e); }

Parser parser = getParser();

public final void parse() throws IOException, TemplateException { // thread policy: // // unsynchronized code elsewhere will access myContent. We must // ensure that any data copied into myContent is ready for public // use--which means dealing with two subtle issues. First, the Block // created by this method must be written back to main memory BEFORE // being referenced by myContent. Second, once we add it to myContent, // our copy of myContent has to be copied back to main memory as well. // // Therefore we synchronize around the access to myContent so as to // accomplish both these things. newContent will be written to main // memory at the start of the synchronized block, and myContent will // be written to main memory at the close. Block newContent = null; HashMap newParameters = null; Reader source = null; Hashtable newFilters = null; try { Parser parser; try { parser = (Parser) _broker.getValue("parser","wm"); } catch (Exception e) { Engine.log.exception(e); throw new TemplateException("Could not load \"wm\" parser:" + e); } Reader in = getReader(); BlockBuilder bb = parser.parseBlock(toString(),in); in.close(); BuildContext bc = new BuildContext(_broker); newParameters = bc.getLocalVariables(); newFilters = bc.getFilters(); newContent = (Block) bb.build(bc); } catch (BuildException be) { newContent = null; _log.error("Template contained invalid data: " + be); throw be; } catch (IOException e) { newContent = null; // don't let the old one survive _log.error("Template: Could not read template: " + this); throw e; } finally { try { source.close(); } catch (Exception e) { } synchronized(this) { myParameters = newParameters; myFilters = newFilters; myContent = newContent; } } }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/78a66b349748346624878ff04bb72f314bdac97c/WMTemplate.java/buggy/webmacro/src/org/webmacro/engine/WMTemplate.java

myParameters = newParameters; myFilters = newFilters; myContent = newContent;

_parameters = newParameters; _filters = newFilters; _content = newContent;

public final void parse() throws IOException, TemplateException { // thread policy: // // unsynchronized code elsewhere will access myContent. We must // ensure that any data copied into myContent is ready for public // use--which means dealing with two subtle issues. First, the Block // created by this method must be written back to main memory BEFORE // being referenced by myContent. Second, once we add it to myContent, // our copy of myContent has to be copied back to main memory as well. // // Therefore we synchronize around the access to myContent so as to // accomplish both these things. newContent will be written to main // memory at the start of the synchronized block, and myContent will // be written to main memory at the close. Block newContent = null; HashMap newParameters = null; Reader source = null; Hashtable newFilters = null; try { Parser parser; try { parser = (Parser) _broker.getValue("parser","wm"); } catch (Exception e) { Engine.log.exception(e); throw new TemplateException("Could not load \"wm\" parser:" + e); } Reader in = getReader(); BlockBuilder bb = parser.parseBlock(toString(),in); in.close(); BuildContext bc = new BuildContext(_broker); newParameters = bc.getLocalVariables(); newFilters = bc.getFilters(); newContent = (Block) bb.build(bc); } catch (BuildException be) { newContent = null; _log.error("Template contained invalid data: " + be); throw be; } catch (IOException e) { newContent = null; // don't let the old one survive _log.error("Template: Could not read template: " + this); throw e; } finally { try { source.close(); } catch (Exception e) { } synchronized(this) { myParameters = newParameters; myFilters = newFilters; myContent = newContent; } } }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/78a66b349748346624878ff04bb72f314bdac97c/WMTemplate.java/buggy/webmacro/src/org/webmacro/engine/WMTemplate.java

public final void write(Writer out, Context data) throws IOException { // thread policy: Access to myContent is unsynchronized here at // the cost of having a slightly stale copy. This is OK, because // you might have requested it slightly earlier anyway. You will // always get a consistent copy--either the current one, or one // that was the current one a few milliseconds ago. This is because // a thread setting myContent may not update main memory immediately, // and this thread may not update its copy of myContent immediately // (it may have a stale copy it read earlier). Block content = myContent; // copy to a local var in case it changes // Make sure that all the contents of "content" are up to date--that // our thread is fully synchronized with main memory, so that we don't // have a half-created version. Synchronize on anything to do this: // we will use an object we don't share with any other thread. synchronized(data) { } if (content == null) { try { synchronized(this) { // double check under the lock if (myContent == null) { parse(); } content = myContent; } } catch (Exception e) { _log.exception(e); _log.error("Template: Unable to read template: " + this); out.write(""); } } try { content.write(out,data); } catch (InvalidContextException e) { _log.exception(e); String warning = "Template: Missing data in Map passed to template " + this; _log.warning(warning); out.write(""); } }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/78a66b349748346624878ff04bb72f314bdac97c/WMTemplate.java/buggy/webmacro/src/org/webmacro/engine/WMTemplate.java

public final void write(Writer out, Context data) throws IOException { // thread policy: Access to myContent is unsynchronized here at // the cost of having a slightly stale copy. This is OK, because // you might have requested it slightly earlier anyway. You will // always get a consistent copy--either the current one, or one // that was the current one a few milliseconds ago. This is because // a thread setting myContent may not update main memory immediately, // and this thread may not update its copy of myContent immediately // (it may have a stale copy it read earlier). Block content = myContent; // copy to a local var in case it changes // Make sure that all the contents of "content" are up to date--that // our thread is fully synchronized with main memory, so that we don't // have a half-created version. Synchronize on anything to do this: // we will use an object we don't share with any other thread. synchronized(data) { } if (content == null) { try { synchronized(this) { // double check under the lock if (myContent == null) { parse(); } content = myContent; } } catch (Exception e) { _log.exception(e); _log.error("Template: Unable to read template: " + this); out.write(""); } } try { content.write(out,data); } catch (InvalidContextException e) { _log.exception(e); String warning = "Template: Missing data in Map passed to template " + this; _log.warning(warning); out.write(""); } }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/78a66b349748346624878ff04bb72f314bdac97c/WMTemplate.java/buggy/webmacro/src/org/webmacro/engine/WMTemplate.java

Block content = myContent;

Block content = _content;

public final void write(Writer out, Context data) throws IOException { // thread policy: Access to myContent is unsynchronized here at // the cost of having a slightly stale copy. This is OK, because // you might have requested it slightly earlier anyway. You will // always get a consistent copy--either the current one, or one // that was the current one a few milliseconds ago. This is because // a thread setting myContent may not update main memory immediately, // and this thread may not update its copy of myContent immediately // (it may have a stale copy it read earlier). Block content = myContent; // copy to a local var in case it changes // Make sure that all the contents of "content" are up to date--that // our thread is fully synchronized with main memory, so that we don't // have a half-created version. Synchronize on anything to do this: // we will use an object we don't share with any other thread. synchronized(data) { } if (content == null) { try { synchronized(this) { // double check under the lock if (myContent == null) { parse(); } content = myContent; } } catch (Exception e) { _log.exception(e); _log.error("Template: Unable to read template: " + this); out.write(""); } } try { content.write(out,data); } catch (InvalidContextException e) { _log.exception(e); String warning = "Template: Missing data in Map passed to template " + this; _log.warning(warning); out.write(""); } }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/78a66b349748346624878ff04bb72f314bdac97c/WMTemplate.java/buggy/webmacro/src/org/webmacro/engine/WMTemplate.java

if (myContent == null) {

if (_content == null) {

public final void write(Writer out, Context data) throws IOException { // thread policy: Access to myContent is unsynchronized here at // the cost of having a slightly stale copy. This is OK, because // you might have requested it slightly earlier anyway. You will // always get a consistent copy--either the current one, or one // that was the current one a few milliseconds ago. This is because // a thread setting myContent may not update main memory immediately, // and this thread may not update its copy of myContent immediately // (it may have a stale copy it read earlier). Block content = myContent; // copy to a local var in case it changes // Make sure that all the contents of "content" are up to date--that // our thread is fully synchronized with main memory, so that we don't // have a half-created version. Synchronize on anything to do this: // we will use an object we don't share with any other thread. synchronized(data) { } if (content == null) { try { synchronized(this) { // double check under the lock if (myContent == null) { parse(); } content = myContent; } } catch (Exception e) { _log.exception(e); _log.error("Template: Unable to read template: " + this); out.write(""); } } try { content.write(out,data); } catch (InvalidContextException e) { _log.exception(e); String warning = "Template: Missing data in Map passed to template " + this; _log.warning(warning); out.write(""); } }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/78a66b349748346624878ff04bb72f314bdac97c/WMTemplate.java/buggy/webmacro/src/org/webmacro/engine/WMTemplate.java

content = myContent;

content = _content;

