h4iku/coconut_java2006 · Datasets at Hugging Face

return (EditArticleView) tab.getPerspective(TASK_ID_EDIT);

return (EditArticleView) tab.getTabView(TASK_ID_EDIT);

protected EditArticleView getEditArticleView(){ WFTabbedPane tab = getWFTabbedPane(); if(tab!=null){ return (EditArticleView) tab.getPerspective(TASK_ID_EDIT); } return null; }

57000 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57000/5db26355cf68616cbd8859fa37cd6aa73d783808/ArticleAdminBlock.java/clean/src/java/com/idega/block/article/component/ArticleAdminBlock.java

public void initializeComponent(FacesContext context){ //TODO Remove this and use newer localization system: WFPage.loadResourceBundles(context); super.initializeComponent(context); String bref = WFPage.CONTENT_BUNDLE + "."; WFTabbedPane tb = new WFTabbedPane(); //tb.setMainAreaStyleClass(WFContainer.DEFAULT_STYLE_CLASS); tb.setId(TASKBAR_ID); add(tb); EditArticleView editArticleBlock = new EditArticleView(); tb.addTabVB(TASK_ID_EDIT, bref + "edit", editArticleBlock); tb.addTabVB(TASK_ID_DETAILS, bref + "details", new ArticleDetailView());// tb.addTabVB(TASK_ID_LIST, bref + "list", new ListArticlesBlock()); tb.addTabVB(TASK_ID_PREVIEW, bref + "preview", new ArticlePreview()); tb.setSelectedMenuItemId(TASK_ID_EDIT); //if (taskbarListener != null) { // tb.addTabListener(taskbarListener); //} String editMode = getEditMode(); if(editMode!=null){ editArticleBlock.setEditMode(editMode); } }

57000 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57000/5db26355cf68616cbd8859fa37cd6aa73d783808/ArticleAdminBlock.java/clean/src/java/com/idega/block/article/component/ArticleAdminBlock.java

super.initializeComponent(context);

UISaveState beanSaveState = new UISaveState(); ValueBinding binding = WFUtil.createValueBinding("#{"+ARTICLE_ITEM_BEAN_ID+"}"); beanSaveState.setId("articleItemBeanSaveState"); beanSaveState.setValueBinding("value",binding); add(beanSaveState);

public void initializeComponent(FacesContext context){ //TODO Remove this and use newer localization system: WFPage.loadResourceBundles(context); super.initializeComponent(context); String bref = WFPage.CONTENT_BUNDLE + "."; WFTabbedPane tb = new WFTabbedPane(); //tb.setMainAreaStyleClass(WFContainer.DEFAULT_STYLE_CLASS); tb.setId(TASKBAR_ID); add(tb); EditArticleView editArticleBlock = new EditArticleView(); tb.addTabVB(TASK_ID_EDIT, bref + "edit", editArticleBlock); tb.addTabVB(TASK_ID_DETAILS, bref + "details", new ArticleDetailView());// tb.addTabVB(TASK_ID_LIST, bref + "list", new ListArticlesBlock()); tb.addTabVB(TASK_ID_PREVIEW, bref + "preview", new ArticlePreview()); tb.setSelectedMenuItemId(TASK_ID_EDIT); //if (taskbarListener != null) { // tb.addTabListener(taskbarListener); //} String editMode = getEditMode(); if(editMode!=null){ editArticleBlock.setEditMode(editMode); } }

57000 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57000/5db26355cf68616cbd8859fa37cd6aa73d783808/ArticleAdminBlock.java/clean/src/java/com/idega/block/article/component/ArticleAdminBlock.java

String bref = WFPage.CONTENT_BUNDLE + "."; WFTabbedPane tb = new WFTabbedPane(); tb.setId(TASKBAR_ID); add(tb); EditArticleView editArticleBlock = new EditArticleView(); tb.addTabVB(TASK_ID_EDIT, bref + "edit", editArticleBlock); tb.addTabVB(TASK_ID_DETAILS, bref + "details", new ArticleDetailView()); tb.addTabVB(TASK_ID_PREVIEW, bref + "preview", new ArticlePreview()); tb.setSelectedMenuItemId(TASK_ID_EDIT); String editMode = getEditMode(); if(editMode!=null){ editArticleBlock.setEditMode(editMode); }

public void initializeComponent(FacesContext context){ //TODO Remove this and use newer localization system: WFPage.loadResourceBundles(context); super.initializeComponent(context); String bref = WFPage.CONTENT_BUNDLE + "."; WFTabbedPane tb = new WFTabbedPane(); //tb.setMainAreaStyleClass(WFContainer.DEFAULT_STYLE_CLASS); tb.setId(TASKBAR_ID); add(tb); EditArticleView editArticleBlock = new EditArticleView(); tb.addTabVB(TASK_ID_EDIT, bref + "edit", editArticleBlock); tb.addTabVB(TASK_ID_DETAILS, bref + "details", new ArticleDetailView());// tb.addTabVB(TASK_ID_LIST, bref + "list", new ListArticlesBlock()); tb.addTabVB(TASK_ID_PREVIEW, bref + "preview", new ArticlePreview()); tb.setSelectedMenuItemId(TASK_ID_EDIT); //if (taskbarListener != null) { // tb.addTabListener(taskbarListener); //} String editMode = getEditMode(); if(editMode!=null){ editArticleBlock.setEditMode(editMode); } }

57000 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57000/5db26355cf68616cbd8859fa37cd6aa73d783808/ArticleAdminBlock.java/clean/src/java/com/idega/block/article/component/ArticleAdminBlock.java

{ int b = control.getGlobalMinimum(); int c = control.getGlobalMaximum(); double a = (double) rangeGraphics/(b-c); return (int) (a*(x-c)+tW); }

int convertRealIntoGraphics(int x) { int b = control.getGlobalMinimum(); int c = control.getGlobalMaximum(); double a = (double) rangeGraphics/(b-c); return (int) (a*(x-c)+tW); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/1722ebf9ac60fc8e45cdc8d0049e85db5b86715c/HistogramDialogManager.java/buggy/SRC/org/openmicroscopy/shoola/agents/rnd/pane/HistogramDialogManager.java

if (presentation != null) { topFrame.addToDesktop(presentation, TopFrame.PALETTE_LAYER); presentation.setVisible(true); }

topFrame.addToDesktop(presentation, TopFrame.PALETTE_LAYER); presentation.setVisible(true);

void showPresentation() { //TODO: add control. if (presentation != null) { topFrame.addToDesktop(presentation, TopFrame.PALETTE_LAYER); presentation.setVisible(true); } }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/e717f628b707987e5b693ea9d57b6ef34b300679/RenderingAgt.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/RenderingAgt.java

_log.debug("Looking for template: " + fileName); for (int i=0; i < _templateDirectory.length; i++) { Template t; String dir = _templateDirectory[i]; File tFile = new File(dir,fileName); if (tFile.canRead()) { _log.debug("TemplateProvider: Found " + fileName + " in " + dir); return tFile; }

_log.debug("Looking for template: " + fileName); for (int i=0; i <_templateDirectory.length; i++) { Template t; String dir = _templateDirectory[i]; File tFile = new File(dir,fileName); if (tFile.canRead()) { _log.debug("TemplateProvider: Found " + fileName + " in " + dir); return tFile; }

final private File findTemplate (String fileName) { _log.debug("Looking for template: " + fileName); for (int i=0; i < _templateDirectory.length; i++) { Template t; String dir = _templateDirectory[i]; File tFile = new File(dir,fileName); if (tFile.canRead()) { _log.debug("TemplateProvider: Found " + fileName + " in " + dir); return tFile; } } return null; }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/48ee8713236f326ad466e62ec2396568a03a90bc/TemplateProvider.java/clean/webmacro/src/org/webmacro/resource/TemplateProvider.java

return null;

final private File findTemplate (String fileName) { _log.debug("Looking for template: " + fileName); for (int i=0; i < _templateDirectory.length; i++) { Template t; String dir = _templateDirectory[i]; File tFile = new File(dir,fileName); if (tFile.canRead()) { _log.debug("TemplateProvider: Found " + fileName + " in " + dir); return tFile; } } return null; }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/48ee8713236f326ad466e62ec2396568a03a90bc/TemplateProvider.java/clean/webmacro/src/org/webmacro/resource/TemplateProvider.java

final public Template getTemplate(String fileName) { File tFile = findTemplate (fileName); Template t = null;

final public Template getTemplate(String fileName) { File tFile = findTemplate (fileName); Template t = null; try { t = new FileTemplate (_broker, tFile); t.parse (); _lastModifiedCache.put (fileName, new Long (tFile.lastModified())); } catch (NullPointerException npe) { _log.warning ("TemplateProvider: Template not found: " + fileName, npe); } catch (Exception e) { // this probably occured b/c of a parsing error. // should throw some kind of ParseErrorException here instead _log.warning ("TemplateProvider: Error occured while getting " + fileName, e); } return t; }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/48ee8713236f326ad466e62ec2396568a03a90bc/TemplateProvider.java/clean/webmacro/src/org/webmacro/resource/TemplateProvider.java

try { t = new FileTemplate (_broker, tFile); t.parse (); _lastModifiedCache.put (fileName, new Long (tFile.lastModified())); } catch (NullPointerException npe) { _log.warning ("TemplateProvider: Template not found: " + fileName, npe); } catch (Exception e) { _log.warning ("TemplateProvider: Error occured while getting " + fileName, e); } return t;

final public Template getTemplate(String fileName) { File tFile = findTemplate (fileName); Template t = null; try { t = new FileTemplate (_broker, tFile); t.parse (); _lastModifiedCache.put (fileName, new Long (tFile.lastModified())); } catch (NullPointerException npe) { _log.warning ("TemplateProvider: Template not found: " + fileName, npe); } catch (Exception e) { // this probably occured b/c of a parsing error. // should throw some kind of ParseErrorException here instead _log.warning ("TemplateProvider: Error occured while getting " + fileName, e); } return t; }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/48ee8713236f326ad466e62ec2396568a03a90bc/TemplateProvider.java/clean/webmacro/src/org/webmacro/resource/TemplateProvider.java

final public boolean shouldReload (String fileName) { File tFile = findTemplate (fileName); Long lm = (Long) _lastModifiedCache.get (fileName); return (lm == null || lm.longValue() != tFile.lastModified()); }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/48ee8713236f326ad466e62ec2396568a03a90bc/TemplateProvider.java/clean/webmacro/src/org/webmacro/resource/TemplateProvider.java

private Editor getDOEditor(TreeViewer model, DataObject hierarchyObject,

private Editor getDOEditor(TreeViewer model, DataObject ho,

private Editor getDOEditor(TreeViewer model, DataObject hierarchyObject, int editorType) { model.addPropertyChangeListener(this); if (editor != null) return editor; EditorModel m = new EditorModel(model, editorType, hierarchyObject); EditorComponent component = new EditorComponent(m); m.initialize(component); component.initialize(); editor = component; return editor; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/d5c797990d356c4ac91ebfe686270c29f4586bd6/EditorFactory.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/editors/EditorFactory.java

EditorModel m = new EditorModel(model, editorType, hierarchyObject);

EditorModel m = new EditorModel(model, editorType, ho);

private Editor getDOEditor(TreeViewer model, DataObject hierarchyObject, int editorType) { model.addPropertyChangeListener(this); if (editor != null) return editor; EditorModel m = new EditorModel(model, editorType, hierarchyObject); EditorComponent component = new EditorComponent(m); m.initialize(component); component.initialize(); editor = component; return editor; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/d5c797990d356c4ac91ebfe686270c29f4586bd6/EditorFactory.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/editors/EditorFactory.java

long modstart = System.currentTimeMillis(); if (ChainBuilderAgent.DEBUG) modstart = System.currentTimeMillis();

public Object getContents() { ChainDataManager chainDataManager = (ChainDataManager) dataManager; if (modData == null) { modData = new ModulesData(); Collection mods = chainDataManager.getModules(); Collection cats = chainDataManager.getModuleCategories(); // find uncategorized modules Iterator iter = mods.iterator(); while (iter.hasNext()) { ChainModuleData m = (ChainModuleData) iter.next(); if (m.getModuleCategory()== null) modData.addUncategorizedModule(m); } // find root categories if (cats != null) { iter = cats.iterator(); while (iter.hasNext()) { ModuleCategoryData c = (ModuleCategoryData) iter.next(); if (c.getParentCategory() == null) modData.addRootModuleCategory(c); findCategoryModules(c,mods); findCategoryChildren(c,cats); } } } return modData; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/a806bf744289bb0eed666b235887c8680d549d94/ModuleLoader.java/clean/SRC/org/openmicroscopy/shoola/agents/chainbuilder/data/ModuleLoader.java

long loadEnd; if (ChainBuilderAgent.DEBUG) { loadEnd= System.currentTimeMillis()-loadStart; System.err.println("time for get modules and get categories.."+loadEnd); }

public Object getContents() { ChainDataManager chainDataManager = (ChainDataManager) dataManager; if (modData == null) { modData = new ModulesData(); Collection mods = chainDataManager.getModules(); Collection cats = chainDataManager.getModuleCategories(); // find uncategorized modules Iterator iter = mods.iterator(); while (iter.hasNext()) { ChainModuleData m = (ChainModuleData) iter.next(); if (m.getModuleCategory()== null) modData.addUncategorizedModule(m); } // find root categories if (cats != null) { iter = cats.iterator(); while (iter.hasNext()) { ModuleCategoryData c = (ModuleCategoryData) iter.next(); if (c.getParentCategory() == null) modData.addRootModuleCategory(c); findCategoryModules(c,mods); findCategoryChildren(c,cats); } } } return modData; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/a806bf744289bb0eed666b235887c8680d549d94/ModuleLoader.java/clean/SRC/org/openmicroscopy/shoola/agents/chainbuilder/data/ModuleLoader.java

if (ChainBuilderAgent.DEBUG) { long modend = System.currentTimeMillis()-modstart; if (modend > 0) System.err.println("total time spent in module get contents.."+modend); }

public Object getContents() { ChainDataManager chainDataManager = (ChainDataManager) dataManager; if (modData == null) { modData = new ModulesData(); Collection mods = chainDataManager.getModules(); Collection cats = chainDataManager.getModuleCategories(); // find uncategorized modules Iterator iter = mods.iterator(); while (iter.hasNext()) { ChainModuleData m = (ChainModuleData) iter.next(); if (m.getModuleCategory()== null) modData.addUncategorizedModule(m); } // find root categories if (cats != null) { iter = cats.iterator(); while (iter.hasNext()) { ModuleCategoryData c = (ModuleCategoryData) iter.next(); if (c.getParentCategory() == null) modData.addRootModuleCategory(c); findCategoryModules(c,mods); findCategoryChildren(c,cats); } } } return modData; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/a806bf744289bb0eed666b235887c8680d549d94/ModuleLoader.java/clean/SRC/org/openmicroscopy/shoola/agents/chainbuilder/data/ModuleLoader.java

defineSingletonMethod("pipe", Arity.noArguments());

protected void initializeClass() { includeModule(getRuntime().getModule("Enumerable")); // TODO: Implement tty? and isatty. We have no real capability to // determine this from java, but if we could set tty status, then // we could invoke jruby differently to allow stdin to return true // on this. This would allow things like cgi.rb to work properly. defineSingletonMethod("foreach", Arity.optional()); defineSingletonMethod("read", Arity.optional()); defineSingletonMethod("readlines", Arity.optional()); defineSingletonMethod("popen", Arity.optional()); defineSingletonMethod("select", Arity.optional()); defineMethod("<<", Arity.singleArgument(), "addString"); defineMethod("binmode", Arity.noArguments()); defineMethod("clone", Arity.noArguments(), "clone_IO"); defineMethod("close", Arity.noArguments()); defineMethod("closed?", Arity.noArguments(), "closed"); defineMethod("each", Arity.optional(), "each_line"); defineMethod("each_byte", Arity.noArguments()); defineMethod("each_line", Arity.optional()); defineMethod("eof", Arity.noArguments()); defineAlias("eof?", "eof"); defineMethod("fcntl", Arity.twoArguments()); defineMethod("fileno", Arity.noArguments()); defineMethod("flush", Arity.noArguments()); defineMethod("fsync", Arity.noArguments()); defineMethod("getc", Arity.noArguments()); defineMethod("gets", Arity.optional()); defineMethod("initialize", Arity.optional()); defineMethod("lineno", Arity.noArguments()); defineMethod("lineno=", Arity.singleArgument(), "lineno_set"); defineMethod("pid", Arity.noArguments()); defineMethod("pos", Arity.noArguments()); defineMethod("pos=", Arity.singleArgument(), "pos_set"); defineMethod("print", Arity.optional()); defineMethod("printf", Arity.optional()); defineMethod("putc", Arity.singleArgument()); defineMethod("puts", Arity.optional()); defineMethod("readpartial", Arity.optional()); defineMethod("read", Arity.optional()); defineMethod("readchar", Arity.noArguments()); defineMethod("readline", Arity.optional()); defineMethod("readlines", Arity.optional()); defineMethod("reopen", Arity.optional()); defineMethod("rewind", Arity.noArguments()); defineMethod("seek", Arity.optional()); defineMethod("sync", Arity.noArguments()); defineMethod("sync=", Arity.singleArgument(), "sync_set"); defineMethod("sysread", Arity.singleArgument()); defineMethod("syswrite", Arity.singleArgument()); defineAlias("tell", "pos"); defineAlias("to_i", "fileno"); defineMethod("to_io", Arity.noArguments()); defineMethod("ungetc", Arity.singleArgument()); defineMethod("write", Arity.singleArgument()); defineMethod("tty?", Arity.noArguments(), "tty"); defineAlias("isatty", "tty?"); // Constants for seek setConstant("SEEK_SET", getRuntime().newFixnum(IOHandler.SEEK_SET)); setConstant("SEEK_CUR", getRuntime().newFixnum(IOHandler.SEEK_CUR)); setConstant("SEEK_END", getRuntime().newFixnum(IOHandler.SEEK_END)); }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/ebb36c83a55d3d046354e5aea24d7b0285ac2c54/IOMetaClass.java/clean/src/org/jruby/runtime/builtin/meta/IOMetaClass.java

throw runtime.newNameError(name() + " is a read-only variable");

throw runtime.newNameError(name() + " is a read-only variable", name());

public IRubyObject set(IRubyObject value) { throw runtime.newNameError(name() + " is a read-only variable"); }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/1278c5bb3507a052d150d814f15453542ae41aed/ReadonlyGlobalVariable.java/clean/src/org/jruby/runtime/ReadonlyGlobalVariable.java

pushCRef(runtime.getObject());

public void preAdoptThread() { pushIter(Iter.ITER_NOT); pushFrame(); getCurrentFrame().newScope(null); pushRubyClass(runtime.getObject()); }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/408ba0b04448fd6ff645ed5c2c99654ac80634bf/ThreadContext.java/clean/src/org/jruby/runtime/ThreadContext.java

private LensMenu(LensComponent lensComponent)

LensMenu(LensComponent lensComponent)

private LensMenu(LensComponent lensComponent) { this.lensComponent = lensComponent; createPopupMenu(); createMenubarMenu(); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/29b0b8d77292efe37e6130bac1e4416901230654/LensMenu.java/clean/SRC/org/openmicroscopy/shoola/util/ui/lens/LensMenu.java