public final void write(Writer out, Context data) throws IOException { // thread policy: Access to myContent is unsynchronized here at // the cost of having a slightly stale copy. This is OK, because // you might have requested it slightly earlier anyway. You will // always get a consistent copy--either the current one, or one // that was the current one a few milliseconds ago. This is because // a thread setting myContent may not update main memory immediately, // and this thread may not update its copy of myContent immediately // (it may have a stale copy it read earlier). Block content = myContent; // copy to a local var in case it changes // Make sure that all the contents of "content" are up to date--that // our thread is fully synchronized with main memory, so that we don't // have a half-created version. Synchronize on anything to do this: // we will use an object we don't share with any other thread. synchronized(data) { } if (content == null) { try { synchronized(this) { // double check under the lock if (myContent == null) { parse(); } content = myContent; } } catch (Exception e) { _log.exception(e); _log.error("Template: Unable to read template: " + this); out.write(""); } } try { content.write(out,data); } catch (InvalidContextException e) { _log.exception(e); String warning = "Template: Missing data in Map passed to template " + this; _log.warning(warning); out.write(""); } }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/78a66b349748346624878ff04bb72f314bdac97c/WMTemplate.java/buggy/webmacro/src/org/webmacro/engine/WMTemplate.java

return (_globals != null) ? _globals.get(name) : null;

if (_globals != null) return _globals.get(name); if (_beanGet != null){ try { return _beanGet.invoke(_bean, new Object[]{ name }); } catch (Exception e){} } return null;

final public Object get(Object name) { return (_globals != null) ? _globals.get(name) : null; }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/504ea334adfb2f014d499c5926b051d4fe3a2bde/Context.java/buggy/webmacro/src/org/webmacro/Context.java

getGlobalVariables().put(name,value);

if (_beanPut != null){ try { _beanPut.invoke(_bean, new Object[]{ name, value }); } catch (Exception e){} } else { getGlobalVariables().put(name,value); }

final public void put(Object name, Object value) { if (_globals == null) { getGlobalVariables().put(name,value); } else { _globals.put(name,value); } }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/504ea334adfb2f014d499c5926b051d4fe3a2bde/Context.java/buggy/webmacro/src/org/webmacro/Context.java

try { _beanGet = bean.getClass().getMethod("get", new Class[]{ java.lang.Object.class }); _beanPut = bean.getClass().getMethod("put", new Class[]{ java.lang.Object.class, java.lang.Object.class }); } catch (Exception e){}

final public void setBean(Object bean) { _bean = bean; }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/504ea334adfb2f014d499c5926b051d4fe3a2bde/Context.java/buggy/webmacro/src/org/webmacro/Context.java

if (isAnnotable() && defaultText) annotationArea.setText("");

if (isAnnotable() && defaultText) { annotationArea.getDocument().removeDocumentListener( annotationAreaListener); annotationArea.setText(""); annotationArea.getDocument().addDocumentListener( annotationAreaListener); }

private void initComponents() { titleLabel = new JLabel(TITLE_MSG+DEFAULT_MSG); saveButton = new JButton("SAVE"); saveButton.setEnabled(false); saveButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { model.save(); } }); annotationArea = new MultilineLabel(); annotationArea.setBackground(Color.WHITE); annotationArea.setBorder(new TitledBorder("Annotation")); deleteBox = new JCheckBox(DELETE_ANNOTATION); listModel = new DefaultListModel(); annotatedByList = new JList(listModel); annotatedByList.setBorder(new TitledBorder("Annotated by")); annotatedByList.setSelectionMode( ListSelectionModel.SINGLE_INTERVAL_SELECTION); annotatedByList.addMouseListener(new MouseAdapter() { public void mouseClicked(MouseEvent e) { if (e.getClickCount() == 1) { showSingleAnnotation(); } } }); annotationAreaListener = new DocumentListener() { /** * Indicates that the object is annotated. * @see DocumentListener#insertUpdate(DocumentEvent) */ public void insertUpdate(DocumentEvent de) { model.setAnnotated(true); } /** * Indicates that the object is annotated. * @see DocumentListener#removeUpdate(DocumentEvent) */ public void removeUpdate(DocumentEvent de) { model.setAnnotated(true); } /** * Required by I/F but no-op implementation in our case. * @see DocumentListener#changedUpdate(DocumentEvent) */ public void changedUpdate(DocumentEvent de) {} }; annotationArea.getDocument().addDocumentListener( annotationAreaListener); annotationArea.addMouseListener(new MouseAdapter() { //Removes default message. public void mouseClicked(MouseEvent e) { if (isAnnotable() && defaultText) annotationArea.setText(""); } }); setComponentsEnabled(false); deleteBox.setSelected(false); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/ea7509babe2344eb702969105eb77096cc5b6bcf/AnnotationPaneUI.java/clean/SRC/org/openmicroscopy/shoola/agents/hiviewer/clipboard/annotator/AnnotationPaneUI.java

defaultText = false;

public void insertUpdate(DocumentEvent de) { model.setAnnotated(true); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/ea7509babe2344eb702969105eb77096cc5b6bcf/AnnotationPaneUI.java/clean/SRC/org/openmicroscopy/shoola/agents/hiviewer/clipboard/annotator/AnnotationPaneUI.java

defaultText = false;

public void removeUpdate(DocumentEvent de) { model.setAnnotated(true); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/ea7509babe2344eb702969105eb77096cc5b6bcf/AnnotationPaneUI.java/clean/SRC/org/openmicroscopy/shoola/agents/hiviewer/clipboard/annotator/AnnotationPaneUI.java

if (isAnnotable() && defaultText) annotationArea.setText("");

if (isAnnotable() && defaultText) { annotationArea.getDocument().removeDocumentListener( annotationAreaListener); annotationArea.setText(""); annotationArea.getDocument().addDocumentListener( annotationAreaListener); }

public void mouseClicked(MouseEvent e) { if (isAnnotable() && defaultText) annotationArea.setText(""); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/ea7509babe2344eb702969105eb77096cc5b6bcf/AnnotationPaneUI.java/clean/SRC/org/openmicroscopy/shoola/agents/hiviewer/clipboard/annotator/AnnotationPaneUI.java

ruby.getRuntime().loadFile((RubyString)arg1, false);

public static RubyObject m_require(Ruby ruby, RubyObject recv, RubyString arg1) { if (arg1.getValue().endsWith(".rb")) { // ruby.getRuntime().load((RubyString)arg1, false); } else if (arg1.getValue().endsWith(".jar")) { File jarFile = new File(arg1.getValue()); if (!jarFile.exists()) { jarFile = new File(new File(ruby.getSourceFile()).getParentFile(), arg1.getValue()); if (!jarFile.exists()) { System.err.println("[Error] Jarfile + \"" + jarFile.getAbsolutePath() + "\"not found."); } } if (jarFile.exists()) { try { ClassLoader javaClassLoader = new URLClassLoader(new URL[] { jarFile.toURL() }, ruby.getJavaClassLoader()); ruby.setJavaClassLoader(javaClassLoader); } catch (MalformedURLException murlExcptn) { } } } return ruby.getNil(); }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/59743974f1f8d5a50153b05647dac2d75d510976/RBKernel.java/buggy/org/jruby/core/RBKernel.java

setSize(240, 310);

public ColourPicker(Color color) { super(); setTitle("Colour Picker Window"); //setSize(250, 350); setModal(true); setResizable(false); float[] vals = new float[4]; vals = color.getComponents(vals); model = new RGBModel(vals[0], vals[1], vals[2], vals[3]); RGBControl control = new RGBControl(model); TabbedPaneUI tabbedPane = new TabbedPaneUI(this, control); setLayout(new GridBagLayout()); GridBagConstraints gbc = new GridBagConstraints(); gbc.gridx = 0; gbc.gridy = 0; gbc.weightx = 80; gbc.weighty = 30; gbc.anchor = GridBagConstraints.CENTER; gbc.fill = GridBagConstraints.BOTH; getContentPane().add(tabbedPane, gbc); pack(); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/d1099f1a40d90a6affae7dfc56a940b82584eb11/ColourPicker.java/buggy/SRC/org/openmicroscopy/shoola/util/ui/colourpicker/ColourPicker.java

log.info("Args:\t"+Arrays.asList(arg0.getArguments()));

log.info("Args:\t"+ (arg0 == null? "()" : Arrays.asList(arg0.getArguments())));