JMenuItem setLensDefaultSize;

private void createMenubarMenu() { JMenu lensOptions; JMenu zoomOptions; JMenu displayOptions; JMenuItem setLensDefaultSize; JMenuItem setLens40x40; JMenuItem setLens60x60; JMenuItem setLens80x80; JMenuItem setLens100x100; JMenuItem setLens150x150; JMenuItem setZoomx3; JMenuItem setZoomx4; JMenuItem setZoomx5; JMenuItem setZoomx10; JRadioButtonMenuItem setDisplayMicrons; JRadioButtonMenuItem setDisplayPixels; menubar = new JMenuBar(); lensOptions = new JMenu(LENS_OPTIONS); zoomOptions = new JMenu(ZOOM_OPTIONS); displayOptions = new JMenu(DISPLAY_UNITS); menubar.add(lensOptions); menubar.add(zoomOptions); menubar.add(displayOptions); setLensDefaultSize = new JMenuItem(new LensAction(lensComponent, LensAction.LENSDEFAULTSIZE)); setLens40x40 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS40x40)); setLens60x60 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS60x60)); setLens80x80 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS80x80)); setLens100x100 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS100x100)); setLens150x150 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS150x150)); setZoomx3 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx3)); setZoomx4 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx4)); setZoomx5 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx5)); setZoomx10 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx10)); lensOptions.add(setLensDefaultSize); lensOptions.add(setLens40x40); lensOptions.add(setLens60x60); lensOptions.add(setLens80x80); lensOptions.add(setLens100x100); lensOptions.add(setLens150x150); zoomOptions.add(setZoomx3); zoomOptions.add(setZoomx4); zoomOptions.add(setZoomx5); zoomOptions.add(setZoomx10); setDisplayMicrons = new JRadioButtonMenuItem(new DisplayAction (lensComponent, DisplayAction.MICRON_OPTION)); setDisplayPixels = new JRadioButtonMenuItem(new DisplayAction (lensComponent, DisplayAction.PIXEL_OPTION)); displayOptions.add(setDisplayMicrons); displayOptions.add(setDisplayPixels); ButtonGroup displayUnits = new ButtonGroup(); displayUnits.add(setDisplayMicrons); displayUnits.add(setDisplayPixels); setDisplayPixels.setSelected(true); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/29b0b8d77292efe37e6130bac1e4416901230654/LensMenu.java/clean/SRC/org/openmicroscopy/shoola/util/ui/lens/LensMenu.java

setLensDefaultSize = new JMenuItem(new LensAction(lensComponent, LensAction.LENSDEFAULTSIZE));

private void createMenubarMenu() { JMenu lensOptions; JMenu zoomOptions; JMenu displayOptions; JMenuItem setLensDefaultSize; JMenuItem setLens40x40; JMenuItem setLens60x60; JMenuItem setLens80x80; JMenuItem setLens100x100; JMenuItem setLens150x150; JMenuItem setZoomx3; JMenuItem setZoomx4; JMenuItem setZoomx5; JMenuItem setZoomx10; JRadioButtonMenuItem setDisplayMicrons; JRadioButtonMenuItem setDisplayPixels; menubar = new JMenuBar(); lensOptions = new JMenu(LENS_OPTIONS); zoomOptions = new JMenu(ZOOM_OPTIONS); displayOptions = new JMenu(DISPLAY_UNITS); menubar.add(lensOptions); menubar.add(zoomOptions); menubar.add(displayOptions); setLensDefaultSize = new JMenuItem(new LensAction(lensComponent, LensAction.LENSDEFAULTSIZE)); setLens40x40 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS40x40)); setLens60x60 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS60x60)); setLens80x80 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS80x80)); setLens100x100 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS100x100)); setLens150x150 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS150x150)); setZoomx3 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx3)); setZoomx4 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx4)); setZoomx5 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx5)); setZoomx10 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx10)); lensOptions.add(setLensDefaultSize); lensOptions.add(setLens40x40); lensOptions.add(setLens60x60); lensOptions.add(setLens80x80); lensOptions.add(setLens100x100); lensOptions.add(setLens150x150); zoomOptions.add(setZoomx3); zoomOptions.add(setZoomx4); zoomOptions.add(setZoomx5); zoomOptions.add(setZoomx10); setDisplayMicrons = new JRadioButtonMenuItem(new DisplayAction (lensComponent, DisplayAction.MICRON_OPTION)); setDisplayPixels = new JRadioButtonMenuItem(new DisplayAction (lensComponent, DisplayAction.PIXEL_OPTION)); displayOptions.add(setDisplayMicrons); displayOptions.add(setDisplayPixels); ButtonGroup displayUnits = new ButtonGroup(); displayUnits.add(setDisplayMicrons); displayUnits.add(setDisplayPixels); setDisplayPixels.setSelected(true); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/29b0b8d77292efe37e6130bac1e4416901230654/LensMenu.java/clean/SRC/org/openmicroscopy/shoola/util/ui/lens/LensMenu.java

LensAction.LENS40x40));

LensAction.LENS40x40)); setLens50x50 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS50x50));

private void createMenubarMenu() { JMenu lensOptions; JMenu zoomOptions; JMenu displayOptions; JMenuItem setLensDefaultSize; JMenuItem setLens40x40; JMenuItem setLens60x60; JMenuItem setLens80x80; JMenuItem setLens100x100; JMenuItem setLens150x150; JMenuItem setZoomx3; JMenuItem setZoomx4; JMenuItem setZoomx5; JMenuItem setZoomx10; JRadioButtonMenuItem setDisplayMicrons; JRadioButtonMenuItem setDisplayPixels; menubar = new JMenuBar(); lensOptions = new JMenu(LENS_OPTIONS); zoomOptions = new JMenu(ZOOM_OPTIONS); displayOptions = new JMenu(DISPLAY_UNITS); menubar.add(lensOptions); menubar.add(zoomOptions); menubar.add(displayOptions); setLensDefaultSize = new JMenuItem(new LensAction(lensComponent, LensAction.LENSDEFAULTSIZE)); setLens40x40 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS40x40)); setLens60x60 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS60x60)); setLens80x80 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS80x80)); setLens100x100 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS100x100)); setLens150x150 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS150x150)); setZoomx3 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx3)); setZoomx4 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx4)); setZoomx5 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx5)); setZoomx10 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx10)); lensOptions.add(setLensDefaultSize); lensOptions.add(setLens40x40); lensOptions.add(setLens60x60); lensOptions.add(setLens80x80); lensOptions.add(setLens100x100); lensOptions.add(setLens150x150); zoomOptions.add(setZoomx3); zoomOptions.add(setZoomx4); zoomOptions.add(setZoomx5); zoomOptions.add(setZoomx10); setDisplayMicrons = new JRadioButtonMenuItem(new DisplayAction (lensComponent, DisplayAction.MICRON_OPTION)); setDisplayPixels = new JRadioButtonMenuItem(new DisplayAction (lensComponent, DisplayAction.PIXEL_OPTION)); displayOptions.add(setDisplayMicrons); displayOptions.add(setDisplayPixels); ButtonGroup displayUnits = new ButtonGroup(); displayUnits.add(setDisplayMicrons); displayUnits.add(setDisplayPixels); setDisplayPixels.setSelected(true); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/29b0b8d77292efe37e6130bac1e4416901230654/LensMenu.java/clean/SRC/org/openmicroscopy/shoola/util/ui/lens/LensMenu.java

lensOptions.add(setLensDefaultSize);

private void createMenubarMenu() { JMenu lensOptions; JMenu zoomOptions; JMenu displayOptions; JMenuItem setLensDefaultSize; JMenuItem setLens40x40; JMenuItem setLens60x60; JMenuItem setLens80x80; JMenuItem setLens100x100; JMenuItem setLens150x150; JMenuItem setZoomx3; JMenuItem setZoomx4; JMenuItem setZoomx5; JMenuItem setZoomx10; JRadioButtonMenuItem setDisplayMicrons; JRadioButtonMenuItem setDisplayPixels; menubar = new JMenuBar(); lensOptions = new JMenu(LENS_OPTIONS); zoomOptions = new JMenu(ZOOM_OPTIONS); displayOptions = new JMenu(DISPLAY_UNITS); menubar.add(lensOptions); menubar.add(zoomOptions); menubar.add(displayOptions); setLensDefaultSize = new JMenuItem(new LensAction(lensComponent, LensAction.LENSDEFAULTSIZE)); setLens40x40 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS40x40)); setLens60x60 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS60x60)); setLens80x80 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS80x80)); setLens100x100 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS100x100)); setLens150x150 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS150x150)); setZoomx3 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx3)); setZoomx4 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx4)); setZoomx5 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx5)); setZoomx10 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx10)); lensOptions.add(setLensDefaultSize); lensOptions.add(setLens40x40); lensOptions.add(setLens60x60); lensOptions.add(setLens80x80); lensOptions.add(setLens100x100); lensOptions.add(setLens150x150); zoomOptions.add(setZoomx3); zoomOptions.add(setZoomx4); zoomOptions.add(setZoomx5); zoomOptions.add(setZoomx10); setDisplayMicrons = new JRadioButtonMenuItem(new DisplayAction (lensComponent, DisplayAction.MICRON_OPTION)); setDisplayPixels = new JRadioButtonMenuItem(new DisplayAction (lensComponent, DisplayAction.PIXEL_OPTION)); displayOptions.add(setDisplayMicrons); displayOptions.add(setDisplayPixels); ButtonGroup displayUnits = new ButtonGroup(); displayUnits.add(setDisplayMicrons); displayUnits.add(setDisplayPixels); setDisplayPixels.setSelected(true); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/29b0b8d77292efe37e6130bac1e4416901230654/LensMenu.java/clean/SRC/org/openmicroscopy/shoola/util/ui/lens/LensMenu.java

zoomOptions.add(setZoomx2);