public Object invoke(MethodInvocation arg0) throws Throwable { log.info("Meth:\t"+arg0.getMethod().getName()); log.info("Args:\t"+Arrays.asList(arg0.getArguments())); Object o; try { o = arg0.proceed(); log.info("Rslt:\t"+o); } catch (Throwable t) { log.debug("Excp:\t"+t); throw t; } log(o); return o; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/42b0a0a257ff174843d0ea6cf14ef8fdd3804b7d/ReturnLogger.java/buggy/components/server/src/ome/aop/ReturnLogger.java

log.info("Rslt:\t"+o);

finalOutput = "Rslt:\t"+o;

public Object invoke(MethodInvocation arg0) throws Throwable { log.info("Meth:\t"+arg0.getMethod().getName()); log.info("Args:\t"+Arrays.asList(arg0.getArguments())); Object o; try { o = arg0.proceed(); log.info("Rslt:\t"+o); } catch (Throwable t) { log.debug("Excp:\t"+t); throw t; } log(o); return o; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/42b0a0a257ff174843d0ea6cf14ef8fdd3804b7d/ReturnLogger.java/buggy/components/server/src/ome/aop/ReturnLogger.java

log.debug("Excp:\t"+t);

finalOutput = "Excp:\t"+t;

public Object invoke(MethodInvocation arg0) throws Throwable { log.info("Meth:\t"+arg0.getMethod().getName()); log.info("Args:\t"+Arrays.asList(arg0.getArguments())); Object o; try { o = arg0.proceed(); log.info("Rslt:\t"+o); } catch (Throwable t) { log.debug("Excp:\t"+t); throw t; } log(o); return o; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/42b0a0a257ff174843d0ea6cf14ef8fdd3804b7d/ReturnLogger.java/buggy/components/server/src/ome/aop/ReturnLogger.java

public Object invoke(MethodInvocation arg0) throws Throwable { log.info("Meth:\t"+arg0.getMethod().getName()); log.info("Args:\t"+Arrays.asList(arg0.getArguments())); Object o; try { o = arg0.proceed(); log.info("Rslt:\t"+o); } catch (Throwable t) { log.debug("Excp:\t"+t); throw t; } log(o); return o; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/42b0a0a257ff174843d0ea6cf14ef8fdd3804b7d/ReturnLogger.java/buggy/components/server/src/ome/aop/ReturnLogger.java

System.err.println ("render: >");

protected String renderGT() { return ">"; }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/0dd98294a4b60b5be523f4e9a86fbe699f49c0da/HTMLPageRenderer.java/clean/wiki/src/org/tcdi/opensource/wiki/renderer/HTMLPageRenderer.java

System.err.println ("render: <");

protected String renderLT() { return "<"; }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/0dd98294a4b60b5be523f4e9a86fbe699f49c0da/HTMLPageRenderer.java/clean/wiki/src/org/tcdi/opensource/wiki/renderer/HTMLPageRenderer.java

.append (text)

.append (replace (replace (text, "<", "<"), ">", ">"))

protected String renderQuotedBlock(String text) { StringBuffer sb = new StringBuffer (text.length()); sb.append ("<pre>") .append (text) .append ("</pre>"); return sb.toString (); }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/0dd98294a4b60b5be523f4e9a86fbe699f49c0da/HTMLPageRenderer.java/clean/wiki/src/org/tcdi/opensource/wiki/renderer/HTMLPageRenderer.java

return "<!-- " + data.getType() + " is an unknown WikiData type";

return "";

protected String renderUnknown(WikiData data) { return "<!-- " + data.getType() + " is an unknown WikiData type"; }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/0dd98294a4b60b5be523f4e9a86fbe699f49c0da/HTMLPageRenderer.java/clean/wiki/src/org/tcdi/opensource/wiki/renderer/HTMLPageRenderer.java

final Block actBlock = ruby.getBlock().getCurrent();

final Block actBlock = ruby.getBlockStack().getCurrent();

public final static Block beginCallArgs(final Ruby ruby) { final Block actBlock = ruby.getBlock().getCurrent(); if (ruby.getCurrentIter().isPre()) { ruby.getBlock().pop(); } ruby.getIterStack().push(Iter.ITER_NOT); return actBlock; }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/8db42974495981011f558bcce15e2dfc28681a76/ArgsUtil.java/clean/org/jruby/ast/util/ArgsUtil.java

ruby.getBlock().pop();

ruby.getBlockStack().pop();

public final static Block beginCallArgs(final Ruby ruby) { final Block actBlock = ruby.getBlock().getCurrent(); if (ruby.getCurrentIter().isPre()) { ruby.getBlock().pop(); } ruby.getIterStack().push(Iter.ITER_NOT); return actBlock; }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/8db42974495981011f558bcce15e2dfc28681a76/ArgsUtil.java/clean/org/jruby/ast/util/ArgsUtil.java

ruby.getBlock().push(actBlock);

ruby.getBlockStack().push(actBlock);

public final static void endCallArgs( final Ruby ruby, final Block actBlock) { if (actBlock != null) { // XXX ruby.getBlock().push(actBlock); // Refresh the next attribute. } ruby.getIterStack().pop(); }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/8db42974495981011f558bcce15e2dfc28681a76/ArgsUtil.java/clean/org/jruby/ast/util/ArgsUtil.java

JPopupMenu menu = PopupMenuFactory.getMenu(node); if(menu != null) { Point2D position = e.getPosition(); e.getCamera().viewToLocal(position); int offsetX = (int)Math.round(position.getX()); int offsetY = (int)Math.round(position.getY()); PCanvas canvas = (PCanvas)e.getComponent(); menu.show(canvas,offsetX,offsetY); }

Thumbnail t = (Thumbnail)node; BrowserEnvironment env = BrowserEnvironment.getInstance(); BrowserAgent agent = env.getBrowserAgent(); agent.loadImage(t);

public void execute(PInputEvent e) { PNode node = e.getPickedNode(); JPopupMenu menu = PopupMenuFactory.getMenu(node); if(menu != null) { Point2D position = e.getPosition(); e.getCamera().viewToLocal(position); int offsetX = (int)Math.round(position.getX()); int offsetY = (int)Math.round(position.getY()); // this could be error prone, but hopefully not in context PCanvas canvas = (PCanvas)e.getComponent(); menu.show(canvas,offsetX,offsetY); } }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/a74dcf148f6dd7ae6d4c17a9e0406afba262a755/PiccoloActions.java/buggy/SRC/org/openmicroscopy/shoola/agents/browser/events/PiccoloActions.java

String newNickname = JOptionPane.showInputDialog(groupChatRoom, Res.getString("label.new.nickname") +":", Res.getString("title.change.nickname"), JOptionPane.QUESTION_MESSAGE);

String newNickname = JOptionPane.showInputDialog(groupChatRoom, Res.getString("label.new.nickname") + ":", Res.getString("title.change.nickname"), JOptionPane.QUESTION_MESSAGE);