private void createMenubarMenu() { JMenu lensOptions; JMenu zoomOptions; JMenu displayOptions; JMenuItem setLensDefaultSize; JMenuItem setLens40x40; JMenuItem setLens60x60; JMenuItem setLens80x80; JMenuItem setLens100x100; JMenuItem setLens150x150; JMenuItem setZoomx3; JMenuItem setZoomx4; JMenuItem setZoomx5; JMenuItem setZoomx10; JRadioButtonMenuItem setDisplayMicrons; JRadioButtonMenuItem setDisplayPixels; menubar = new JMenuBar(); lensOptions = new JMenu(LENS_OPTIONS); zoomOptions = new JMenu(ZOOM_OPTIONS); displayOptions = new JMenu(DISPLAY_UNITS); menubar.add(lensOptions); menubar.add(zoomOptions); menubar.add(displayOptions); setLensDefaultSize = new JMenuItem(new LensAction(lensComponent, LensAction.LENSDEFAULTSIZE)); setLens40x40 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS40x40)); setLens60x60 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS60x60)); setLens80x80 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS80x80)); setLens100x100 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS100x100)); setLens150x150 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS150x150)); setZoomx3 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx3)); setZoomx4 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx4)); setZoomx5 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx5)); setZoomx10 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx10)); lensOptions.add(setLensDefaultSize); lensOptions.add(setLens40x40); lensOptions.add(setLens60x60); lensOptions.add(setLens80x80); lensOptions.add(setLens100x100); lensOptions.add(setLens150x150); zoomOptions.add(setZoomx3); zoomOptions.add(setZoomx4); zoomOptions.add(setZoomx5); zoomOptions.add(setZoomx10); setDisplayMicrons = new JRadioButtonMenuItem(new DisplayAction (lensComponent, DisplayAction.MICRON_OPTION)); setDisplayPixels = new JRadioButtonMenuItem(new DisplayAction (lensComponent, DisplayAction.PIXEL_OPTION)); displayOptions.add(setDisplayMicrons); displayOptions.add(setDisplayPixels); ButtonGroup displayUnits = new ButtonGroup(); displayUnits.add(setDisplayMicrons); displayUnits.add(setDisplayPixels); setDisplayPixels.setSelected(true); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/29b0b8d77292efe37e6130bac1e4416901230654/LensMenu.java/clean/SRC/org/openmicroscopy/shoola/util/ui/lens/LensMenu.java

JMenuItem setLensDefaultSize;

private void createPopupMenu() { JMenu lensOptions; JMenu zoomOptions; JMenuItem topOption; JMenu displayOptions; JMenuItem setLensDefaultSize; JMenuItem setLens40x40; JMenuItem setLens60x60; JMenuItem setLens80x80; JMenuItem setLens100x100; JMenuItem setLens150x150; JMenuItem setZoomx3; JMenuItem setZoomx4; JMenuItem setZoomx5; JMenuItem setZoomx10; JRadioButtonMenuItem setDisplayMicrons; JRadioButtonMenuItem setDisplayPixels; popupMenu = new JPopupMenu(POPUP_MENU_DESCRIPTION); topOption = new JMenuItem(POPUP_MENU_TOPOPTION); popupMenu.add(topOption); popupMenu.addSeparator(); lensOptions = new JMenu(LENS_OPTIONS); zoomOptions = new JMenu(ZOOM_OPTIONS); displayOptions = new JMenu(DISPLAY_UNITS); popupMenu.add(lensOptions); popupMenu.add(zoomOptions); popupMenu.add(displayOptions); setLensDefaultSize = new JMenuItem(new LensAction(lensComponent, LensAction.LENSDEFAULTSIZE)); setLens40x40 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS40x40)); setLens60x60 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS60x60)); setLens80x80 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS80x80)); setLens100x100 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS100x100)); setLens150x150 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS150x150)); setZoomx3 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx3)); setZoomx4 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx4)); setZoomx5 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx5)); setZoomx10 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx10)); lensOptions.add(setLensDefaultSize); lensOptions.add(setLens40x40); lensOptions.add(setLens60x60); lensOptions.add(setLens80x80); lensOptions.add(setLens100x100); lensOptions.add(setLens150x150); zoomOptions.add(setZoomx3); zoomOptions.add(setZoomx4); zoomOptions.add(setZoomx5); zoomOptions.add(setZoomx10); setDisplayMicrons = new JRadioButtonMenuItem(new DisplayAction (lensComponent, DisplayAction.MICRON_OPTION)); setDisplayPixels = new JRadioButtonMenuItem(new DisplayAction (lensComponent, DisplayAction.PIXEL_OPTION)); displayOptions.add(setDisplayMicrons); displayOptions.add(setDisplayPixels); ButtonGroup displayUnits = new ButtonGroup(); displayUnits.add(setDisplayMicrons); displayUnits.add(setDisplayPixels); setDisplayPixels.setSelected(true); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/29b0b8d77292efe37e6130bac1e4416901230654/LensMenu.java/clean/SRC/org/openmicroscopy/shoola/util/ui/lens/LensMenu.java

setLensDefaultSize = new JMenuItem(new LensAction(lensComponent, LensAction.LENSDEFAULTSIZE));

private void createPopupMenu() { JMenu lensOptions; JMenu zoomOptions; JMenuItem topOption; JMenu displayOptions; JMenuItem setLensDefaultSize; JMenuItem setLens40x40; JMenuItem setLens60x60; JMenuItem setLens80x80; JMenuItem setLens100x100; JMenuItem setLens150x150; JMenuItem setZoomx3; JMenuItem setZoomx4; JMenuItem setZoomx5; JMenuItem setZoomx10; JRadioButtonMenuItem setDisplayMicrons; JRadioButtonMenuItem setDisplayPixels; popupMenu = new JPopupMenu(POPUP_MENU_DESCRIPTION); topOption = new JMenuItem(POPUP_MENU_TOPOPTION); popupMenu.add(topOption); popupMenu.addSeparator(); lensOptions = new JMenu(LENS_OPTIONS); zoomOptions = new JMenu(ZOOM_OPTIONS); displayOptions = new JMenu(DISPLAY_UNITS); popupMenu.add(lensOptions); popupMenu.add(zoomOptions); popupMenu.add(displayOptions); setLensDefaultSize = new JMenuItem(new LensAction(lensComponent, LensAction.LENSDEFAULTSIZE)); setLens40x40 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS40x40)); setLens60x60 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS60x60)); setLens80x80 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS80x80)); setLens100x100 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS100x100)); setLens150x150 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS150x150)); setZoomx3 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx3)); setZoomx4 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx4)); setZoomx5 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx5)); setZoomx10 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx10)); lensOptions.add(setLensDefaultSize); lensOptions.add(setLens40x40); lensOptions.add(setLens60x60); lensOptions.add(setLens80x80); lensOptions.add(setLens100x100); lensOptions.add(setLens150x150); zoomOptions.add(setZoomx3); zoomOptions.add(setZoomx4); zoomOptions.add(setZoomx5); zoomOptions.add(setZoomx10); setDisplayMicrons = new JRadioButtonMenuItem(new DisplayAction (lensComponent, DisplayAction.MICRON_OPTION)); setDisplayPixels = new JRadioButtonMenuItem(new DisplayAction (lensComponent, DisplayAction.PIXEL_OPTION)); displayOptions.add(setDisplayMicrons); displayOptions.add(setDisplayPixels); ButtonGroup displayUnits = new ButtonGroup(); displayUnits.add(setDisplayMicrons); displayUnits.add(setDisplayPixels); setDisplayPixels.setSelected(true); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/29b0b8d77292efe37e6130bac1e4416901230654/LensMenu.java/clean/SRC/org/openmicroscopy/shoola/util/ui/lens/LensMenu.java

ZoomAction.ZOOMx3));

private void createPopupMenu() { JMenu lensOptions; JMenu zoomOptions; JMenuItem topOption; JMenu displayOptions; JMenuItem setLensDefaultSize; JMenuItem setLens40x40; JMenuItem setLens60x60; JMenuItem setLens80x80; JMenuItem setLens100x100; JMenuItem setLens150x150; JMenuItem setZoomx3; JMenuItem setZoomx4; JMenuItem setZoomx5; JMenuItem setZoomx10; JRadioButtonMenuItem setDisplayMicrons; JRadioButtonMenuItem setDisplayPixels; popupMenu = new JPopupMenu(POPUP_MENU_DESCRIPTION); topOption = new JMenuItem(POPUP_MENU_TOPOPTION); popupMenu.add(topOption); popupMenu.addSeparator(); lensOptions = new JMenu(LENS_OPTIONS); zoomOptions = new JMenu(ZOOM_OPTIONS); displayOptions = new JMenu(DISPLAY_UNITS); popupMenu.add(lensOptions); popupMenu.add(zoomOptions); popupMenu.add(displayOptions); setLensDefaultSize = new JMenuItem(new LensAction(lensComponent, LensAction.LENSDEFAULTSIZE)); setLens40x40 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS40x40)); setLens60x60 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS60x60)); setLens80x80 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS80x80)); setLens100x100 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS100x100)); setLens150x150 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS150x150)); setZoomx3 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx3)); setZoomx4 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx4)); setZoomx5 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx5)); setZoomx10 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx10)); lensOptions.add(setLensDefaultSize); lensOptions.add(setLens40x40); lensOptions.add(setLens60x60); lensOptions.add(setLens80x80); lensOptions.add(setLens100x100); lensOptions.add(setLens150x150); zoomOptions.add(setZoomx3); zoomOptions.add(setZoomx4); zoomOptions.add(setZoomx5); zoomOptions.add(setZoomx10); setDisplayMicrons = new JRadioButtonMenuItem(new DisplayAction (lensComponent, DisplayAction.MICRON_OPTION)); setDisplayPixels = new JRadioButtonMenuItem(new DisplayAction (lensComponent, DisplayAction.PIXEL_OPTION)); displayOptions.add(setDisplayMicrons); displayOptions.add(setDisplayPixels); ButtonGroup displayUnits = new ButtonGroup(); displayUnits.add(setDisplayMicrons); displayUnits.add(setDisplayPixels); setDisplayPixels.setSelected(true); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/29b0b8d77292efe37e6130bac1e4416901230654/LensMenu.java/clean/SRC/org/openmicroscopy/shoola/util/ui/lens/LensMenu.java

lensOptions.add(setLensDefaultSize);

private void createPopupMenu() { JMenu lensOptions; JMenu zoomOptions; JMenuItem topOption; JMenu displayOptions; JMenuItem setLensDefaultSize; JMenuItem setLens40x40; JMenuItem setLens60x60; JMenuItem setLens80x80; JMenuItem setLens100x100; JMenuItem setLens150x150; JMenuItem setZoomx3; JMenuItem setZoomx4; JMenuItem setZoomx5; JMenuItem setZoomx10; JRadioButtonMenuItem setDisplayMicrons; JRadioButtonMenuItem setDisplayPixels; popupMenu = new JPopupMenu(POPUP_MENU_DESCRIPTION); topOption = new JMenuItem(POPUP_MENU_TOPOPTION); popupMenu.add(topOption); popupMenu.addSeparator(); lensOptions = new JMenu(LENS_OPTIONS); zoomOptions = new JMenu(ZOOM_OPTIONS); displayOptions = new JMenu(DISPLAY_UNITS); popupMenu.add(lensOptions); popupMenu.add(zoomOptions); popupMenu.add(displayOptions); setLensDefaultSize = new JMenuItem(new LensAction(lensComponent, LensAction.LENSDEFAULTSIZE)); setLens40x40 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS40x40)); setLens60x60 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS60x60)); setLens80x80 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS80x80)); setLens100x100 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS100x100)); setLens150x150 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS150x150)); setZoomx3 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx3)); setZoomx4 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx4)); setZoomx5 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx5)); setZoomx10 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx10)); lensOptions.add(setLensDefaultSize); lensOptions.add(setLens40x40); lensOptions.add(setLens60x60); lensOptions.add(setLens80x80); lensOptions.add(setLens100x100); lensOptions.add(setLens150x150); zoomOptions.add(setZoomx3); zoomOptions.add(setZoomx4); zoomOptions.add(setZoomx5); zoomOptions.add(setZoomx10); setDisplayMicrons = new JRadioButtonMenuItem(new DisplayAction (lensComponent, DisplayAction.MICRON_OPTION)); setDisplayPixels = new JRadioButtonMenuItem(new DisplayAction (lensComponent, DisplayAction.PIXEL_OPTION)); displayOptions.add(setDisplayMicrons); displayOptions.add(setDisplayPixels); ButtonGroup displayUnits = new ButtonGroup(); displayUnits.add(setDisplayMicrons); displayUnits.add(setDisplayPixels); setDisplayPixels.setSelected(true); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/29b0b8d77292efe37e6130bac1e4416901230654/LensMenu.java/clean/SRC/org/openmicroscopy/shoola/util/ui/lens/LensMenu.java

zoomOptions.add(setZoomx2);

private void createPopupMenu() { JMenu lensOptions; JMenu zoomOptions; JMenuItem topOption; JMenu displayOptions; JMenuItem setLensDefaultSize; JMenuItem setLens40x40; JMenuItem setLens60x60; JMenuItem setLens80x80; JMenuItem setLens100x100; JMenuItem setLens150x150; JMenuItem setZoomx3; JMenuItem setZoomx4; JMenuItem setZoomx5; JMenuItem setZoomx10; JRadioButtonMenuItem setDisplayMicrons; JRadioButtonMenuItem setDisplayPixels; popupMenu = new JPopupMenu(POPUP_MENU_DESCRIPTION); topOption = new JMenuItem(POPUP_MENU_TOPOPTION); popupMenu.add(topOption); popupMenu.addSeparator(); lensOptions = new JMenu(LENS_OPTIONS); zoomOptions = new JMenu(ZOOM_OPTIONS); displayOptions = new JMenu(DISPLAY_UNITS); popupMenu.add(lensOptions); popupMenu.add(zoomOptions); popupMenu.add(displayOptions); setLensDefaultSize = new JMenuItem(new LensAction(lensComponent, LensAction.LENSDEFAULTSIZE)); setLens40x40 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS40x40)); setLens60x60 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS60x60)); setLens80x80 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS80x80)); setLens100x100 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS100x100)); setLens150x150 = new JMenuItem(new LensAction(lensComponent, LensAction.LENS150x150)); setZoomx3 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx3)); setZoomx4 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx4)); setZoomx5 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx5)); setZoomx10 = new JMenuItem(new ZoomAction(lensComponent, ZoomAction.ZOOMx10)); lensOptions.add(setLensDefaultSize); lensOptions.add(setLens40x40); lensOptions.add(setLens60x60); lensOptions.add(setLens80x80); lensOptions.add(setLens100x100); lensOptions.add(setLens150x150); zoomOptions.add(setZoomx3); zoomOptions.add(setZoomx4); zoomOptions.add(setZoomx5); zoomOptions.add(setZoomx10); setDisplayMicrons = new JRadioButtonMenuItem(new DisplayAction (lensComponent, DisplayAction.MICRON_OPTION)); setDisplayPixels = new JRadioButtonMenuItem(new DisplayAction (lensComponent, DisplayAction.PIXEL_OPTION)); displayOptions.add(setDisplayMicrons); displayOptions.add(setDisplayPixels); ButtonGroup displayUnits = new ButtonGroup(); displayUnits.add(setDisplayMicrons); displayUnits.add(setDisplayPixels); setDisplayPixels.setSelected(true); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/29b0b8d77292efe37e6130bac1e4416901230654/LensMenu.java/clean/SRC/org/openmicroscopy/shoola/util/ui/lens/LensMenu.java

return ref.menubar;

return menubar;

JMenuBar getMenubar() { return ref.menubar; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/29b0b8d77292efe37e6130bac1e4416901230654/LensMenu.java/clean/SRC/org/openmicroscopy/shoola/util/ui/lens/LensMenu.java

return ref.popupMenu;

return popupMenu;

JPopupMenu getPopupMenu() { return ref.popupMenu; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/29b0b8d77292efe37e6130bac1e4416901230654/LensMenu.java/clean/SRC/org/openmicroscopy/shoola/util/ui/lens/LensMenu.java

double y = (double) x; verifyInput(y); return Math.log(y);

return Math.log(verifyInput((double) x));

public double transform(int x, double k) { double y = (double) x; verifyInput(y); return Math.log(y); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/003d5b181ea715c02dffec4523e09bc34e884765/LogarithmicMap.java/buggy/SRC/org/openmicroscopy/shoola/env/rnd/quantum/LogarithmicMap.java

private void verifyInput(double x)

private double verifyInput(double x)

private void verifyInput(double x) { if (x <= 0) throw new IllegalArgumentException("Value not consistent. " + "The value must be > 0."); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/003d5b181ea715c02dffec4523e09bc34e884765/LogarithmicMap.java/buggy/SRC/org/openmicroscopy/shoola/env/rnd/quantum/LogarithmicMap.java

if (x <= 0) throw new IllegalArgumentException("Value not consistent. " + "The value must be > 0.");

if (x <= 0) x = 1.0; return x;

private void verifyInput(double x) { if (x <= 0) throw new IllegalArgumentException("Value not consistent. " + "The value must be > 0."); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/003d5b181ea715c02dffec4523e09bc34e884765/LogarithmicMap.java/buggy/SRC/org/openmicroscopy/shoola/env/rnd/quantum/LogarithmicMap.java

public RubyScope() {

public RubyScope(Ruby ruby) { this.ruby = ruby;

public RubyScope() { }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/d69d4a4ad55400b629f71574f9f1c20c617cc2ca/RubyScope.java/buggy/org/jruby/runtime/RubyScope.java

ruby.setActMethodScope(oldActMethodScope);

public void pop() { this.superObject = old.superObject; this.localTbl = old.localTbl; this.localVars = old.localVars; this.flags = old.flags; this.old = old.old; }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/d69d4a4ad55400b629f71574f9f1c20c617cc2ca/RubyScope.java/buggy/org/jruby/runtime/RubyScope.java

old = new RubyScope(this);

oldActMethodScope = ruby.getActMethodScope(); ruby.setActMethodScope(Constants.NOEX_PUBLIC); old = new RubyScope(this, ruby);

public void push() { old = new RubyScope(this); localTbl = null; localVars = null; flags = 0; }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/d69d4a4ad55400b629f71574f9f1c20c617cc2ca/RubyScope.java/buggy/org/jruby/runtime/RubyScope.java

final JDialog optionsDialog = new JDialog(SparkManager.getMainWindow(), Res.getString("title.set.status.message "), true);

final JDialog optionsDialog = new JDialog(SparkManager.getMainWindow(), Res.getString("title.set.status.message"), true);