private void checkPopup(MouseEvent evt) { final int index = list.locationToIndex(evt.getPoint()); list.setSelectedIndex(index); final String selectedUser = getSelectedUser(); final String groupJID = (String)userMap.get(selectedUser); String groupJIDNickname = StringUtils.parseResource(groupJID); final String nickname = groupChatRoom.getNickname(); final Occupant occupant = userManager.getOccupant(groupChatRoom, selectedUser); final boolean admin = SparkManager.getUserManager().isOwnerOrAdmin(groupChatRoom, chat.getNickname()); final boolean moderator = SparkManager.getUserManager().isModerator(groupChatRoom, chat.getNickname()); final boolean userIsAdmin = userManager.isOwnerOrAdmin(occupant); final boolean userIsModerator = userManager.isModerator(occupant); boolean isMe = groupJIDNickname.equals(nickname); JPopupMenu popup = new JPopupMenu(); if (isMe) { Action changeNicknameAction = new AbstractAction() { public void actionPerformed(ActionEvent actionEvent) { String newNickname = JOptionPane.showInputDialog(groupChatRoom, Res.getString("label.new.nickname") +":", Res.getString("title.change.nickname"), JOptionPane.QUESTION_MESSAGE); if (ModelUtil.hasLength(newNickname)) { while (true) { newNickname = newNickname.trim(); try { chat.changeNickname(newNickname); break; } catch (XMPPException e1) { newNickname = JOptionPane.showInputDialog(groupChatRoom, Res.getString("message.nickname.in.use") + ":", Res.getString("title.change.nickname"), JOptionPane.QUESTION_MESSAGE); if (!ModelUtil.hasLength(newNickname)) { break; } } } } } }; changeNicknameAction.putValue(Action.NAME, Res.getString("menuitem.change.nickname")); changeNicknameAction.putValue(Action.SMALL_ICON, SparkRes.getImageIcon(SparkRes.DESKTOP_IMAGE)); if (allowNicknameChange) { popup.add(changeNicknameAction); } } Action chatAction = new AbstractAction() { public void actionPerformed(ActionEvent actionEvent) { String selectedUser = getSelectedUser(); startChat(groupChatRoom, (String)userMap.get(selectedUser)); } }; chatAction.putValue(Action.NAME, Res.getString("menuitem.start.a.chat")); chatAction.putValue(Action.SMALL_ICON, SparkRes.getImageIcon(SparkRes.SMALL_MESSAGE_IMAGE)); if (!isMe) { popup.add(chatAction); } Action blockAction = new AbstractAction() { public void actionPerformed(ActionEvent e) { ImageIcon icon = (ImageIcon)list.getSelectedValue(); String description = icon.getDescription(); if (groupChatRoom.isBlocked(groupJID)) { groupChatRoom.removeBlockedUser(groupJID); icon = getImageIcon(groupJID); model.setElementAt(icon, index); } else { groupChatRoom.addBlockedUser(groupJID); icon = SparkRes.getImageIcon(SparkRes.BRICKWALL_IMAGE); icon.setDescription(description); model.setElementAt(icon, index); } } }; blockAction.putValue(Action.NAME, Res.getString("menuitem.block.user")); blockAction.putValue(Action.SMALL_ICON, SparkRes.getImageIcon(SparkRes.BRICKWALL_IMAGE)); if (!isMe) { if (groupChatRoom.isBlocked(groupJID)) { blockAction.putValue(Action.NAME, Res.getString("menuitem.unblock.user")); } popup.add(blockAction); } Action kickAction = new AbstractAction() { public void actionPerformed(ActionEvent actionEvent) { kickUser(selectedUser); } }; kickAction.putValue(Action.NAME, Res.getString("menuitem.kick.user")); kickAction.putValue(Action.SMALL_ICON, SparkRes.getImageIcon(SparkRes.SMALL_DELETE)); if (moderator && !userIsAdmin && !isMe) { popup.add(kickAction); } // Handle Voice Operations Action voiceAction = new AbstractAction() { public void actionPerformed(ActionEvent actionEvent) { if (userManager.hasVoice(groupChatRoom, selectedUser)) { revokeVoice(selectedUser); } else { grantVoice(selectedUser); } } }; voiceAction.putValue(Action.NAME, Res.getString("menuitem.voice")); voiceAction.putValue(Action.SMALL_ICON, SparkRes.getImageIcon(SparkRes.MEGAPHONE_16x16)); if (moderator && !userIsModerator && !isMe) { if (userManager.hasVoice(groupChatRoom, selectedUser)) { voiceAction.putValue(Action.NAME, Res.getString("menuitem.revoke.voice")); } else { voiceAction.putValue(Action.NAME, Res.getString("menuitem.grant.voice")); } popup.add(voiceAction); } Action banAction = new AbstractAction() { public void actionPerformed(ActionEvent actionEvent) { banUser(selectedUser); } }; banAction.putValue(Action.NAME, Res.getString("menuitem.ban.user")); banAction.putValue(Action.SMALL_ICON, SparkRes.getImageIcon(SparkRes.RED_FLAG_16x16)); if (admin && !userIsModerator && !isMe) { popup.add(banAction); } Action moderatorAction = new AbstractAction() { public void actionPerformed(ActionEvent actionEvent) { if (!userIsModerator) { grantModerator(selectedUser); } else { revokeModerator(selectedUser); } } }; moderatorAction.putValue(Action.SMALL_ICON, SparkRes.getImageIcon(SparkRes.MODERATOR_IMAGE)); if (admin && !userIsModerator) { moderatorAction.putValue(Action.NAME, Res.getString("menuitem.grant.moderator")); popup.add(moderatorAction); } else if (admin && userIsModerator && !isMe) { moderatorAction.putValue(Action.NAME, Res.getString("menuitem.revoke.moderator")); popup.add(moderatorAction); } // Handle Unbanning of users. Action unbanAction = new AbstractAction() { public void actionPerformed(ActionEvent actionEvent) { String jid = ((JMenuItem)actionEvent.getSource()).getText(); unbanUser(jid); } }; if (admin) { JMenu unbanMenu = new JMenu(Res.getString("menuitem.unban")); Iterator bannedUsers = null; try { bannedUsers = chat.getOutcasts().iterator(); } catch (XMPPException e) { Log.error("Error loading all banned users", e); } while (bannedUsers != null && bannedUsers.hasNext()) { Affiliate bannedUser = (Affiliate)bannedUsers.next(); ImageIcon icon = SparkRes.getImageIcon(SparkRes.RED_BALL); JMenuItem bannedItem = new JMenuItem(bannedUser.getJid(), icon); unbanMenu.add(bannedItem); bannedItem.addActionListener(unbanAction); } if (unbanMenu.getMenuComponentCount() > 0) { popup.add(unbanMenu); } } Action inviteAction = new AbstractAction() { public void actionPerformed(ActionEvent actionEvent) { ConferenceUtils.inviteUsersToRoom(groupChatRoom.getConferenceService(), groupChatRoom.getRoomname(), null); } }; inviteAction.putValue(Action.NAME, Res.getString("menuitem.invite.users")); inviteAction.putValue(Action.SMALL_ICON, SparkRes.getImageIcon(SparkRes.CONFERENCE_IMAGE_16x16)); popup.addSeparator(); popup.add(inviteAction); popup.show(list, evt.getX(), evt.getY()); }

52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/78464cb447e4e3046a3cf7c554642f9e12b07fef/ConferenceRoomInfo.java/buggy/src/java/org/jivesoftware/spark/ui/conferences/ConferenceRoomInfo.java

String newNickname = JOptionPane.showInputDialog(groupChatRoom, Res.getString("label.new.nickname") +":", Res.getString("title.change.nickname"), JOptionPane.QUESTION_MESSAGE);

String newNickname = JOptionPane.showInputDialog(groupChatRoom, Res.getString("label.new.nickname") + ":", Res.getString("title.change.nickname"), JOptionPane.QUESTION_MESSAGE);

public void actionPerformed(ActionEvent actionEvent) { String newNickname = JOptionPane.showInputDialog(groupChatRoom, Res.getString("label.new.nickname") +":", Res.getString("title.change.nickname"), JOptionPane.QUESTION_MESSAGE); if (ModelUtil.hasLength(newNickname)) { while (true) { newNickname = newNickname.trim(); try { chat.changeNickname(newNickname); break; } catch (XMPPException e1) { newNickname = JOptionPane.showInputDialog(groupChatRoom, Res.getString("message.nickname.in.use") + ":", Res.getString("title.change.nickname"), JOptionPane.QUESTION_MESSAGE); if (!ModelUtil.hasLength(newNickname)) { break; } } } } }

52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/78464cb447e4e3046a3cf7c554642f9e12b07fef/ConferenceRoomInfo.java/buggy/src/java/org/jivesoftware/spark/ui/conferences/ConferenceRoomInfo.java

if (room != groupChatRoom) { return; }

public void userHasLeft(ChatRoom room, String userid) { int index = getIndex(userid); if (index != -1) { model.removeElementAt(index); } }

52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/78464cb447e4e3046a3cf7c554642f9e12b07fef/ConferenceRoomInfo.java/buggy/src/java/org/jivesoftware/spark/ui/conferences/ConferenceRoomInfo.java

public boolean isOwnerOrAdmin(Occupant occupant) {

public boolean isOwnerOrAdmin(GroupChatRoom groupChatRoom, String nickname) { Occupant occupant = getOccupant(groupChatRoom, nickname);

public boolean isOwnerOrAdmin(Occupant occupant) { if (occupant != null) { String affiliation = occupant.getAffiliation(); if ("owner".equals(affiliation) || "admin".equals(affiliation)) { return true; } } return false; }

52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/274dbf0ef077e2132bf5036ee54b9dbe4b819268/UserManager.java/buggy/src/java/org/jivesoftware/spark/UserManager.java

public boolean isModerator(Occupant occupant) {

public boolean isModerator(GroupChatRoom groupChatRoom, String nickname) { Occupant occupant = getOccupant(groupChatRoom, nickname);

public boolean isModerator(Occupant occupant) { if (occupant != null) { String role = occupant.getRole(); if ("moderator".equals(role)) { return true; } } return false; }

52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/274dbf0ef077e2132bf5036ee54b9dbe4b819268/UserManager.java/buggy/src/java/org/jivesoftware/spark/UserManager.java