public void invoke(String selectedType) { final StatusBar statusBar = SparkManager.getWorkspace().getStatusBar(); // Construct main panel w/ layout. final JPanel mainPanel = new JPanel(); mainPanel.setLayout(new BorderLayout()); // The user should only be able to close this dialog. Object[] options = {Res.getString("ok"), Res.getString("cancel")}; final JOptionPane optionPane = new JOptionPane(this, JOptionPane.PLAIN_MESSAGE, JOptionPane.OK_CANCEL_OPTION, null, options, options[0]); mainPanel.add(optionPane, BorderLayout.CENTER); final JDialog optionsDialog = new JDialog(SparkManager.getMainWindow(), Res.getString("title.set.status.message "), true); optionsDialog.setContentPane(mainPanel); optionsDialog.pack(); if (selectedType != null) { int count = typeBox.getItemCount(); for (int i = 0; i < count; i++) { ImageIcon icon = (ImageIcon)typeBox.getItemAt(i); if (icon.getDescription().equals(selectedType)) { typeBox.setSelectedIndex(i); break; } } persistBox.setSelected(true); } optionsDialog.setLocationRelativeTo(SparkManager.getMainWindow()); optionPane.addPropertyChangeListener(new PropertyChangeListener() { public void propertyChange(PropertyChangeEvent propertyChangeEvent) { String value = (String)optionPane.getValue(); if (Res.getString("cancel").equals(value)) { optionsDialog.setVisible(false); } else if (Res.getString("ok").equals(value)) { if (!persistBox.isSelected()) { // Change presence and quit. StatusItem item = statusBar.getStatusItem(getType()); Presence oldPresence = item.getPresence(); Presence presence = StatusBar.copyPresence(oldPresence); presence.setStatus(getStatus()); presence.setPriority(getPriority()); statusBar.changeAvailability(presence); statusBar.setStatus(getStatus()); optionsDialog.setVisible(false); return; } List list = load(); CustomStatusItem customStatusItem = new CustomStatusItem(); customStatusItem.setPriority(getPriority()); customStatusItem.setStatus(getStatus()); customStatusItem.setType(getType()); Iterator customListIterator = list.iterator(); boolean exists = false; while (customListIterator.hasNext()) { CustomStatusItem customItem = (CustomStatusItem)customListIterator.next(); String type = customItem.getType(); String status = customItem.getStatus(); if (type.equals(customStatusItem.getType()) && status.equals(customStatusItem.getStatus())) { exists = true; } } // Otherwise save. if (!exists) { list.add(customStatusItem); // Update current status. StatusItem item = statusBar.getStatusItem(getType()); Presence oldPresence = item.getPresence(); Presence presence = StatusBar.copyPresence(oldPresence); presence.setStatus(getStatus()); presence.setPriority(getPriority()); statusBar.changeAvailability(presence); statusBar.setStatus(getStatus()); // Persist new item. save(list); } optionsDialog.setVisible(false); } } }); optionsDialog.setVisible(true); optionsDialog.toFront(); optionsDialog.requestFocus(); }

52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/19e17d68c2c9589c1eea9caba87ba9f18813b1c4/CustomMessages.java/buggy/src/java/org/jivesoftware/spark/ui/status/CustomMessages.java

bar.add(Box.createRigidArea(VBOX)); bar.add(colorPickerButton);

private JToolBar buildToolBar() { JToolBar bar = new JToolBar(JToolBar.VERTICAL); bar.setFloatable(false); bar.setRollover(true); bar.setBorder(null); bar.add(colorModelButton); bar.add(Box.createRigidArea(VBOX)); bar.add(channelMovieButton); return bar; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/bbd964029121f2811ba2b7cf47a392087032888c/ControlPane.java/buggy/SRC/org/openmicroscopy/shoola/agents/imviewer/view/ControlPane.java

button.setPreferredSize(new Dimension(30, 30));

button.setPreferredSize(ChannelButton.DEFAULT_MIN_SIZE);

private JPanel createChannelsPane() { JPanel p = new JPanel(); p.setLayout(new BoxLayout(p, BoxLayout.Y_AXIS)); ChannelMetadata[] data = model.getChannelData(); ChannelButton button; ChannelMetadata d; p.add(Box.createRigidArea(VBOX)); boolean gs = model.getColorModel().equals(ImViewer.GREY_SCALE_MODEL); for (int k = 0; k < data.length; k++) { d = data[k]; button = new ChannelButton(""+d.getEmissionWavelength(), model.getChannelColor(k), k, model.isChannelActive(k)); if (gs) button.setGrayedOut(gs); button.addPropertyChangeListener(controller); button.setPreferredSize(new Dimension(30, 30)); channelButtons.add(button); p.add(button); p.add(Box.createRigidArea(VBOX)); } JPanel controls = new JPanel(); controls.setLayout(new BoxLayout(controls,BoxLayout.Y_AXIS)); controls.add(Box.createVerticalStrut(20)); controls.add(buildToolBar()); controls.add(p); return UIUtilities.buildComponentPanel(controls); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/bbd964029121f2811ba2b7cf47a392087032888c/ControlPane.java/buggy/SRC/org/openmicroscopy/shoola/agents/imviewer/view/ControlPane.java

ViewerAction a = controller.getAction(ImViewerControl.COLOR_PICKER); colorPickerButton = new JButton(a); colorPickerButton.addMouseListener((ColorPickerAction) a); UIUtilities.unifiedButtonLookAndFeel(colorPickerButton);

private void initComponents() { ViewerAction[] zoomingActions = new ViewerAction[12]; zoomingActions[0] = controller.getAction(ImViewerControl.ZOOM_25); zoomingActions[1] = controller.getAction(ImViewerControl.ZOOM_50); zoomingActions[2] = controller.getAction(ImViewerControl.ZOOM_75); zoomingActions[3] = controller.getAction(ImViewerControl.ZOOM_100); zoomingActions[4] = controller.getAction(ImViewerControl.ZOOM_125); zoomingActions[5] = controller.getAction(ImViewerControl.ZOOM_150); zoomingActions[6] = controller.getAction(ImViewerControl.ZOOM_175); zoomingActions[7] = controller.getAction(ImViewerControl.ZOOM_200); zoomingActions[8] = controller.getAction(ImViewerControl.ZOOM_225); zoomingActions[9] = controller.getAction(ImViewerControl.ZOOM_250); zoomingActions[10] = controller.getAction(ImViewerControl.ZOOM_275); zoomingActions[11] = controller.getAction(ImViewerControl.ZOOM_300); zoomingBox = new JComboBox(zoomingActions); zoomingBox.setEnabled(false); ViewerAction[] ratingActions = new ViewerAction[5]; ratingActions[0] = controller.getAction(ImViewerControl.RATING_ONE); ratingActions[1] = controller.getAction(ImViewerControl.RATING_TWO); ratingActions[2] = controller.getAction(ImViewerControl.RATING_THREE); ratingActions[3] = controller.getAction(ImViewerControl.RATING_FOUR); ratingActions[4] = controller.getAction(ImViewerControl.RATING_FIVE); ratingBox = new JComboBox(ratingActions); ratingBox.setEnabled(false); zSlider = new OneKnobSlider(JSlider.VERTICAL, 0, 1, 0); zSlider.setEnabled(false); tSlider = new OneKnobSlider(JSlider.VERTICAL, 0, 1, 0); tSlider.setEnabled(false); //zSlider.addChangeListener(this); //tSlider.addChangeListener(this); channelMovieButton = new JButton( controller.getAction(ImViewerControl.CHANNEL_MOVIE)); UIUtilities.unifiedButtonLookAndFeel(channelMovieButton); colorModelButton = new JButton(); UIUtilities.unifiedButtonLookAndFeel(colorModelButton); colorModelButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { String m = model.getColorModel(); ViewerAction a = null; if (m.equals(ImViewer.RGB_MODEL) || m.equals(ImViewer.HSB_MODEL)) { a = controller.getAction(ImViewerControl.GREY_SCALE_MODEL); } else if (m.equals(ImViewer.GREY_SCALE_MODEL)) { a = controller.getAction(ImViewerControl.RGB_MODEL); } a.actionPerformed(e); } }); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/bbd964029121f2811ba2b7cf47a392087032888c/ControlPane.java/buggy/SRC/org/openmicroscopy/shoola/agents/imviewer/view/ControlPane.java

} catch (Exception excptn) { excptn.printStackTrace(getErrorStream());

/*} catch (Exception excptn) { excptn.printStackTrace(getErrorStream());*/

public void loadScript(RubyString scriptName, RubyString source, boolean wrap) { RubyObject self = ruby.getRubyTopSelf(); CRefNode savedCRef = ruby.getCRef(); // TMP_PROTECT; if (wrap && ruby.getSafeLevel() >= 4) { // Check_Type(fname, T_STRING); } else { // Check_SafeStr(fname); } // volatile ID last_func; // ruby_errinfo = Qnil; /* ensure */ RubyVarmap.push(ruby); ruby.pushClass(); RubyModule wrapper = ruby.getWrapper(); ruby.setCRef(ruby.getTopCRef()); if (!wrap) { ruby.secure(4); /* should alter global state */ ruby.setRubyClass(ruby.getClasses().getObjectClass()); ruby.setWrapper(null); } else { /* load in anonymous module as toplevel */ ruby.setWrapper(RubyModule.newModule(ruby)); ruby.setRubyClass(ruby.getWrapper()); self = ruby.getRubyTopSelf().rbClone(); self.extendObject(ruby.getRubyClass()); ruby.getCRef().push(ruby.getWrapper()); } ruby.getRubyFrame().push(); ruby.getRubyFrame().setLastFunc(null); ruby.getRubyFrame().setLastClass(null); ruby.getRubyFrame().setSelf(self); ruby.getRubyFrame().setCbase(new CRefNode(ruby.getRubyClass(), null)); ruby.getScope().push(); /* default visibility is private at loading toplevel */ ruby.setActMethodScope(Constants.SCOPE_PRIVATE); String last_func = ruby.getRubyFrame().getLastFunc(); try { // RubyId last_func = ruby.getRubyFrame().getLastFunc(); // DEFER_INTS; ruby.setInEval(ruby.getInEval() + 1); ruby.getRubyParser().compileString(scriptName.getValue(), source, 0); // --- ruby.setInEval(ruby.getInEval() - 1); self.evalNode(ruby.getParserHelper().getEvalTree()); } catch (Exception excptn) { excptn.printStackTrace(getErrorStream()); } finally { ruby.getRubyFrame().setLastFunc(last_func); /*if (ruby.getRubyScope().getFlags() == SCOPE_ALLOCA && ruby.getRubyClass() == ruby.getClasses().getObjectClass()) { if (ruby_scope->local_tbl) free(ruby_scope->local_tbl); }*/ ruby.setCRef(savedCRef); ruby.getScope().pop(); ruby.getRubyFrame().pop(); ruby.popClass(); RubyVarmap.pop(ruby); ruby.setWrapper(wrapper); } /*if (ruby_nerrs > 0) { ruby_nerrs = 0; rb_exc_raise(ruby_errinfo); }*/ }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/774c5d3d592dfd020e3a8f961b73f629c4c55cf0/RubyRuntime.java/buggy/org/jruby/runtime/RubyRuntime.java

List names = new ArrayList();

ArrayList names = new ArrayList();

public RubyArray instance_variables() { List names = new ArrayList(); Iterator iter = instanceVariables.keySet().iterator(); while (iter.hasNext()) { String name = (String) iter.next(); names.add(RubyString.newString(getRuby(), name)); } return RubyArray.newArray(ruby, names); }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/a42a5780d9d19f5b3f27bdc079684319c5596e54/RubyObject.java/buggy/org/jruby/RubyObject.java

rootResource.putMethod(getWebdavServletURL(iwuc)+getFolderLocation()+"/"+filename+".xml",articleDoc.toString());

rootResource.putMethod(getWebdavServletURL(iwuc)+getFolderLocation()+"/"+filename+ARTICLE_SUFFIX,articleDoc.toString());

public void store() throws IDOStoreException{// public Boolean store() { boolean storeOk = true; clearErrorKeys(); ArticleDocument articleDoc = ArticleDocument.Factory.newInstance(); ArticleDocument.Article article = articleDoc.addNewArticle(); if (getHeadline().trim().equals("")) { addErrorKey(KEY_ERROR_HEADLINE_EMPTY); storeOk = false; } if (getBody().trim().equals("")) { addErrorKey(KEY_ERROR_BODY_EMPTY); storeOk = false; } // if (getRequestedStatus() != null && getRequestedStatus().equals(ContentItemCase.STATUS_PUBLISHED)) {// if (getCase().getPublishedFromDate() == null) {// addErrorKey(KEY_ERROR_PUBLISHED_FROM_DATE_EMPTY);// storeOk = false;// }// } article.setHeadline(getHeadline()); article.setBody(getBody()); article.setTeaser(getTeaser()); article.setAuthor(getAuthor()); article.setSource(getSource()); article.setComment(getComment()); String filename = getHeadline(); if(null==filename || filename.length()==0) { filename = "empty"; }/* File path = new File(getFolder()); if(!path.exists()) { path.mkdirs(); }*/ try { IWUserContext iwuc = IWContext.getInstance(); IWApplicationContext iwac = iwuc.getApplicationContext(); IWSlideSession session = (IWSlideSession)IBOLookup.getSessionInstance(iwuc,IWSlideSession.class); IWSlideService service = (IWSlideService)IBOLookup.getServiceInstance(iwac,IWSlideService.class); WebdavRootResource rootResource = session.getWebdavRootResource(); String uri = service.getWebdavServerURI(); String folderLoaction = getFolderLocation();// String filePath = service.getWebdavServerURI()+getFolderLocation();// boolean success = rootResource.mkcolMethod(filePath);// createPath(getFolderLocation()); IWSlideService slideService = (IWSlideService)IBOLookup.getServiceInstance(iwac,IWSlideService.class); slideService.createAllFoldersInPath(getFolderLocation()); System.out.println("URI = "+uri); System.out.println("Folder location = "+folderLoaction); // System.out.println("success "+success);// success = rootResource.putMethod(getWebdavServletURL(iwuc)+getFolderLocation()+"/"+filename+".xml",articleDoc.toString());// System.out.println("success "+success);// String webdavServletURL = getWebdavServletURL(iwuc)+"/"+getFolder();// System.out.println("webdavServletURL = "+webdavServletURL);// System.out.println("webdavServerURL = "+service.getWebdavServerURL());// WebdavResource webdavResource = session.getWebdavResource(session.getWebdavServerURL().toString());// WebdavResource webdavResource = session.getWebdavResource("http://localhost:8080/servlet/webdav");// WebdavResource webdavResource = new WebdavResource("http://localhost:8080/servlet/webdav/"); // WebdavFile webdavFile = session.getWebdavFile();// WebdavFile path = new WebdavFile(webdavFile, getFolder());// path.mkdirs();// webdavResource = session.getWebdavResource(getWebdavServletURL(iwuc)+getFolder()+"/"+filename+".xml");// WebdavResource webdavResource = session.getWebdavResource("http://localhost:8080/servlet/webdav/"+filename+".xml");// IWSlideService iwss = new IWSlideService();// HttpURL root = new HttpURL("http://localhost:8080/servlet/webdav/files/");// WebdavResource webdavResource = new WebdavResource("http://localhost:8080/servlet/webdav/files/"+filename+".xml");// WebdavFile webdavFile = session.getWebdavFile();// webdavResource.putMethod(new File(filename+".xml")); /* HttpURL root = new HttpURL("http://localhost:8080/servlet/webdav/files/"+filename+".xml"); root.setUserinfo("root","root"); WebdavFile webdavFile = new WebdavFile(webdavResource.getHttpURL()); webdavResource.close(); */// HttpURL root = new HttpURL("http://localhost:8080/servlet/webdav/files/"+filename+".xml", "root", "root");// root.setUserinfo("root","root"); // WebdavFile webdavFile = new WebdavFile("http://localhost:8080/servlet/webdav/files/"+filename+".xml", "root", "root");// webdavFile.createNewFile();// if(!webdavFile.exists()) {// } // articleDoc.save(new File(getFolder()+"/"+filename+".xml"));// articleDoc.save(webdavFile);// webdavFile.close(); } catch (IOException e1) { storeOk = false; // TODO Auto-generated catch block e1.printStackTrace(); } if (storeOk) { if (getRequestedStatus() != null) { setStatus(getRequestedStatus()); setRequestedStatus(null); } }else { throw new ArticleStoreException(); } }

57000 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57000/e75e5a35d9b917c44d8a58d117a43ccf5ad660b4/ArticleItemBean.java/buggy/src/java/com/idega/block/article/bean/ArticleItemBean.java

public void store() throws IDOStoreException{// public Boolean store() { boolean storeOk = true; clearErrorKeys(); ArticleDocument articleDoc = ArticleDocument.Factory.newInstance(); ArticleDocument.Article article = articleDoc.addNewArticle(); if (getHeadline().trim().equals("")) { addErrorKey(KEY_ERROR_HEADLINE_EMPTY); storeOk = false; } if (getBody().trim().equals("")) { addErrorKey(KEY_ERROR_BODY_EMPTY); storeOk = false; } // if (getRequestedStatus() != null && getRequestedStatus().equals(ContentItemCase.STATUS_PUBLISHED)) {// if (getCase().getPublishedFromDate() == null) {// addErrorKey(KEY_ERROR_PUBLISHED_FROM_DATE_EMPTY);// storeOk = false;// }// } article.setHeadline(getHeadline()); article.setBody(getBody()); article.setTeaser(getTeaser()); article.setAuthor(getAuthor()); article.setSource(getSource()); article.setComment(getComment()); String filename = getHeadline(); if(null==filename || filename.length()==0) { filename = "empty"; }/* File path = new File(getFolder()); if(!path.exists()) { path.mkdirs(); }*/ try { IWUserContext iwuc = IWContext.getInstance(); IWApplicationContext iwac = iwuc.getApplicationContext(); IWSlideSession session = (IWSlideSession)IBOLookup.getSessionInstance(iwuc,IWSlideSession.class); IWSlideService service = (IWSlideService)IBOLookup.getServiceInstance(iwac,IWSlideService.class); WebdavRootResource rootResource = session.getWebdavRootResource(); String uri = service.getWebdavServerURI(); String folderLoaction = getFolderLocation();// String filePath = service.getWebdavServerURI()+getFolderLocation();// boolean success = rootResource.mkcolMethod(filePath);// createPath(getFolderLocation()); IWSlideService slideService = (IWSlideService)IBOLookup.getServiceInstance(iwac,IWSlideService.class); slideService.createAllFoldersInPath(getFolderLocation()); System.out.println("URI = "+uri); System.out.println("Folder location = "+folderLoaction); // System.out.println("success "+success);// success = rootResource.putMethod(getWebdavServletURL(iwuc)+getFolderLocation()+"/"+filename+".xml",articleDoc.toString());// System.out.println("success "+success);// String webdavServletURL = getWebdavServletURL(iwuc)+"/"+getFolder();// System.out.println("webdavServletURL = "+webdavServletURL);// System.out.println("webdavServerURL = "+service.getWebdavServerURL());// WebdavResource webdavResource = session.getWebdavResource(session.getWebdavServerURL().toString());// WebdavResource webdavResource = session.getWebdavResource("http://localhost:8080/servlet/webdav");// WebdavResource webdavResource = new WebdavResource("http://localhost:8080/servlet/webdav/"); // WebdavFile webdavFile = session.getWebdavFile();// WebdavFile path = new WebdavFile(webdavFile, getFolder());// path.mkdirs();// webdavResource = session.getWebdavResource(getWebdavServletURL(iwuc)+getFolder()+"/"+filename+".xml");// WebdavResource webdavResource = session.getWebdavResource("http://localhost:8080/servlet/webdav/"+filename+".xml");// IWSlideService iwss = new IWSlideService();// HttpURL root = new HttpURL("http://localhost:8080/servlet/webdav/files/");// WebdavResource webdavResource = new WebdavResource("http://localhost:8080/servlet/webdav/files/"+filename+".xml");// WebdavFile webdavFile = session.getWebdavFile();// webdavResource.putMethod(new File(filename+".xml")); /* HttpURL root = new HttpURL("http://localhost:8080/servlet/webdav/files/"+filename+".xml"); root.setUserinfo("root","root"); WebdavFile webdavFile = new WebdavFile(webdavResource.getHttpURL()); webdavResource.close(); */// HttpURL root = new HttpURL("http://localhost:8080/servlet/webdav/files/"+filename+".xml", "root", "root");// root.setUserinfo("root","root"); // WebdavFile webdavFile = new WebdavFile("http://localhost:8080/servlet/webdav/files/"+filename+".xml", "root", "root");// webdavFile.createNewFile();// if(!webdavFile.exists()) {// } // articleDoc.save(new File(getFolder()+"/"+filename+".xml"));// articleDoc.save(webdavFile);// webdavFile.close(); } catch (IOException e1) { storeOk = false; // TODO Auto-generated catch block e1.printStackTrace(); } if (storeOk) { if (getRequestedStatus() != null) { setStatus(getRequestedStatus()); setRequestedStatus(null); } }else { throw new ArticleStoreException(); } }