Set cat = new HashSet(1); cat.add(parent); classify(children, cat); return ;

public void addExistingObjects(DataObject parent, Set children) throws DSOutOfServiceException, DSAccessException { if (parent instanceof ProjectData) { try { children.toArray(new DatasetData[] {}); } catch (ArrayStoreException ase) { throw new IllegalArgumentException( "items can only be datasets."); } } else if (parent instanceof DatasetData) { try { children.toArray(new ImageData[] {}); } catch (ArrayStoreException ase) { throw new IllegalArgumentException( "items can only be images."); } } else if (parent instanceof CategoryGroupData) { try { children.toArray(new CategoryData[] {}); } catch (ArrayStoreException ase) { throw new IllegalArgumentException( "items can only be categories."); } } else if (parent instanceof CategoryData) { try { children.toArray(new ImageData[] {}); } catch (ArrayStoreException ase) { throw new IllegalArgumentException( "items can only be images."); } Set cat = new HashSet(1); cat.add(parent); classify(children, cat); return ; } else throw new IllegalArgumentException("parent object not supported"); List objects = new ArrayList(); if (parent instanceof ProjectData) { Project mParent = parent.asProject(); ProjectDatasetLink l; Iterator child = children.iterator(); while (child.hasNext()) { l = new ProjectDatasetLink(); l.link(mParent, ((DataObject) child.next()).asDataset()); objects.add(l); } } else if (parent instanceof DatasetData) { Dataset mParent = parent.asDataset(); DatasetImageLink l; Iterator child = children.iterator(); while (child.hasNext()) { l = new DatasetImageLink(); l.link(mParent, ((DataObject) child.next()).asImage()); objects.add(l); } } else if (parent instanceof CategoryGroupData) { CategoryGroup mParent = parent.asCategoryGroup(); CategoryGroupCategoryLink l; Iterator child = children.iterator(); while (child.hasNext()) { l = new CategoryGroupCategoryLink(); l.link(mParent, ((DataObject) child.next()).asCategory()); objects.add(l); } } if (objects.size() != 0) { Iterator i = objects.iterator(); IObject[] array = new IObject[objects.size()]; int index = 0; while (i.hasNext()) { array[index] = (IObject) i.next(); index++; } gateway.createObjects(array, (new PojoOptions()).map()); } }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3be9d381a3d593d28d0b987df4bc2963a9fa97b8/OmeroDataServiceImpl.java/clean/SRC/org/openmicroscopy/shoola/env/data/OmeroDataServiceImpl.java

if (parent instanceof ProjectData) { Project mParent = parent.asProject(); ProjectDatasetLink l; Iterator child = children.iterator(); while (child.hasNext()) { l = new ProjectDatasetLink(); l.link(mParent, ((DataObject) child.next()).asDataset()); objects.add(l); } } else if (parent instanceof DatasetData) { Dataset mParent = parent.asDataset(); DatasetImageLink l; Iterator child = children.iterator(); while (child.hasNext()) { l = new DatasetImageLink(); l.link(mParent, ((DataObject) child.next()).asImage()); objects.add(l); } } else if (parent instanceof CategoryGroupData) { CategoryGroup mParent = parent.asCategoryGroup(); CategoryGroupCategoryLink l; Iterator child = children.iterator(); while (child.hasNext()) { l = new CategoryGroupCategoryLink(); l.link(mParent, ((DataObject) child.next()).asCategory()); objects.add(l); }

IObject ioParent = parent.asIObject(); IObject ioChild; Iterator child = children.iterator(); while (child.hasNext()) { ioChild = ((DataObject) child.next()).asIObject(); objects.add(ModelMapper.linkParentToChild(ioChild, ioParent));

public void addExistingObjects(DataObject parent, Set children) throws DSOutOfServiceException, DSAccessException { if (parent instanceof ProjectData) { try { children.toArray(new DatasetData[] {}); } catch (ArrayStoreException ase) { throw new IllegalArgumentException( "items can only be datasets."); } } else if (parent instanceof DatasetData) { try { children.toArray(new ImageData[] {}); } catch (ArrayStoreException ase) { throw new IllegalArgumentException( "items can only be images."); } } else if (parent instanceof CategoryGroupData) { try { children.toArray(new CategoryData[] {}); } catch (ArrayStoreException ase) { throw new IllegalArgumentException( "items can only be categories."); } } else if (parent instanceof CategoryData) { try { children.toArray(new ImageData[] {}); } catch (ArrayStoreException ase) { throw new IllegalArgumentException( "items can only be images."); } Set cat = new HashSet(1); cat.add(parent); classify(children, cat); return ; } else throw new IllegalArgumentException("parent object not supported"); List objects = new ArrayList(); if (parent instanceof ProjectData) { Project mParent = parent.asProject(); ProjectDatasetLink l; Iterator child = children.iterator(); while (child.hasNext()) { l = new ProjectDatasetLink(); l.link(mParent, ((DataObject) child.next()).asDataset()); objects.add(l); } } else if (parent instanceof DatasetData) { Dataset mParent = parent.asDataset(); DatasetImageLink l; Iterator child = children.iterator(); while (child.hasNext()) { l = new DatasetImageLink(); l.link(mParent, ((DataObject) child.next()).asImage()); objects.add(l); } } else if (parent instanceof CategoryGroupData) { CategoryGroup mParent = parent.asCategoryGroup(); CategoryGroupCategoryLink l; Iterator child = children.iterator(); while (child.hasNext()) { l = new CategoryGroupCategoryLink(); l.link(mParent, ((DataObject) child.next()).asCategory()); objects.add(l); } } if (objects.size() != 0) { Iterator i = objects.iterator(); IObject[] array = new IObject[objects.size()]; int index = 0; while (i.hasNext()) { array[index] = (IObject) i.next(); index++; } gateway.createObjects(array, (new PojoOptions()).map()); } }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3be9d381a3d593d28d0b987df4bc2963a9fa97b8/OmeroDataServiceImpl.java/clean/SRC/org/openmicroscopy/shoola/env/data/OmeroDataServiceImpl.java

Category mParent; CategoryImageLink l;

IObject ioParent, ioChild;

public void classify(Set images, Set categories) throws DSOutOfServiceException, DSAccessException { try { images.toArray(new ImageData[] {}); } catch (ArrayStoreException ase) { throw new IllegalArgumentException( "images only contains ImageData elements."); } try { categories.toArray(new CategoryData[] {}); } catch (ArrayStoreException ase) { throw new IllegalArgumentException( "categories only contains CategoryData elements."); } Iterator category = categories.iterator(); Iterator image; List objects = new ArrayList(); Category mParent; CategoryImageLink l; while (category.hasNext()) { mParent = ((DataObject) category.next()).asCategory(); image = images.iterator(); while (image.hasNext()) { l = new CategoryImageLink(); l.link(mParent, ((DataObject) image.next()).asImage()); objects.add(l); } } if (objects.size() != 0) { Iterator i = objects.iterator(); IObject[] array = new IObject[objects.size()]; int index = 0; while (i.hasNext()) { array[index] = (IObject) i.next(); index++; } gateway.createObjects(array, (new PojoOptions()).map()); } }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3be9d381a3d593d28d0b987df4bc2963a9fa97b8/OmeroDataServiceImpl.java/clean/SRC/org/openmicroscopy/shoola/env/data/OmeroDataServiceImpl.java

mParent = ((DataObject) category.next()).asCategory();

ioParent = ((DataObject) category.next()).asIObject();

public void classify(Set images, Set categories) throws DSOutOfServiceException, DSAccessException { try { images.toArray(new ImageData[] {}); } catch (ArrayStoreException ase) { throw new IllegalArgumentException( "images only contains ImageData elements."); } try { categories.toArray(new CategoryData[] {}); } catch (ArrayStoreException ase) { throw new IllegalArgumentException( "categories only contains CategoryData elements."); } Iterator category = categories.iterator(); Iterator image; List objects = new ArrayList(); Category mParent; CategoryImageLink l; while (category.hasNext()) { mParent = ((DataObject) category.next()).asCategory(); image = images.iterator(); while (image.hasNext()) { l = new CategoryImageLink(); l.link(mParent, ((DataObject) image.next()).asImage()); objects.add(l); } } if (objects.size() != 0) { Iterator i = objects.iterator(); IObject[] array = new IObject[objects.size()]; int index = 0; while (i.hasNext()) { array[index] = (IObject) i.next(); index++; } gateway.createObjects(array, (new PojoOptions()).map()); } }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3be9d381a3d593d28d0b987df4bc2963a9fa97b8/OmeroDataServiceImpl.java/clean/SRC/org/openmicroscopy/shoola/env/data/OmeroDataServiceImpl.java

l = new CategoryImageLink(); l.link(mParent, ((DataObject) image.next()).asImage()); objects.add(l);

ioChild = ((DataObject) image.next()).asIObject(); objects.add(ModelMapper.linkParentToChild(ioChild, ioParent));

public void classify(Set images, Set categories) throws DSOutOfServiceException, DSAccessException { try { images.toArray(new ImageData[] {}); } catch (ArrayStoreException ase) { throw new IllegalArgumentException( "images only contains ImageData elements."); } try { categories.toArray(new CategoryData[] {}); } catch (ArrayStoreException ase) { throw new IllegalArgumentException( "categories only contains CategoryData elements."); } Iterator category = categories.iterator(); Iterator image; List objects = new ArrayList(); Category mParent; CategoryImageLink l; while (category.hasNext()) { mParent = ((DataObject) category.next()).asCategory(); image = images.iterator(); while (image.hasNext()) { l = new CategoryImageLink(); l.link(mParent, ((DataObject) image.next()).asImage()); objects.add(l); } } if (objects.size() != 0) { Iterator i = objects.iterator(); IObject[] array = new IObject[objects.size()]; int index = 0; while (i.hasNext()) { array[index] = (IObject) i.next(); index++; } gateway.createObjects(array, (new PojoOptions()).map()); } }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3be9d381a3d593d28d0b987df4bc2963a9fa97b8/OmeroDataServiceImpl.java/clean/SRC/org/openmicroscopy/shoola/env/data/OmeroDataServiceImpl.java

IObject created = gateway.createObject(obj, (new PojoOptions()).map()); if (parent != null) ModelMapper.linkParentToChild(created, parent.asIObject());

Map options = (new PojoOptions()).map(); IObject created = gateway.createObject(obj, options); if (parent != null) { ModelMapper.linkParentToNewChild(created, parent.asIObject()); }

public DataObject createDataObject(DataObject child, DataObject parent) throws DSOutOfServiceException, DSAccessException { if (child == null) throw new IllegalArgumentException("The child cannot be null."); IObject obj = ModelMapper.createIObject(child, parent); if (obj == null) throw new NullPointerException("Cannot convert object."); IObject created = gateway.createObject(obj, (new PojoOptions()).map()); if (parent != null) ModelMapper.linkParentToChild(created, parent.asIObject()); return PojoMapper.asDataObject(created); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3be9d381a3d593d28d0b987df4bc2963a9fa97b8/OmeroDataServiceImpl.java/clean/SRC/org/openmicroscopy/shoola/env/data/OmeroDataServiceImpl.java

gateway.deleteObject(link, (new PojoOptions()).map());

gateway.deleteObject(link);

public void cutAndPaste(Map toPaste, Map toCut) throws DSOutOfServiceException, DSAccessException { /* try { if ((toPaste == null || toCut == null) || (toPaste.size() == 0 || toCut.size() == 0)) { throw new IllegalArgumentException("No data to cut and Paste."); } Iterator i = toPaste.keySet().iterator(); DataObject parent; while (i.hasNext()) { parent = (DataObject) i.next(); paste(parent, (Set) toPaste.get(parent)); } i = toCut.keySet().iterator(); while (i.hasNext()) { parent = (DataObject) i.next(); //removeDataObjects((Set) toCut.get(parent), parent); cut(parent, (Set) toCut.get(parent)); } } catch (Exception e) { e.printStackTrace(); } */ Iterator i = toPaste.keySet().iterator(); DataObject parent = null; IObject[] children; ImageData img = null; while (i.hasNext()) { System.out.println("to paste 0"); parent = (DataObject) i.next(); Set imgs = (Set) toPaste.get(parent); Iterator j = imgs.iterator(); while (j.hasNext()) { img = (ImageData) j.next(); } } Image ioObject = null; Dataset mParent = parent.asDataset(); DatasetImageLink l = new DatasetImageLink(); ioObject = (Image) gateway.updateObject(img.asIObject(), (new PojoOptions()).map()); l.link(mParent, ioObject); gateway.createObject(l, (new PojoOptions()).map()); i = toCut.keySet().iterator(); while (i.hasNext()) { System.out.println("to remove 0"); parent = (DataObject) i.next(); Set imgs = (Set) toCut.get(parent); Iterator k = imgs.iterator(); while (k.hasNext()) { img = (ImageData) k.next(); } ioObject = (Image) gateway.updateObject(img.asIObject(), (new PojoOptions()).map()); } mParent = parent.asDataset(); List links = ioObject.collectDatasetLinks(null); i = links.iterator(); DatasetImageLink link = null; while (i.hasNext()) { System.out.println("to remove"); link = (DatasetImageLink) i.next(); if (link.getParent().getId() == mParent.getId()) break; } gateway.deleteObject(link, (new PojoOptions()).map()); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3be9d381a3d593d28d0b987df4bc2963a9fa97b8/OmeroDataServiceImpl.java/clean/SRC/org/openmicroscopy/shoola/env/data/OmeroDataServiceImpl.java

link = ModelMapper.unlinkChildFromParent( ((DataObject) i.next()).asImage(), mParent); if (link != null) links.add(link);

link = gateway.findLink(Category.class, mParent, ((DataObject) i.next()).asImage()); if (link != null) links.add(link);

public void declassify(Set images, Set categories) throws DSOutOfServiceException, DSAccessException { try { images.toArray(new ImageData[] {}); } catch (ArrayStoreException ase) { throw new IllegalArgumentException( "The images set only contains ImageData elements."); } try { categories.toArray(new CategoryData[] {}); } catch (ArrayStoreException ase) { throw new IllegalArgumentException( "The categories set only contains CategoryData elements."); } Iterator category = categories.iterator(); List links = new ArrayList(); Iterator i; IObject mParent; IObject link; while (category.hasNext()) { mParent = ((DataObject) category.next()).asIObject(); i = images.iterator(); while (i.hasNext()) { link = ModelMapper.unlinkChildFromParent( ((DataObject) i.next()).asImage(), mParent); if (link != null) links.add(link); } } if (links != null) { gateway.deleteObjects((IObject[]) links.toArray(new IObject[links.size()])); } }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3be9d381a3d593d28d0b987df4bc2963a9fa97b8/OmeroDataServiceImpl.java/clean/SRC/org/openmicroscopy/shoola/env/data/OmeroDataServiceImpl.java

Map options = (new PojoOptions()).map(); gateway.deleteObject(data.asIObject(), options);

gateway.deleteObject(data.asIObject());

public DataObject removeAnnotationFrom(DataObject annotatedObject, AnnotationData data) throws DSOutOfServiceException, DSAccessException { if (data == null) throw new IllegalArgumentException("No annotation to delete."); if (annotatedObject == null) throw new IllegalArgumentException("No annotated DataObject."); if (!(annotatedObject instanceof ImageData) && !(annotatedObject instanceof DatasetData)) throw new IllegalArgumentException("This method only supports " + "ImageData and DatasetData objects."); Map options = (new PojoOptions()).map(); gateway.deleteObject(data.asIObject(), options); return updateDataObject(annotatedObject); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3be9d381a3d593d28d0b987df4bc2963a9fa97b8/OmeroDataServiceImpl.java/clean/SRC/org/openmicroscopy/shoola/env/data/OmeroDataServiceImpl.java

DataObject child;

public Set removeDataObjects(Set children, DataObject parent) throws DSOutOfServiceException, DSAccessException { if (children == null) throw new IllegalArgumentException("The children cannot be null."); if (children.size() == 0) throw new IllegalArgumentException("The children cannot be null."); Iterator i = children.iterator(); if (parent == null) { int index = 0; IObject[] ioObjects = new IObject[children.size()]; while (i.hasNext()) { ioObjects[index] = ((DataObject) i.next()).asIObject(); index++; } gateway.deleteObjects(ioObjects); } else { DataObject child; IObject p = parent.asIObject(); Image img; IObject link; List links = null; List toUpdate = new ArrayList(); while (i.hasNext()) { child = (DataObject) i.next(); if (child instanceof ImageData) { img = child.asImage(); link = ModelMapper.unlinkChildFromParent(img, p); if (links == null) links = new ArrayList(); if (link != null) links.add(link); if (!(toUpdate.contains(p))) toUpdate.add(p); } else { toUpdate.add(ModelMapper.removeIObject(child.asIObject(), p)); } } if (links != null) { gateway.deleteObjects((IObject[]) links.toArray(new IObject[links.size()])); } IObject[] results = gateway.updateObjects( (IObject[]) toUpdate.toArray( new IObject[toUpdate.size()]), (new PojoOptions()).map()); for (int j = 0; j < results.length; j++) PojoMapper.asDataObject(results[j]); } return children; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3be9d381a3d593d28d0b987df4bc2963a9fa97b8/OmeroDataServiceImpl.java/clean/SRC/org/openmicroscopy/shoola/env/data/OmeroDataServiceImpl.java

Image img;

IObject ioChild;

public Set removeDataObjects(Set children, DataObject parent) throws DSOutOfServiceException, DSAccessException { if (children == null) throw new IllegalArgumentException("The children cannot be null."); if (children.size() == 0) throw new IllegalArgumentException("The children cannot be null."); Iterator i = children.iterator(); if (parent == null) { int index = 0; IObject[] ioObjects = new IObject[children.size()]; while (i.hasNext()) { ioObjects[index] = ((DataObject) i.next()).asIObject(); index++; } gateway.deleteObjects(ioObjects); } else { DataObject child; IObject p = parent.asIObject(); Image img; IObject link; List links = null; List toUpdate = new ArrayList(); while (i.hasNext()) { child = (DataObject) i.next(); if (child instanceof ImageData) { img = child.asImage(); link = ModelMapper.unlinkChildFromParent(img, p); if (links == null) links = new ArrayList(); if (link != null) links.add(link); if (!(toUpdate.contains(p))) toUpdate.add(p); } else { toUpdate.add(ModelMapper.removeIObject(child.asIObject(), p)); } } if (links != null) { gateway.deleteObjects((IObject[]) links.toArray(new IObject[links.size()])); } IObject[] results = gateway.updateObjects( (IObject[]) toUpdate.toArray( new IObject[toUpdate.size()]), (new PojoOptions()).map()); for (int j = 0; j < results.length; j++) PojoMapper.asDataObject(results[j]); } return children; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3be9d381a3d593d28d0b987df4bc2963a9fa97b8/OmeroDataServiceImpl.java/clean/SRC/org/openmicroscopy/shoola/env/data/OmeroDataServiceImpl.java

child = (DataObject) i.next(); if (child instanceof ImageData) { img = child.asImage(); link = ModelMapper.unlinkChildFromParent(img, p); if (links == null) links = new ArrayList(); if (link != null) links.add(link); if (!(toUpdate.contains(p))) toUpdate.add(p); } else { toUpdate.add(ModelMapper.removeIObject(child.asIObject(), p)); }

ioChild = ((DataObject) i.next()).asIObject(); link = ModelMapper.unlinkChildFromParent(ioChild, p); if (links == null) links = new ArrayList(); if (link != null) links.add(link); if (!(toUpdate.contains(p))) toUpdate.add(p);

public Set removeDataObjects(Set children, DataObject parent) throws DSOutOfServiceException, DSAccessException { if (children == null) throw new IllegalArgumentException("The children cannot be null."); if (children.size() == 0) throw new IllegalArgumentException("The children cannot be null."); Iterator i = children.iterator(); if (parent == null) { int index = 0; IObject[] ioObjects = new IObject[children.size()]; while (i.hasNext()) { ioObjects[index] = ((DataObject) i.next()).asIObject(); index++; } gateway.deleteObjects(ioObjects); } else { DataObject child; IObject p = parent.asIObject(); Image img; IObject link; List links = null; List toUpdate = new ArrayList(); while (i.hasNext()) { child = (DataObject) i.next(); if (child instanceof ImageData) { img = child.asImage(); link = ModelMapper.unlinkChildFromParent(img, p); if (links == null) links = new ArrayList(); if (link != null) links.add(link); if (!(toUpdate.contains(p))) toUpdate.add(p); } else { toUpdate.add(ModelMapper.removeIObject(child.asIObject(), p)); } } if (links != null) { gateway.deleteObjects((IObject[]) links.toArray(new IObject[links.size()])); } IObject[] results = gateway.updateObjects( (IObject[]) toUpdate.toArray( new IObject[toUpdate.size()]), (new PojoOptions()).map()); for (int j = 0; j < results.length; j++) PojoMapper.asDataObject(results[j]); } return children; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3be9d381a3d593d28d0b987df4bc2963a9fa97b8/OmeroDataServiceImpl.java/clean/SRC/org/openmicroscopy/shoola/env/data/OmeroDataServiceImpl.java

for (int j = 0; j < results.length; j++) PojoMapper.asDataObject(results[j]);

*/

public Set removeDataObjects(Set children, DataObject parent) throws DSOutOfServiceException, DSAccessException { if (children == null) throw new IllegalArgumentException("The children cannot be null."); if (children.size() == 0) throw new IllegalArgumentException("The children cannot be null."); Iterator i = children.iterator(); if (parent == null) { int index = 0; IObject[] ioObjects = new IObject[children.size()]; while (i.hasNext()) { ioObjects[index] = ((DataObject) i.next()).asIObject(); index++; } gateway.deleteObjects(ioObjects); } else { DataObject child; IObject p = parent.asIObject(); Image img; IObject link; List links = null; List toUpdate = new ArrayList(); while (i.hasNext()) { child = (DataObject) i.next(); if (child instanceof ImageData) { img = child.asImage(); link = ModelMapper.unlinkChildFromParent(img, p); if (links == null) links = new ArrayList(); if (link != null) links.add(link); if (!(toUpdate.contains(p))) toUpdate.add(p); } else { toUpdate.add(ModelMapper.removeIObject(child.asIObject(), p)); } } if (links != null) { gateway.deleteObjects((IObject[]) links.toArray(new IObject[links.size()])); } IObject[] results = gateway.updateObjects( (IObject[]) toUpdate.toArray( new IObject[toUpdate.size()]), (new PojoOptions()).map()); for (int j = 0; j < results.length; j++) PojoMapper.asDataObject(results[j]); } return children; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3be9d381a3d593d28d0b987df4bc2963a9fa97b8/OmeroDataServiceImpl.java/clean/SRC/org/openmicroscopy/shoola/env/data/OmeroDataServiceImpl.java

IObject updated = gateway.updateObject(annotatedObject.asIObject(), options);

IObject object = annotatedObject.asIObject(); ModelMapper.unloadCollections(object); IObject updated = gateway.updateObject(object, options);

public DataObject updateAnnotationFor(DataObject annotatedObject, AnnotationData data) throws DSOutOfServiceException, DSAccessException { if (data == null) throw new IllegalArgumentException("No annotation to update."); if (annotatedObject == null) throw new IllegalArgumentException("No annotated DataObject."); if (!(annotatedObject instanceof ImageData) && !(annotatedObject instanceof DatasetData)) throw new IllegalArgumentException("This method only supports " + "ImageData and DatasetData objects."); Map options = (new PojoOptions()).map(); IObject updated = gateway.updateObject(annotatedObject.asIObject(), options); IObject toUpdate = data.asIObject(); ModelMapper.setAnnotatedObject(updated, toUpdate); gateway.updateObject(toUpdate, options); return PojoMapper.asDataObject(updated); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3be9d381a3d593d28d0b987df4bc2963a9fa97b8/OmeroDataServiceImpl.java/clean/SRC/org/openmicroscopy/shoola/env/data/OmeroDataServiceImpl.java

ModelMapper.unloadCollections(ob);;

ModelMapper.unloadCollections(ob);

public DataObject updateDataObject(DataObject object) throws DSOutOfServiceException, DSAccessException { if (object == null) throw new DSAccessException("No object to update."); IObject ob = object.asIObject(); ModelMapper.unloadCollections(ob);; IObject updated = gateway.updateObject(ob, (new PojoOptions()).map()); return PojoMapper.asDataObject(updated); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3be9d381a3d593d28d0b987df4bc2963a9fa97b8/OmeroDataServiceImpl.java/clean/SRC/org/openmicroscopy/shoola/env/data/OmeroDataServiceImpl.java

return service.createDataObjects(objects, options);

IObject[] results = service.createDataObjects(objects, options); return results;

IObject[] createObjects(IObject[] objects, Map options) throws DSOutOfServiceException, DSAccessException { try { IPojos service = getIPojosService(); return service.createDataObjects(objects, options); } catch (Exception e) { handleException(e, "Cannot update the object."); } return null; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3be9d381a3d593d28d0b987df4bc2963a9fa97b8/OMEROGateway.java/buggy/SRC/org/openmicroscopy/shoola/env/data/OMEROGateway.java

return "1.1.9.6";

return "1.1.9.7";

public static String getVersion() { return "1.1.9.6"; }

52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/7645851bdaa2a933966642360f8bb4b56e708043/JiveInfo.java/buggy/src/java/org/jivesoftware/sparkimpl/settings/JiveInfo.java

public static void main(String args[]) throws IOException { int n = Integer.parseInt(args[0]); boolean val = true; Toggle toggle = new Toggle(val); for (int i=0; i<n; i++) { val = toggle.activate().value(); } System.out.println((val) ? "true" : "false"); val = true; NthToggle ntoggle = new NthToggle(true, 3); for (int i=0; i<n; i++) { val = ntoggle.activate().value(); } System.out.println((val) ? "true" : "false"); }

53330 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/53330/eb6c850277407b38bcaefb81155941da0f27b849/methcall.java/buggy/tests/shootout/java-start/methcall.java

public static Annotator getAnnotator(Set objects, Registry ctx) { if (registry == null) registry = ctx; if (objects == null || objects.size() == 0) return null; return singleton.createAnnotator(objects); }

public static Annotator getAnnotator(JFrame parent, Set objects, Registry ctx) { if (registry == null) registry = ctx; if (parent == null) owner = parent; if (objects == null || objects.size() == 0) return null; return singleton.createAnnotator(objects); }

public static Annotator getAnnotator(Set objects, Registry ctx) { if (registry == null) registry = ctx; if (objects == null || objects.size() == 0) return null; return singleton.createAnnotator(objects); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/464efde90db6bc5095c0a7e5952f51ad0f37ca86/AnnotatorFactory.java/buggy/SRC/org/openmicroscopy/shoola/agents/util/annotator/view/AnnotatorFactory.java

public static Classifier getClassifier(Set objects, Class rootType, long rootID, int m, Registry ctx)

public static Classifier getClassifier(JFrame parent, Set objects, Class rootType, long rootID, int m, Registry ctx)

public static Classifier getClassifier(Set objects, Class rootType, long rootID, int m, Registry ctx) { if (registry == null) registry = ctx; if (objects == null || objects.size() == 0) return null; return singleton.createClassifier(objects, rootType, rootID, m); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/464efde90db6bc5095c0a7e5952f51ad0f37ca86/ClassifierFactory.java/buggy/SRC/org/openmicroscopy/shoola/agents/util/classifier/view/ClassifierFactory.java

if (owner == null) owner = parent;

public static Classifier getClassifier(Set objects, Class rootType, long rootID, int m, Registry ctx) { if (registry == null) registry = ctx; if (objects == null || objects.size() == 0) return null; return singleton.createClassifier(objects, rootType, rootID, m); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/464efde90db6bc5095c0a7e5952f51ad0f37ca86/ClassifierFactory.java/buggy/SRC/org/openmicroscopy/shoola/agents/util/classifier/view/ClassifierFactory.java

public CommandlineParser(String[] arguments, PrintStream outStream) {

public CommandlineParser(Main main, String[] arguments) {

public CommandlineParser(String[] arguments, PrintStream outStream) { this.arguments = arguments; this.outStream = outStream; processArguments(); }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/b4a189a27604d62c317938f16a124fb9dab1e94a/CommandlineParser.java/clean/src/org/jruby/util/CommandlineParser.java

this.outStream = outStream;

this.main = main;

public CommandlineParser(String[] arguments, PrintStream outStream) { this.arguments = arguments; this.outStream = outStream; processArguments(); }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/b4a189a27604d62c317938f16a124fb9dab1e94a/CommandlineParser.java/clean/src/org/jruby/util/CommandlineParser.java

System.err.println("Error opening script file: " + e.getMessage()); systemExit();

throw new MainExitException(1, "Error opening script file: " + e.getMessage());

public Reader getScriptSource() { if (hasInlineScript()) { return new StringReader(inlineScript()); } else if (isSourceFromStdin()) { return new InputStreamReader(System.in); } else { File file = new File(getScriptFileName()); try { return new BufferedReader(new FileReader(file)); } catch (IOException e) { System.err.println("Error opening script file: " + e.getMessage()); systemExit(); } } assert false; return null; }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/b4a189a27604d62c317938f16a124fb9dab1e94a/CommandlineParser.java/clean/src/org/jruby/util/CommandlineParser.java

assert false; return null;

public Reader getScriptSource() { if (hasInlineScript()) { return new StringReader(inlineScript()); } else if (isSourceFromStdin()) { return new InputStreamReader(System.in); } else { File file = new File(getScriptFileName()); try { return new BufferedReader(new FileReader(file)); } catch (IOException e) { System.err.println("Error opening script file: " + e.getMessage()); systemExit(); } } assert false; return null; }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/b4a189a27604d62c317938f16a124fb9dab1e94a/CommandlineParser.java/clean/src/org/jruby/util/CommandlineParser.java

System.err.println("invalid argument " + argumentIndex); System.err.println(errorMessage); Main.printUsage(outStream); systemExit(); return null;

MainExitException mee = new MainExitException(1, "invalid argument " + argumentIndex + "\n" + errorMessage); mee.setUsageError(true); throw mee;

private String grabValue(String errorMessage) { characterIndex++; if (characterIndex < arguments[argumentIndex].length()) { return arguments[argumentIndex].substring(characterIndex); } argumentIndex++; if (argumentIndex < arguments.length) { return arguments[argumentIndex]; } System.err.println("invalid argument " + argumentIndex); System.err.println(errorMessage); Main.printUsage(outStream); systemExit(); return null; }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/b4a189a27604d62c317938f16a124fb9dab1e94a/CommandlineParser.java/clean/src/org/jruby/util/CommandlineParser.java

Main.printUsage(outStream);

main.printUsage();

private void processArgument() { String argument = arguments[argumentIndex]; FOR : for (characterIndex = 1; characterIndex < argument.length(); characterIndex++) { switch (argument.charAt(characterIndex)) { case 'h' : Main.printUsage(outStream); shouldRunInterpreter = false; break; case 'I' : loadPaths.add(grabValue(" -I must be followed by a directory name to add to lib path")); break FOR; case 'r' : requiredLibraries.add(grabValue("-r must be followed by a package to require")); break FOR; case 'e' : inlineScript.append(grabValue(" -e must be followed by an expression to evaluate")); inlineScript.append('\n'); break FOR; case 'b' : benchmarking = true; break; case 'p' : assumePrinting = true; assumeLoop = true; break; case 'n' : assumeLoop = true; break; case 'a' : split = true; break; case 'l' : processLineEnds = true; break; case 'v' : verbose = true; setShowVersion(true); break; case 'w' : verbose = true; break; case '-' : if (argument.equals("--version")) { setShowVersion(true); break FOR; } else { if (argument.equals("--")) { // ruby interpreter compatibilty // Usage: ruby [switches] [--] [programfile] [arguments]) break FOR; } } default : System.err.println("unknown option " + argument.charAt(characterIndex)); systemExit(); } } }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/b4a189a27604d62c317938f16a124fb9dab1e94a/CommandlineParser.java/clean/src/org/jruby/util/CommandlineParser.java

System.err.println("unknown option " + argument.charAt(characterIndex)); systemExit();

throw new MainExitException(1, "unknown option " + argument.charAt(characterIndex));

private void processArgument() { String argument = arguments[argumentIndex]; FOR : for (characterIndex = 1; characterIndex < argument.length(); characterIndex++) { switch (argument.charAt(characterIndex)) { case 'h' : Main.printUsage(outStream); shouldRunInterpreter = false; break; case 'I' : loadPaths.add(grabValue(" -I must be followed by a directory name to add to lib path")); break FOR; case 'r' : requiredLibraries.add(grabValue("-r must be followed by a package to require")); break FOR; case 'e' : inlineScript.append(grabValue(" -e must be followed by an expression to evaluate")); inlineScript.append('\n'); break FOR; case 'b' : benchmarking = true; break; case 'p' : assumePrinting = true; assumeLoop = true; break; case 'n' : assumeLoop = true; break; case 'a' : split = true; break; case 'l' : processLineEnds = true; break; case 'v' : verbose = true; setShowVersion(true); break; case 'w' : verbose = true; break; case '-' : if (argument.equals("--version")) { setShowVersion(true); break FOR; } else { if (argument.equals("--")) { // ruby interpreter compatibilty // Usage: ruby [switches] [--] [programfile] [arguments]) break FOR; } } default : System.err.println("unknown option " + argument.charAt(characterIndex)); systemExit(); } } }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/b4a189a27604d62c317938f16a124fb9dab1e94a/CommandlineParser.java/clean/src/org/jruby/util/CommandlineParser.java

protected void leave(Node iVisited) {}

protected void leave(Node iVisited) { }

protected void leave(Node iVisited) {}