57000 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57000/e75e5a35d9b917c44d8a58d117a43ccf5ad660b4/ArticleItemBean.java/buggy/src/java/com/idega/block/article/bean/ArticleItemBean.java

public void store() throws IDOStoreException{// public Boolean store() { boolean storeOk = true; clearErrorKeys(); ArticleDocument articleDoc = ArticleDocument.Factory.newInstance(); ArticleDocument.Article article = articleDoc.addNewArticle(); if (getHeadline().trim().equals("")) { addErrorKey(KEY_ERROR_HEADLINE_EMPTY); storeOk = false; } if (getBody().trim().equals("")) { addErrorKey(KEY_ERROR_BODY_EMPTY); storeOk = false; } // if (getRequestedStatus() != null && getRequestedStatus().equals(ContentItemCase.STATUS_PUBLISHED)) {// if (getCase().getPublishedFromDate() == null) {// addErrorKey(KEY_ERROR_PUBLISHED_FROM_DATE_EMPTY);// storeOk = false;// }// } article.setHeadline(getHeadline()); article.setBody(getBody()); article.setTeaser(getTeaser()); article.setAuthor(getAuthor()); article.setSource(getSource()); article.setComment(getComment()); String filename = getHeadline(); if(null==filename || filename.length()==0) { filename = "empty"; }/* File path = new File(getFolder()); if(!path.exists()) { path.mkdirs(); }*/ try { IWUserContext iwuc = IWContext.getInstance(); IWApplicationContext iwac = iwuc.getApplicationContext(); IWSlideSession session = (IWSlideSession)IBOLookup.getSessionInstance(iwuc,IWSlideSession.class); IWSlideService service = (IWSlideService)IBOLookup.getServiceInstance(iwac,IWSlideService.class); WebdavRootResource rootResource = session.getWebdavRootResource(); String uri = service.getWebdavServerURI(); String folderLoaction = getFolderLocation();// String filePath = service.getWebdavServerURI()+getFolderLocation();// boolean success = rootResource.mkcolMethod(filePath);// createPath(getFolderLocation()); IWSlideService slideService = (IWSlideService)IBOLookup.getServiceInstance(iwac,IWSlideService.class); slideService.createAllFoldersInPath(getFolderLocation()); System.out.println("URI = "+uri); System.out.println("Folder location = "+folderLoaction); // System.out.println("success "+success);// success = rootResource.putMethod(getWebdavServletURL(iwuc)+getFolderLocation()+"/"+filename+".xml",articleDoc.toString());// System.out.println("success "+success);// String webdavServletURL = getWebdavServletURL(iwuc)+"/"+getFolder();// System.out.println("webdavServletURL = "+webdavServletURL);// System.out.println("webdavServerURL = "+service.getWebdavServerURL());// WebdavResource webdavResource = session.getWebdavResource(session.getWebdavServerURL().toString());// WebdavResource webdavResource = session.getWebdavResource("http://localhost:8080/servlet/webdav");// WebdavResource webdavResource = new WebdavResource("http://localhost:8080/servlet/webdav/"); // WebdavFile webdavFile = session.getWebdavFile();// WebdavFile path = new WebdavFile(webdavFile, getFolder());// path.mkdirs();// webdavResource = session.getWebdavResource(getWebdavServletURL(iwuc)+getFolder()+"/"+filename+".xml");// WebdavResource webdavResource = session.getWebdavResource("http://localhost:8080/servlet/webdav/"+filename+".xml");// IWSlideService iwss = new IWSlideService();// HttpURL root = new HttpURL("http://localhost:8080/servlet/webdav/files/");// WebdavResource webdavResource = new WebdavResource("http://localhost:8080/servlet/webdav/files/"+filename+".xml");// WebdavFile webdavFile = session.getWebdavFile();// webdavResource.putMethod(new File(filename+".xml")); /* HttpURL root = new HttpURL("http://localhost:8080/servlet/webdav/files/"+filename+".xml"); root.setUserinfo("root","root"); WebdavFile webdavFile = new WebdavFile(webdavResource.getHttpURL()); webdavResource.close(); */// HttpURL root = new HttpURL("http://localhost:8080/servlet/webdav/files/"+filename+".xml", "root", "root");// root.setUserinfo("root","root"); // WebdavFile webdavFile = new WebdavFile("http://localhost:8080/servlet/webdav/files/"+filename+".xml", "root", "root");// webdavFile.createNewFile();// if(!webdavFile.exists()) {// } // articleDoc.save(new File(getFolder()+"/"+filename+".xml"));// articleDoc.save(webdavFile);// webdavFile.close(); } catch (IOException e1) { storeOk = false; // TODO Auto-generated catch block e1.printStackTrace(); } if (storeOk) { if (getRequestedStatus() != null) { setStatus(getRequestedStatus()); setRequestedStatus(null); } }else { throw new ArticleStoreException(); } }

57000 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57000/e75e5a35d9b917c44d8a58d117a43ccf5ad660b4/ArticleItemBean.java/buggy/src/java/com/idega/block/article/bean/ArticleItemBean.java

public void store() throws IDOStoreException{// public Boolean store() { boolean storeOk = true; clearErrorKeys(); ArticleDocument articleDoc = ArticleDocument.Factory.newInstance(); ArticleDocument.Article article = articleDoc.addNewArticle(); if (getHeadline().trim().equals("")) { addErrorKey(KEY_ERROR_HEADLINE_EMPTY); storeOk = false; } if (getBody().trim().equals("")) { addErrorKey(KEY_ERROR_BODY_EMPTY); storeOk = false; } // if (getRequestedStatus() != null && getRequestedStatus().equals(ContentItemCase.STATUS_PUBLISHED)) {// if (getCase().getPublishedFromDate() == null) {// addErrorKey(KEY_ERROR_PUBLISHED_FROM_DATE_EMPTY);// storeOk = false;// }// } article.setHeadline(getHeadline()); article.setBody(getBody()); article.setTeaser(getTeaser()); article.setAuthor(getAuthor()); article.setSource(getSource()); article.setComment(getComment()); String filename = getHeadline(); if(null==filename || filename.length()==0) { filename = "empty"; }/* File path = new File(getFolder()); if(!path.exists()) { path.mkdirs(); }*/ try { IWUserContext iwuc = IWContext.getInstance(); IWApplicationContext iwac = iwuc.getApplicationContext(); IWSlideSession session = (IWSlideSession)IBOLookup.getSessionInstance(iwuc,IWSlideSession.class); IWSlideService service = (IWSlideService)IBOLookup.getServiceInstance(iwac,IWSlideService.class); WebdavRootResource rootResource = session.getWebdavRootResource(); String uri = service.getWebdavServerURI(); String folderLoaction = getFolderLocation();// String filePath = service.getWebdavServerURI()+getFolderLocation();// boolean success = rootResource.mkcolMethod(filePath);// createPath(getFolderLocation()); IWSlideService slideService = (IWSlideService)IBOLookup.getServiceInstance(iwac,IWSlideService.class); slideService.createAllFoldersInPath(getFolderLocation()); System.out.println("URI = "+uri); System.out.println("Folder location = "+folderLoaction); // System.out.println("success "+success);// success = rootResource.putMethod(getWebdavServletURL(iwuc)+getFolderLocation()+"/"+filename+".xml",articleDoc.toString());// System.out.println("success "+success);// String webdavServletURL = getWebdavServletURL(iwuc)+"/"+getFolder();// System.out.println("webdavServletURL = "+webdavServletURL);// System.out.println("webdavServerURL = "+service.getWebdavServerURL());// WebdavResource webdavResource = session.getWebdavResource(session.getWebdavServerURL().toString());// WebdavResource webdavResource = session.getWebdavResource("http://localhost:8080/servlet/webdav");// WebdavResource webdavResource = new WebdavResource("http://localhost:8080/servlet/webdav/"); // WebdavFile webdavFile = session.getWebdavFile();// WebdavFile path = new WebdavFile(webdavFile, getFolder());// path.mkdirs();// webdavResource = session.getWebdavResource(getWebdavServletURL(iwuc)+getFolder()+"/"+filename+".xml");// WebdavResource webdavResource = session.getWebdavResource("http://localhost:8080/servlet/webdav/"+filename+".xml");// IWSlideService iwss = new IWSlideService();// HttpURL root = new HttpURL("http://localhost:8080/servlet/webdav/files/");// WebdavResource webdavResource = new WebdavResource("http://localhost:8080/servlet/webdav/files/"+filename+".xml");// WebdavFile webdavFile = session.getWebdavFile();// webdavResource.putMethod(new File(filename+".xml")); /* HttpURL root = new HttpURL("http://localhost:8080/servlet/webdav/files/"+filename+".xml"); root.setUserinfo("root","root"); WebdavFile webdavFile = new WebdavFile(webdavResource.getHttpURL()); webdavResource.close(); */// HttpURL root = new HttpURL("http://localhost:8080/servlet/webdav/files/"+filename+".xml", "root", "root");// root.setUserinfo("root","root"); // WebdavFile webdavFile = new WebdavFile("http://localhost:8080/servlet/webdav/files/"+filename+".xml", "root", "root");// webdavFile.createNewFile();// if(!webdavFile.exists()) {// } // articleDoc.save(new File(getFolder()+"/"+filename+".xml"));// articleDoc.save(webdavFile);// webdavFile.close(); } catch (IOException e1) { storeOk = false; // TODO Auto-generated catch block e1.printStackTrace(); } if (storeOk) { if (getRequestedStatus() != null) { setStatus(getRequestedStatus()); setRequestedStatus(null); } }else { throw new ArticleStoreException(); } }

57000 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57000/e75e5a35d9b917c44d8a58d117a43ccf5ad660b4/ArticleItemBean.java/buggy/src/java/com/idega/block/article/bean/ArticleItemBean.java

HttpURL root = new HttpURL("http: