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coconut_java2006

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if (ChainBuilderAgent.DEBUG) System.err.println("starting mmodule target link..."+modLink);
private void startModuleTargetLink(ModuleLinkTarget modLink) { moduleLinkOriginTarget = modLink; //System.err.println("starting mmodule target link..."+modLink); moduleLink = new ModuleLink(linkLayer,moduleLinkOriginTarget); moduleLink.setPickable(false); linkState = LINKING_MODULE_TARGETS; }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/a806bf744289bb0eed666b235887c8680d549d94/ChainCreationEventHandler.java/buggy/SRC/org/openmicroscopy/shoola/agents/chainbuilder/piccolo/ChainCreationEventHandler.java
if (ChainBuilderAgent.DEBUG) { System.err.println("mouse pressing and starting link"); System.err.println("start param link. link state is LINKING_PARAMS"); }
private void startParamLink(FormalParameter param) { ////System.err.println("mouse pressing and starting link"); linkOrigin = param; link = new ParamLink(); linkLayer.addChild(link); link.setStartParam(linkOrigin); link.setPickable(false); //System.err.println("start param link. link state is LINKING_PARAMS"); linkState = LINKING_PARAMS; }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/a806bf744289bb0eed666b235887c8680d549d94/ChainCreationEventHandler.java/buggy/SRC/org/openmicroscopy/shoola/agents/chainbuilder/piccolo/ChainCreationEventHandler.java
private void startParamLink(FormalParameter param) { ////System.err.println("mouse pressing and starting link"); linkOrigin = param; link = new ParamLink(); linkLayer.addChild(link); link.setStartParam(linkOrigin); link.setPickable(false); //System.err.println("start param link. link state is LINKING_PARAMS"); linkState = LINKING_PARAMS; }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/a806bf744289bb0eed666b235887c8680d549d94/ChainCreationEventHandler.java/buggy/SRC/org/openmicroscopy/shoola/agents/chainbuilder/piccolo/ChainCreationEventHandler.java
if (index == -1) return;
public void copyPlaneArea(PlaneArea pa, int newZ, int newT) { int index = presentation.getToolBar().getSelectedIndex(); abstraction.copyPlaneArea(pa, index, newZ, newT); if (newT == getCurrentT() && newZ == getCurrentZ()) { PlaneArea p = abstraction.getPlaneArea(newZ, newT, index); if (p != null) { p.scale(abstraction.getMagFactor()); drawingCanvas.setPlaneArea(p, index); } } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/82a0758855f6c1b189a9820fbc91ef09f7c7863a/ROIAgtCtrl.java/clean/SRC/org/openmicroscopy/shoola/agents/roi/ROIAgtCtrl.java
int index = presentation.getToolBar().getSelectedIndex(); if (index == -1) return;
public void removeAllPlaneAreas() { abstraction.removeAllPlaneAreas(); drawingCanvas.clearPreviousView(); drawingCanvas.repaint(); ToolBarMng tbm = presentation.getToolBar().getManager(); tbm.removeCurrentPlane(getCurrentZ(), getCurrentT()); ScreenROI roi = getScreenROI(); drawingCanvas.getManager().setDefault(roi.getIndex(), roi.getAreaColor(), ROIAgtUIF.CONSTRUCTING); setROIThumbnail(); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/82a0758855f6c1b189a9820fbc91ef09f7c7863a/ROIAgtCtrl.java/clean/SRC/org/openmicroscopy/shoola/agents/roi/ROIAgtCtrl.java
return setInstanceVariable(name, value, "Insecure: can't set constant",
IRubyObject result = setInstanceVariable(name, value, "Insecure: can't set constant",
public IRubyObject setConstant(String name, IRubyObject value) { return setInstanceVariable(name, value, "Insecure: can't set constant", "class/module"); }
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/d27bd5bcb36c7670bce31c6a2a4c22b11fdfa5c4/RubyModule.java/buggy/src/org/jruby/RubyModule.java
if (value instanceof RubyModule) { RubyModule module = (RubyModule)value; if (module.getBaseName() == null) { module.setBaseName(name); } } return result;
public IRubyObject setConstant(String name, IRubyObject value) { return setInstanceVariable(name, value, "Insecure: can't set constant", "class/module"); }
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/d27bd5bcb36c7670bce31c6a2a4c22b11fdfa5c4/RubyModule.java/buggy/src/org/jruby/RubyModule.java
public UserCredentials getUserCredentials()
public UserCredentials getUserCredentials(final boolean init)
public UserCredentials getUserCredentials() { //First off, let's make sure that this.open() has already been called. //If not we return to prevent deadlock. if (!isValid) return null; //Construct request of mehtod execution. final SplashScreenFuture future = new SplashScreenFuture(); Runnable doCollectUserCredentials = new Runnable() { public void run() { servant.collectUserCredentials(future); } }; //Schedule execution within Swing dispatching thread. SwingUtilities.invokeLater(doCollectUserCredentials); //Now we can safely wait for the user to enter their credentials. return (UserCredentials) future.get(); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/84042cbca2e8aeaf65ca18c85ea2224ea4c04d55/SplashScreenProxy.java/clean/SRC/org/openmicroscopy/shoola/env/ui/SplashScreenProxy.java
public void run() { servant.collectUserCredentials(future); }
public void run() { servant.collectUserCredentials(future, init); }
public UserCredentials getUserCredentials() { //First off, let's make sure that this.open() has already been called. //If not we return to prevent deadlock. if (!isValid) return null; //Construct request of mehtod execution. final SplashScreenFuture future = new SplashScreenFuture(); Runnable doCollectUserCredentials = new Runnable() { public void run() { servant.collectUserCredentials(future); } }; //Schedule execution within Swing dispatching thread. SwingUtilities.invokeLater(doCollectUserCredentials); //Now we can safely wait for the user to enter their credentials. return (UserCredentials) future.get(); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/84042cbca2e8aeaf65ca18c85ea2224ea4c04d55/SplashScreenProxy.java/clean/SRC/org/openmicroscopy/shoola/env/ui/SplashScreenProxy.java
public void run() { servant.collectUserCredentials(future); }
public void run() { servant.collectUserCredentials(future, init); }
public void run() { servant.collectUserCredentials(future); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/84042cbca2e8aeaf65ca18c85ea2224ea4c04d55/SplashScreenProxy.java/clean/SRC/org/openmicroscopy/shoola/env/ui/SplashScreenProxy.java
out.println(pkg == null ? "All Packages" : pkg.getName());
out.println(pkg == null ? "All Packages" : generatePackageName(pkg));
private void generateClassList(Package pkg) throws IOException { String filename; Collection classes; if (pkg == null) { filename = "frame-classes.html"; classes = coverage.getClassesSortedByBasename().values(); } else { filename = "frame-classes-" + pkg.getName() + ".html"; classes = pkg.getClasses(); } File file = new File(outputDir, filename); PrintStream out = null; try { out = new PrintStream(new FileOutputStream(file)); out.println("<html>"); out.println("<head>"); out.println("<title>Coverage Report Classes</title>"); out .println("<link title=\"Style\" type=\"text/css\" rel=\"stylesheet\" href=\"css/main.css\" />"); out.println("</head>"); out.println("<body>"); out.println("<h5>"); out.println(pkg == null ? "All Packages" : pkg.getName()); out.println("</h5>"); out.println("<h5>Classes</h5>"); out.println("<table width=\"100%\">"); for (Iterator iter = classes.iterator(); iter.hasNext();) { Clazz clazz = (Clazz)iter.next(); out.println("<tr>"); String percentCovered; if (clazz.getNumberOfLines() > 0) percentCovered = getPercentValue(clazz .getLineCoverageRate()); else percentCovered = "N/A"; out .println("<td nowrap=\"nowrap\"><a target=\"summary\" href=\"" + clazz.getLongName() + ".html\">" + clazz.getName() + "</a> <i>(" + percentCovered + ")</i></td>"); out.println("</tr>"); } out.println("</td>"); out.println("</tr>"); out.println("</table>"); out.println("</body>"); out.println("</html>"); } finally { if (out != null) { out.close(); } } }
50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/bc68f2316e279affb4a8c05a3d93558ff5689828/HTMLReport.java/buggy/cobertura/src/net/sourceforge/cobertura/reporting/html/HTMLReport.java
out.print(pkg == null ? "All Packages" : pkg.getName());
out.print(pkg == null ? "All Packages" : generatePackageName(pkg));
private void generateOverview(Package pkg) throws IOException { String filename; if (pkg == null) { filename = "frame-summary.html"; } else { filename = "frame-summary-" + pkg.getName() + ".html"; } File file = new File(outputDir, filename); PrintStream out = null; try { out = new PrintStream(new FileOutputStream(file)); out.println("<html>"); out.println("<head>"); out.println("<title>Coverage Report</title>"); out .println("<link title=\"Style\" type=\"text/css\" rel=\"stylesheet\" href=\"css/main.css\" />"); out .println("<link title=\"Style\" type=\"text/css\" rel=\"stylesheet\" href=\"css/sortabletable.css\" />"); out .println("<script type=\"text/javascript\" src=\"js/popup.js\"></script>"); out .println("<script type=\"text/javascript\" src=\"js/sortabletable.js\"></script>"); out .println("<script type=\"text/javascript\" src=\"js/percentagesorttype.js\"></script>"); out.println("</head>"); out.println("<body>"); out.print("<h5>Coverage Report - "); out.print(pkg == null ? "All Packages" : pkg.getName()); out.println("</h5>"); out.println("<p>"); out.println("<table class=\"report\" id=\"packageResults\">"); out.println("<thead>"); out.println("<tr>"); out.println(" <td class=\"heading\">Package</td>"); out.println(" <td class=\"heading\"># Classes</td>"); out.println(generateCommonTableColumns()); out.println("</tr>"); out.println("</thead>"); out.println("<tbody>"); Set packages; if (pkg == null) { // Output a summary line for all packages out.println(generateTableRowForTotal()); // Get packages packages = coverage.getPackages(); } else { // Output a line for the current package out.println(generateTableRowForPackage(pkg)); // Get subpackages packages = coverage.getSubPackages(pkg); } // Output a line for each package or subpackage if (packages.size() > 0) { Iterator iter = packages.iterator(); while (iter.hasNext()) { Package subpkg = (Package)iter.next(); out.println(generateTableRowForPackage(subpkg)); } } out.println("</tbody>"); out.println("</table>"); out.println("<script type=\"text/javascript\">"); out .println("var packageTable = new SortableTable(document.getElementById(\"packageResults\"),"); out .println(" [\"String\", \"Number\", \"Percentage\", \"Percentage\", \"Number\", \"Number\", \"Number\"]);"); out.println("packageTable.sort(0);"); out.println("</script>"); out.println("</p>"); // Get the list of classes in this package Set classes; if (pkg == null) { classes = new TreeSet(); if (coverage.getNumberOfClasses() > 0) { Iterator iter = coverage.getClasses().iterator(); while (iter.hasNext()) { Clazz clazz = (Clazz)iter.next(); if (clazz.getPackageName() == null) { classes.add(clazz); } } } } else { classes = pkg.getClasses(); } // Output a line for each class if (classes.size() > 0) { out.println("<p>"); out.println("<table class=\"report\" id=\"classResults\">"); out.println(generateTableHeaderForClasses()); out.println("<tbody>"); Iterator iter = classes.iterator(); while (iter.hasNext()) { Clazz clazz = (Clazz)iter.next(); out.println(generateTableRowForClass(clazz)); } out.println("</tbody>"); out.println("</table>"); out.println("<script type=\"text/javascript\">"); out .println("var classTable = new SortableTable(document.getElementById(\"classResults\"),"); out .println(" [\"String\", \"Percentage\", \"Percentage\", \"Number\", \"Number\", \"Number\"]);"); out.println("classTable.sort(0);"); out.println("</script>"); out.println("</p>"); } out.println("<div class=\"footer\">"); out .println("Reports generated by <a href=\"http://cobertura.sourceforge.net/\" target=\"_top\">Cobertura</a>."); out.println("</div>"); out.println("</body>"); out.println("</html>"); } finally { if (out != null) { out.close(); } } }
50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/bc68f2316e279affb4a8c05a3d93558ff5689828/HTMLReport.java/buggy/cobertura/src/net/sourceforge/cobertura/reporting/html/HTMLReport.java
private void generateOverview(Package pkg) throws IOException { String filename; if (pkg == null) { filename = "frame-summary.html"; } else { filename = "frame-summary-" + pkg.getName() + ".html"; } File file = new File(outputDir, filename); PrintStream out = null; try { out = new PrintStream(new FileOutputStream(file)); out.println("<html>"); out.println("<head>"); out.println("<title>Coverage Report</title>"); out .println("<link title=\"Style\" type=\"text/css\" rel=\"stylesheet\" href=\"css/main.css\" />"); out .println("<link title=\"Style\" type=\"text/css\" rel=\"stylesheet\" href=\"css/sortabletable.css\" />"); out .println("<script type=\"text/javascript\" src=\"js/popup.js\"></script>"); out .println("<script type=\"text/javascript\" src=\"js/sortabletable.js\"></script>"); out .println("<script type=\"text/javascript\" src=\"js/percentagesorttype.js\"></script>"); out.println("</head>"); out.println("<body>"); out.print("<h5>Coverage Report - "); out.print(pkg == null ? "All Packages" : pkg.getName()); out.println("</h5>"); out.println("<p>"); out.println("<table class=\"report\" id=\"packageResults\">"); out.println("<thead>"); out.println("<tr>"); out.println(" <td class=\"heading\">Package</td>"); out.println(" <td class=\"heading\"># Classes</td>"); out.println(generateCommonTableColumns()); out.println("</tr>"); out.println("</thead>"); out.println("<tbody>"); Set packages; if (pkg == null) { // Output a summary line for all packages out.println(generateTableRowForTotal()); // Get packages packages = coverage.getPackages(); } else { // Output a line for the current package out.println(generateTableRowForPackage(pkg)); // Get subpackages packages = coverage.getSubPackages(pkg); } // Output a line for each package or subpackage if (packages.size() > 0) { Iterator iter = packages.iterator(); while (iter.hasNext()) { Package subpkg = (Package)iter.next(); out.println(generateTableRowForPackage(subpkg)); } } out.println("</tbody>"); out.println("</table>"); out.println("<script type=\"text/javascript\">"); out .println("var packageTable = new SortableTable(document.getElementById(\"packageResults\"),"); out .println(" [\"String\", \"Number\", \"Percentage\", \"Percentage\", \"Number\", \"Number\", \"Number\"]);"); out.println("packageTable.sort(0);"); out.println("</script>"); out.println("</p>"); // Get the list of classes in this package Set classes; if (pkg == null) { classes = new TreeSet(); if (coverage.getNumberOfClasses() > 0) { Iterator iter = coverage.getClasses().iterator(); while (iter.hasNext()) { Clazz clazz = (Clazz)iter.next(); if (clazz.getPackageName() == null) { classes.add(clazz); } } } } else { classes = pkg.getClasses(); } // Output a line for each class if (classes.size() > 0) { out.println("<p>"); out.println("<table class=\"report\" id=\"classResults\">"); out.println(generateTableHeaderForClasses()); out.println("<tbody>"); Iterator iter = classes.iterator(); while (iter.hasNext()) { Clazz clazz = (Clazz)iter.next(); out.println(generateTableRowForClass(clazz)); } out.println("</tbody>"); out.println("</table>"); out.println("<script type=\"text/javascript\">"); out .println("var classTable = new SortableTable(document.getElementById(\"classResults\"),"); out .println(" [\"String\", \"Percentage\", \"Percentage\", \"Number\", \"Number\", \"Number\"]);"); out.println("classTable.sort(0);"); out.println("</script>"); out.println("</p>"); } out.println("<div class=\"footer\">"); out .println("Reports generated by <a href=\"http://cobertura.sourceforge.net/\" target=\"_top\">Cobertura</a>."); out.println("</div>"); out.println("</body>"); out.println("</html>"); } finally { if (out != null) { out.close(); } } }
50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/bc68f2316e279affb4a8c05a3d93558ff5689828/HTMLReport.java/buggy/cobertura/src/net/sourceforge/cobertura/reporting/html/HTMLReport.java
+ url2 + "\"' target=\"summary\">" + pkg.getName()
+ url2 + "\"' target=\"summary\">" + generatePackageName(pkg)
private void generatePackageList() throws IOException { File file = new File(outputDir, "frame-packages.html"); PrintStream out = null; try { out = new PrintStream(new FileOutputStream(file)); out.println("<html>"); out.println("<head>"); out.println("<title>Coverage Report</title>"); out .println("<link title=\"Style\" type=\"text/css\" rel=\"stylesheet\" href=\"css/main.css\" />"); out.println("</head>"); out.println("<body>"); out.println("<h5>Packages</h5>"); out.println("<table width=\"100%\">"); out.println("<tr>"); out .println("<td nowrap=\"nowrap\"><a href=\"frame-summary.html\" onClick='parent.classList.location.href=\"frame-classes.html\"' target=\"summary\">All</a></td>"); out.println("</tr>"); Iterator iter = coverage.getPackages().iterator(); while (iter.hasNext()) { Package pkg = (Package)iter.next(); String url1 = "frame-summary-" + pkg.getName() + ".html"; String url2 = "frame-classes-" + pkg.getName() + ".html"; out.println("<tr>"); out.println("<td nowrap=\"nowrap\"><a href=\"" + url1 + "\" onClick='parent.classList.location.href=\"" + url2 + "\"' target=\"summary\">" + pkg.getName() + "</a></td>"); out.println("</tr>"); } out.println("</table>"); out.println("</body>"); out.println("</html>"); } finally { if (out != null) { out.close(); } } }
50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/bc68f2316e279affb4a8c05a3d93558ff5689828/HTMLReport.java/buggy/cobertura/src/net/sourceforge/cobertura/reporting/html/HTMLReport.java
if (clazz.getPackageName() != null)
String classPackageName = clazz.getPackageName(); if ((classPackageName != null) && classPackageName.length() > 0)
private void generateSourceFile(Clazz clazz) throws IOException { String filename = clazz.getLongName() + ".html"; File file = new File(outputDir, filename); PrintStream out = null; try { out = new PrintStream(new FileOutputStream(file)); out.println("<html>"); out.println("<head>"); out.println("<title>Coverage Report</title>"); out .println("<link title=\"Style\" type=\"text/css\" rel=\"stylesheet\" href=\"css/main.css\" />"); out .println("<script type=\"text/javascript\" src=\"js/popup.js\"></script>"); out.println("</head>"); out.println("<body>"); out.print("<h5>Coverage Report - "); if (clazz.getPackageName() != null) { out.print(clazz.getPackageName() + "."); } out.print(clazz.getName()); out.println("</h5>"); // Output the coverage summary for this class out.println("<p>"); out.println("<table class=\"report\">"); out.println(generateTableHeaderForClasses()); out.println(generateTableRowForClass(clazz)); out.println("</table>"); out.println("</p>"); // Output this class's source code with syntax and coverage highlighting out.println("<p>"); out .println("<table cellspacing=\"0\" cellpadding=\"0\" class=\"src\">"); BufferedReader br = null; try { br = new BufferedReader(new FileReader(new File(sourceDir, clazz.getLongFileName()))); String lineStr; JavaToHtml javaToHtml = new JavaToHtml(); int lineNumber = 1; while ((lineStr = br.readLine()) != null) { out.println("<tr>"); if (clazz.isValidSourceLine(lineNumber)) { long numberOfHits = clazz.getNumberOfHits(lineNumber); out.println(" <td class=\"numLineCover\">&nbsp;" + lineNumber + "</td>"); if (numberOfHits > 0) { out .println(" <td class=\"nbHitsCovered\">&nbsp;" + numberOfHits + "</td>"); out .println(" <td class=\"src\"><pre class=\"src\">&nbsp;" + javaToHtml.process(lineStr) + "</pre></td>"); } else { out .println(" <td class=\"nbHitsUncovered\">&nbsp;" + numberOfHits + "</td>"); out .println(" <td class=\"src\"><pre class=\"src\"><span class=\"srcUncovered\">&nbsp;" + javaToHtml.process(lineStr) + "</span></pre></td>"); } } else { out.println(" <td class=\"numLine\">&nbsp;" + lineNumber + "</td>"); out.println(" <td class=\"nbHits\">&nbsp;</td>"); out .println(" <td class=\"src\"><pre class=\"src\">&nbsp;" + javaToHtml.process(lineStr) + "</pre></td>"); } out.println("</tr>"); lineNumber++; } } finally { if (br != null) { br.close(); } } out.println("</table>"); out.println("</p>"); out.println("<div class=\"footer\">"); out .println("Reports generated by <a href=\"http://cobertura.sourceforge.net/\" target=\"_top\">Cobertura</a>."); out.println("</div>"); out.println("</body>"); out.println("</html>"); } finally { if (out != null) { out.close(); } } }
50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/bc68f2316e279affb4a8c05a3d93558ff5689828/HTMLReport.java/buggy/cobertura/src/net/sourceforge/cobertura/reporting/html/HTMLReport.java
+ "\"'>" + pkg.getName() + "</a></td>");
+ "\"'>" + generatePackageName(pkg) + "</a></td>");
private String generateTableRowForPackage(Package pkg) { StringBuffer ret = new StringBuffer(); String url1 = "frame-summary-" + pkg.getName() + ".html"; String url2 = "frame-classes-" + pkg.getName() + ".html"; double lineCoverage = pkg.getLineCoverageRate(); double branchCoverage = pkg.getBranchCoverageRate(); double ccn = Util.getCCN(new File(sourceDir, pkg.getFileName()), false); ret.append(" <tr>"); ret.append("<td class=\"text\"><a href=\"" + url1 + "\" onClick='parent.classList.location.href=\"" + url2 + "\"'>" + pkg.getName() + "</a></td>"); ret .append("<td class=\"value\">" + pkg.getClasses().size() + "</td>"); ret.append(generateTableColumnsFromData(lineCoverage, branchCoverage, ccn)); ret.append("</tr>"); return ret.toString(); }
50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/bc68f2316e279affb4a8c05a3d93558ff5689828/HTMLReport.java/buggy/cobertura/src/net/sourceforge/cobertura/reporting/html/HTMLReport.java
long start = System.currentTimeMillis();
if (ChainBuilderAgent.DEBUG) { start = System.currentTimeMillis(); }
public synchronized Collection getChainExecutions() { // if we're done, go for it. if (chainExecutions != null) { return chainExecutions.getExecutions(); } if (gettingExecutions == false) { long start = System.currentTimeMillis(); gettingExecutions = true; retrieveChainExecutions(); gettingExecutions = false; notifyAll(); long getTime = System.currentTimeMillis()-start; System.err.println("time for executions is "+getTime); return chainExecutions.getExecutions(); } else {// in progress try{ wait(); return chainExecutions.getExecutions(); } catch (InterruptedException e) { return null; } } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/a806bf744289bb0eed666b235887c8680d549d94/ChainDataManager.java/buggy/SRC/org/openmicroscopy/shoola/agents/chainbuilder/ChainDataManager.java
long getTime = System.currentTimeMillis()-start; System.err.println("time for executions is "+getTime);
if (ChainBuilderAgent.DEBUG) { long getTime = System.currentTimeMillis()-start; System.err.println("time for executions is "+getTime); }
public synchronized Collection getChainExecutions() { // if we're done, go for it. if (chainExecutions != null) { return chainExecutions.getExecutions(); } if (gettingExecutions == false) { long start = System.currentTimeMillis(); gettingExecutions = true; retrieveChainExecutions(); gettingExecutions = false; notifyAll(); long getTime = System.currentTimeMillis()-start; System.err.println("time for executions is "+getTime); return chainExecutions.getExecutions(); } else {// in progress try{ wait(); return chainExecutions.getExecutions(); } catch (InterruptedException e) { return null; } } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/a806bf744289bb0eed666b235887c8680d549d94/ChainDataManager.java/buggy/SRC/org/openmicroscopy/shoola/agents/chainbuilder/ChainDataManager.java
long start = System.currentTimeMillis();
if (ChainBuilderAgent.DEBUG) { start = System.currentTimeMillis(); }
public synchronized Collection getChains() { Collection res = null; // if we're done, go for it. if (chainHash != null && chainHash.size() > 0) { res = chainHash.values(); } else { if (gettingChains == false) { long start = System.currentTimeMillis(); gettingChains = true; retrieveChains(); gettingChains = false; notifyAll(); long end = System.currentTimeMillis()-start; System.err.println("time for retrieving chains.. "+end); res = chainHash.values(); } else {// in progress try{ wait(); res = chainHash.values(); } catch (InterruptedException e) { res = null; } } } return res; }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/a806bf744289bb0eed666b235887c8680d549d94/ChainDataManager.java/buggy/SRC/org/openmicroscopy/shoola/agents/chainbuilder/ChainDataManager.java
long end = System.currentTimeMillis()-start; System.err.println("time for retrieving chains.. "+end);
if (ChainBuilderAgent.DEBUG) { long end = System.currentTimeMillis()-start; System.err.println("time for retrieving chains.. "+end); }
public synchronized Collection getChains() { Collection res = null; // if we're done, go for it. if (chainHash != null && chainHash.size() > 0) { res = chainHash.values(); } else { if (gettingChains == false) { long start = System.currentTimeMillis(); gettingChains = true; retrieveChains(); gettingChains = false; notifyAll(); long end = System.currentTimeMillis()-start; System.err.println("time for retrieving chains.. "+end); res = chainHash.values(); } else {// in progress try{ wait(); res = chainHash.values(); } catch (InterruptedException e) { res = null; } } } return res; }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/a806bf744289bb0eed666b235887c8680d549d94/ChainDataManager.java/buggy/SRC/org/openmicroscopy/shoola/agents/chainbuilder/ChainDataManager.java
return Collections.EMPTY_LIST;
return EMPTY_LIST;
public List childNodes() { return Collections.EMPTY_LIST; }
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/b1293eda8454686e846e2a9837b348e2983bb423/UndefNode.java/buggy/src/org/jruby/ast/UndefNode.java
PlayerManager manager = new PlayerManager(this, control, max,
manager = new PlayerManager(this, control, max,
private void init(ViewerCtrl control, int maxT, int maxZ, MovieSettings settings) { int max = maxT; int s = settings.getStartT(), e = settings.getEndT(); if (maxT == 0) { s = settings.getStartZ(); e = settings.getEndZ(); max = maxZ; } PlayerManager manager = new PlayerManager(this, control, max, settings.getMovieIndex(), s, e); player = new PlayerUI(manager, control.getRegistry(), maxT, maxZ, settings); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0a711d50cfe02a185f8d314b378ca4c49e92ab2f/Player.java/clean/SRC/org/openmicroscopy/shoola/agents/viewer/movie/Player.java
if ((broadcast || message.getType() == Message.Type.NORMAL) && message.getBody() != null) {
if ((broadcast || (message.getType() == Message.Type.NORMAL) || message.getType() == Message.Type.HEADLINE) && message.getBody() != null) {
public void processPacket(final Packet packet) { SwingUtilities.invokeLater(new Runnable() { public void run() { final Message message = (Message)packet; boolean broadcast = message.getProperty("broadcast") != null; if ((broadcast || message.getType() == Message.Type.NORMAL) && message.getBody() != null) { showAlert((Message)packet); } else { String host = SparkManager.getSessionManager().getServerAddress(); String from = packet.getFrom() != null ? packet.getFrom() : ""; if (host.equalsIgnoreCase(from) || !ModelUtil.hasLength(from)) { showAlert((Message)packet); } } } }); }
52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/7645851bdaa2a933966642360f8bb4b56e708043/BroadcastPlugin.java/buggy/src/java/org/jivesoftware/sparkimpl/plugin/alerts/BroadcastPlugin.java
if ((broadcast || message.getType() == Message.Type.NORMAL) && message.getBody() != null) {
if ((broadcast || (message.getType() == Message.Type.NORMAL) || message.getType() == Message.Type.HEADLINE) && message.getBody() != null) {
public void run() { final Message message = (Message)packet; boolean broadcast = message.getProperty("broadcast") != null; if ((broadcast || message.getType() == Message.Type.NORMAL) && message.getBody() != null) { showAlert((Message)packet); } else { String host = SparkManager.getSessionManager().getServerAddress(); String from = packet.getFrom() != null ? packet.getFrom() : ""; if (host.equalsIgnoreCase(from) || !ModelUtil.hasLength(from)) { showAlert((Message)packet); } } }
52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/7645851bdaa2a933966642360f8bb4b56e708043/BroadcastPlugin.java/buggy/src/java/org/jivesoftware/sparkimpl/plugin/alerts/BroadcastPlugin.java
pathToTestOutput, "--source", pathToSourceCode };
pathToTestOutput, pathToSourceCode };
public void testXMLReportValidity() throws Exception { String[] args; // Serialize the current coverage data to disk ProjectData.saveGlobalProjectData(); String dataFileName = CoverageDataFileHandler.getDefaultDataFile() .getAbsolutePath(); // Then we need to generate the XML report args = new String[] { "--format", "xml", "--datafile", dataFileName, "--destination", pathToTestOutput, "--source", pathToSourceCode }; net.sourceforge.cobertura.reporting.Main.main(args); // Create a validating XML document parser DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setValidating(true); DocumentBuilder documentBuilder = factory.newDocumentBuilder(); documentBuilder.setEntityResolver(new JUnitXMLParserEntityResolver( basedir)); documentBuilder.setErrorHandler(new JUnitXMLParserErrorHandler()); // Parse the XML report InputStream inputStream = null; try { inputStream = new FileInputStream(pathToXMLReport); documentBuilder.parse(inputStream); } finally { if (inputStream != null) inputStream.close(); } }
50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/c26f5a170c752d9d1d5b884dd7eb60b982637269/XMLReportTest.java/buggy/cobertura/test/net/sourceforge/cobertura/reporting/xml/XMLReportTest.java
public void finished() { if (data != null) { searchResults.showUsersFound(data); } else { JOptionPane.showMessageDialog(searchResults, Res.getString("message.no.results.found"), Res.getString("title.notification"), JOptionPane.ERROR_MESSAGE); } }
52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/4639786a0c9bdc8bd2c5848f7b9e59c4d32dc2e5/SearchForm.java/buggy/src/java/org/jivesoftware/sparkimpl/search/users/SearchForm.java
} catch (IOException e)
} catch (Exception e)
public byte[] calculateMessageDigest() { errorIfNotLoaded(); try { return buffer.calculateMessageDigest(); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
e.printStackTrace(); throw new RuntimeException("Unimplemented exception.");
handleException(e);
public byte[] calculateMessageDigest() { errorIfNotLoaded(); try { return buffer.calculateMessageDigest(); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
return null;
public byte[] calculateMessageDigest() { errorIfNotLoaded(); try { return buffer.calculateMessageDigest(); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
MappedByteBuffer plane;
MappedByteBuffer plane = null;
public byte[] getPlane(Integer arg0, Integer arg1, Integer arg2) { errorIfNotLoaded(); MappedByteBuffer plane; try { plane = buffer.getPlane(arg0, arg1, arg2); } catch (Exception e) { throw new RuntimeException(e); } return bufferAsByteArrayWithExceptionIfNull( plane ); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
throw new RuntimeException(e);
handleException(e);
public byte[] getPlane(Integer arg0, Integer arg1, Integer arg2) { errorIfNotLoaded(); MappedByteBuffer plane; try { plane = buffer.getPlane(arg0, arg1, arg2); } catch (Exception e) { throw new RuntimeException(e); } return bufferAsByteArrayWithExceptionIfNull( plane ); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
return bufferAsByteArrayWithExceptionIfNull( plane );
return bufferAsByteArrayWithExceptionIfNull(plane);
public byte[] getPlane(Integer arg0, Integer arg1, Integer arg2) { errorIfNotLoaded(); MappedByteBuffer plane; try { plane = buffer.getPlane(arg0, arg1, arg2); } catch (Exception e) { throw new RuntimeException(e); } return bufferAsByteArrayWithExceptionIfNull( plane ); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
} catch (DimensionsOutOfBoundsException e)
} catch (Exception e)
public Long getPlaneOffset(Integer arg0, Integer arg1, Integer arg2) { errorIfNotLoaded(); try { return buffer.getPlaneOffset(arg0, arg1, arg2); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
e.printStackTrace(); throw new RuntimeException("Unimplemented exception.");
handleException(e);
public Long getPlaneOffset(Integer arg0, Integer arg1, Integer arg2) { errorIfNotLoaded(); try { return buffer.getPlaneOffset(arg0, arg1, arg2); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
return null;
public Long getPlaneOffset(Integer arg0, Integer arg1, Integer arg2) { errorIfNotLoaded(); try { return buffer.getPlaneOffset(arg0, arg1, arg2); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
MappedByteBuffer region;
MappedByteBuffer region = null;
public byte[] getRegion(Integer arg0, Long arg1) { errorIfNotLoaded(); MappedByteBuffer region; try { region = buffer.getRegion(arg0, arg1); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } return bufferAsByteArrayWithExceptionIfNull( region ); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
} catch (IOException e)
} catch (Exception e)
public byte[] getRegion(Integer arg0, Long arg1) { errorIfNotLoaded(); MappedByteBuffer region; try { region = buffer.getRegion(arg0, arg1); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } return bufferAsByteArrayWithExceptionIfNull( region ); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
e.printStackTrace(); throw new RuntimeException("Unimplemented exception.");
handleException(e);
public byte[] getRegion(Integer arg0, Long arg1) { errorIfNotLoaded(); MappedByteBuffer region; try { region = buffer.getRegion(arg0, arg1); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } return bufferAsByteArrayWithExceptionIfNull( region ); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
return bufferAsByteArrayWithExceptionIfNull( region );
return bufferAsByteArrayWithExceptionIfNull(region);
public byte[] getRegion(Integer arg0, Long arg1) { errorIfNotLoaded(); MappedByteBuffer region; try { region = buffer.getRegion(arg0, arg1); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } return bufferAsByteArrayWithExceptionIfNull( region ); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
MappedByteBuffer row;
MappedByteBuffer row = null;
public byte[] getRow(Integer arg0, Integer arg1, Integer arg2, Integer arg3) { errorIfNotLoaded(); MappedByteBuffer row; try { row = buffer.getRow(arg0, arg1, arg2, arg3); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } return bufferAsByteArrayWithExceptionIfNull( row ); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
} catch (IOException e)
} catch (Exception e)
public byte[] getRow(Integer arg0, Integer arg1, Integer arg2, Integer arg3) { errorIfNotLoaded(); MappedByteBuffer row; try { row = buffer.getRow(arg0, arg1, arg2, arg3); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } return bufferAsByteArrayWithExceptionIfNull( row ); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception.");
handleException(e);
public byte[] getRow(Integer arg0, Integer arg1, Integer arg2, Integer arg3) { errorIfNotLoaded(); MappedByteBuffer row; try { row = buffer.getRow(arg0, arg1, arg2, arg3); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } return bufferAsByteArrayWithExceptionIfNull( row ); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
} catch (DimensionsOutOfBoundsException e)
} catch (Exception e)
public Long getRowOffset(Integer arg0, Integer arg1, Integer arg2, Integer arg3) { errorIfNotLoaded(); try { return buffer.getRowOffset(arg0, arg1, arg2, arg3); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
e.printStackTrace(); throw new RuntimeException("Unimplemented exception.");
handleException(e);
public Long getRowOffset(Integer arg0, Integer arg1, Integer arg2, Integer arg3) { errorIfNotLoaded(); try { return buffer.getRowOffset(arg0, arg1, arg2, arg3); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
return null;
public Long getRowOffset(Integer arg0, Integer arg1, Integer arg2, Integer arg3) { errorIfNotLoaded(); try { return buffer.getRowOffset(arg0, arg1, arg2, arg3); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
MappedByteBuffer stack;
MappedByteBuffer stack = null;
public byte[] getStack(Integer arg0, Integer arg1) { errorIfNotLoaded(); MappedByteBuffer stack; try { stack = buffer.getStack(arg0, arg1); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } return bufferAsByteArrayWithExceptionIfNull( stack ); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
} catch (IOException e)
} catch (Exception e)
public byte[] getStack(Integer arg0, Integer arg1) { errorIfNotLoaded(); MappedByteBuffer stack; try { stack = buffer.getStack(arg0, arg1); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } return bufferAsByteArrayWithExceptionIfNull( stack ); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception.");
handleException(e);
public byte[] getStack(Integer arg0, Integer arg1) { errorIfNotLoaded(); MappedByteBuffer stack; try { stack = buffer.getStack(arg0, arg1); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } return bufferAsByteArrayWithExceptionIfNull( stack ); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
} catch (DimensionsOutOfBoundsException e)
} catch (Exception e)
public Long getStackOffset(Integer arg0, Integer arg1) { errorIfNotLoaded(); try { return buffer.getStackOffset(arg0, arg1); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
e.printStackTrace(); throw new RuntimeException("Unimplemented exception.");
handleException(e);
public Long getStackOffset(Integer arg0, Integer arg1) { errorIfNotLoaded(); try { return buffer.getStackOffset(arg0, arg1); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
return null;
public Long getStackOffset(Integer arg0, Integer arg1) { errorIfNotLoaded(); try { return buffer.getStackOffset(arg0, arg1); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
MappedByteBuffer timepoint;
MappedByteBuffer timepoint = null;
public byte[] getTimepoint(Integer arg0) { errorIfNotLoaded(); MappedByteBuffer timepoint; try { timepoint = buffer.getTimepoint(arg0); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } return bufferAsByteArrayWithExceptionIfNull( timepoint ); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
} catch (IOException e)
} catch (Exception e)
public byte[] getTimepoint(Integer arg0) { errorIfNotLoaded(); MappedByteBuffer timepoint; try { timepoint = buffer.getTimepoint(arg0); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } return bufferAsByteArrayWithExceptionIfNull( timepoint ); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception.");
handleException(e);
public byte[] getTimepoint(Integer arg0) { errorIfNotLoaded(); MappedByteBuffer timepoint; try { timepoint = buffer.getTimepoint(arg0); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } return bufferAsByteArrayWithExceptionIfNull( timepoint ); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
return bufferAsByteArrayWithExceptionIfNull( timepoint );
return bufferAsByteArrayWithExceptionIfNull(timepoint);
public byte[] getTimepoint(Integer arg0) { errorIfNotLoaded(); MappedByteBuffer timepoint; try { timepoint = buffer.getTimepoint(arg0); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } return bufferAsByteArrayWithExceptionIfNull( timepoint ); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
} catch (DimensionsOutOfBoundsException e)
} catch (Exception e)
public Long getTimepointOffset(Integer arg0) { errorIfNotLoaded(); try { return buffer.getTimepointOffset(arg0); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
e.printStackTrace(); throw new RuntimeException("Unimplemented exception.");
handleException(e);
public Long getTimepointOffset(Integer arg0) { errorIfNotLoaded(); try { return buffer.getTimepointOffset(arg0); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
return null;
public Long getTimepointOffset(Integer arg0) { errorIfNotLoaded(); try { return buffer.getTimepointOffset(arg0); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
} catch (BufferOverflowException e)
} catch (Exception e)
public void setPlane(byte[] arg0, Integer arg1, Integer arg2, Integer arg3) { errorIfNotLoaded(); try { buffer.setPlane(arg0, arg1, arg2, arg3); } catch (BufferOverflowException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception.");
handleException(e);
public void setPlane(byte[] arg0, Integer arg1, Integer arg2, Integer arg3) { errorIfNotLoaded(); try { buffer.setPlane(arg0, arg1, arg2, arg3); } catch (BufferOverflowException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
} catch (BufferOverflowException e)
} catch (Exception e)
public void setRegion(Integer arg0, Long arg1, byte[] arg2) { errorIfNotLoaded(); try { buffer.setRegion(arg0, arg1, arg2); } catch (BufferOverflowException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception.");
handleException(e);
public void setRegion(Integer arg0, Long arg1, byte[] arg2) { errorIfNotLoaded(); try { buffer.setRegion(arg0, arg1, arg2); } catch (BufferOverflowException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
throw new RuntimeException("Not implemented yet.");
try { ByteBuffer buf = ByteBuffer.wrap(arg0); buffer.setRow(buf, arg1, arg2, arg3, arg4); } catch (Exception e) { handleException(e); }
public void setRow(byte[] arg0, Integer arg1, Integer arg2, Integer arg3, Integer arg4) { errorIfNotLoaded(); // FIXME buffer.setRow(arg0, arg1, arg2, arg3, arg4); throw new RuntimeException("Not implemented yet."); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
} catch (BufferOverflowException e)
} catch (Exception e)
public void setStack(byte[] arg0, Integer arg1, Integer arg2, Integer arg3) { errorIfNotLoaded(); try { buffer.setStack(arg0, arg1, arg2, arg3); } catch (BufferOverflowException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception.");
handleException(e);
public void setStack(byte[] arg0, Integer arg1, Integer arg2, Integer arg3) { errorIfNotLoaded(); try { buffer.setStack(arg0, arg1, arg2, arg3); } catch (BufferOverflowException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
} catch (BufferOverflowException e)
} catch (Exception e)
public void setTimepoint(byte[] arg0, Integer arg1) { errorIfNotLoaded(); try { buffer.setTimepoint(arg0, arg1); } catch (BufferOverflowException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception.");
handleException(e);
public void setTimepoint(byte[] arg0, Integer arg1) { errorIfNotLoaded(); try { buffer.setTimepoint(arg0, arg1); } catch (BufferOverflowException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } catch (DimensionsOutOfBoundsException e) { e.printStackTrace(); throw new RuntimeException("Unimplemented exception."); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/65a3b02bf58c957397c6c8ccacffb5f328940fc9/RawPixelsBean.java/clean/components/server/src/ome/services/RawPixelsBean.java
if (response.isOnOff()) presentation.deIconify(); else {
if (response.isOnOff()) { if (presentation != null) presentation.deIconify(); } else {
private void handleDisplayViewerRelatedAgents(DisplayViewerRelatedAgent response) { if (response.isOnOff()) presentation.deIconify(); else { if (presentation != null) removePresentation(); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/821d4f7a003d25f9dccd2eaf7e886336cbdefc95/RenderingAgt.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/RenderingAgt.java
nodesToReset = new HashSet();
BrowserUI() { sorter = new ViewerSorter(); listener = new TreeExpansionListener() { public void treeCollapsed(TreeExpansionEvent e) { onNodeNavigation(e, false); } public void treeExpanded(TreeExpansionEvent e) { onNodeNavigation(e, true); } }; }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9e74eb87688bcf709c72b37a05e54a0314b1974e/BrowserUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java
List expanded = new ArrayList();
private void buildTreeNode(TreeImageDisplay parent, Collection nodes, DefaultTreeModel tm) { if (nodes.size() == 0) { tm.insertNodeInto(new DefaultMutableTreeNode(EMPTY_MSG), parent, parent.getChildCount()); return; } Iterator i = nodes.iterator(); TreeImageDisplay display; Set children; parent.removeAllChildren(); List expanded = new ArrayList(); while (i.hasNext()) { display = (TreeImageDisplay) i.next(); tm.insertNodeInto(display, parent, parent.getChildCount()); if (display instanceof TreeImageSet) { children = display.getChildrenDisplay(); if (children.size() != 0) { if (display.containsImages()) { expanded.add(display); display.setExpanded(true); setExpandedParent(display, false); buildTreeNode(display, sorter.sort(children), tm); expandNode(display); tm.reload(display); } else { buildTreeNode(display, sorter.sort(children), tm); } } else { tm.insertNodeInto(new DefaultMutableTreeNode(EMPTY_MSG), display, display.getChildCount()); } } else reloadRoot = false; } if (parent.isExpanded()) { expandNode(parent); tm.reload(parent); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9e74eb87688bcf709c72b37a05e54a0314b1974e/BrowserUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java
expanded.add(display);
private void buildTreeNode(TreeImageDisplay parent, Collection nodes, DefaultTreeModel tm) { if (nodes.size() == 0) { tm.insertNodeInto(new DefaultMutableTreeNode(EMPTY_MSG), parent, parent.getChildCount()); return; } Iterator i = nodes.iterator(); TreeImageDisplay display; Set children; parent.removeAllChildren(); List expanded = new ArrayList(); while (i.hasNext()) { display = (TreeImageDisplay) i.next(); tm.insertNodeInto(display, parent, parent.getChildCount()); if (display instanceof TreeImageSet) { children = display.getChildrenDisplay(); if (children.size() != 0) { if (display.containsImages()) { expanded.add(display); display.setExpanded(true); setExpandedParent(display, false); buildTreeNode(display, sorter.sort(children), tm); expandNode(display); tm.reload(display); } else { buildTreeNode(display, sorter.sort(children), tm); } } else { tm.insertNodeInto(new DefaultMutableTreeNode(EMPTY_MSG), display, display.getChildCount()); } } else reloadRoot = false; } if (parent.isExpanded()) { expandNode(parent); tm.reload(parent); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9e74eb87688bcf709c72b37a05e54a0314b1974e/BrowserUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java
} else reloadRoot = false;
}
private void buildTreeNode(TreeImageDisplay parent, Collection nodes, DefaultTreeModel tm) { if (nodes.size() == 0) { tm.insertNodeInto(new DefaultMutableTreeNode(EMPTY_MSG), parent, parent.getChildCount()); return; } Iterator i = nodes.iterator(); TreeImageDisplay display; Set children; parent.removeAllChildren(); List expanded = new ArrayList(); while (i.hasNext()) { display = (TreeImageDisplay) i.next(); tm.insertNodeInto(display, parent, parent.getChildCount()); if (display instanceof TreeImageSet) { children = display.getChildrenDisplay(); if (children.size() != 0) { if (display.containsImages()) { expanded.add(display); display.setExpanded(true); setExpandedParent(display, false); buildTreeNode(display, sorter.sort(children), tm); expandNode(display); tm.reload(display); } else { buildTreeNode(display, sorter.sort(children), tm); } } else { tm.insertNodeInto(new DefaultMutableTreeNode(EMPTY_MSG), display, display.getChildCount()); } } else reloadRoot = false; } if (parent.isExpanded()) { expandNode(parent); tm.reload(parent); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9e74eb87688bcf709c72b37a05e54a0314b1974e/BrowserUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java
reloadRoot = true;
void clearTree() { DefaultTreeModel dtm = (DefaultTreeModel) treeDisplay.getModel(); TreeImageDisplay root = (TreeImageDisplay) dtm.getRoot(); root.removeAllChildren(); root.removeAllChildrenDisplay(); buildEmptyNode(root); dtm.reload(); collapsePath(root); if (!model.isMainTree()) loadGoIntoTree(); reloadRoot = true; }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9e74eb87688bcf709c72b37a05e54a0314b1974e/BrowserUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java
reloadRoot = true;
private void loadGoIntoTree() { DefaultTreeModel dtm = (DefaultTreeModel) goIntoTree.getModel(); DefaultMutableTreeNode r = (DefaultMutableTreeNode) dtm.getRoot(); TreeImageDisplay d = model.getLastSelectedDisplay(); r.removeAllChildren(); TreeImageDisplay copy = d.copy(); dtm.insertNodeInto(copy, r, r.getChildCount()); buildTreeNode(copy, sorter.sort(copy.getChildrenDisplay()), dtm); reloadRoot = true; dtm.reload(r); if (copy.isChildrenLoaded()) expandGoIntoTreeNode(copy); scrollPane.getViewport().removeAll(); scrollPane.getViewport().add(goIntoTree); repaint(); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9e74eb87688bcf709c72b37a05e54a0314b1974e/BrowserUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java
void removeNodes(List nodes, TreeImageDisplay parentDisplay) { if (parentDisplay == null) parentDisplay = getTreeRoot(); Iterator i = nodes.iterator(); TreeImageDisplay node; TreeImageDisplay parent; DefaultTreeModel dtm = (DefaultTreeModel) treeDisplay.getModel(); while (i.hasNext()) { node = (TreeImageDisplay) i.next(); parent = node.getParentDisplay(); if (parent.isChildrenLoaded()) { parent.removeChildDisplay(node); parent.remove(node); dtm.reload(parent); if (parent.equals(parentDisplay)) treeDisplay.setSelectionPath( new TreePath(parent.getPath())); } } //if (reloadRoot) dtm.reload(getTreeRoot()); if (!model.isMainTree()) loadGoIntoTree(); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9e74eb87688bcf709c72b37a05e54a0314b1974e/BrowserUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java
reloadRoot = true;
void selectFoundNode(TreeImageDisplay node) { TreePath path = new TreePath(node.getPath()); treeDisplay.setSelectionPath(path); TreeCellRenderer renderer = (TreeCellRenderer) treeDisplay.getCellRenderer(); //treeDisplay.requestFocus(); renderer.getTreeCellRendererComponent(treeDisplay, node, treeDisplay.isPathSelected(path), false, true, 0, false); if (!model.isMainTree()) { loadGoIntoTree(); selectGoIntoTreeFoundNode(node); } reloadRoot = true; }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9e74eb87688bcf709c72b37a05e54a0314b1974e/BrowserUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java
reloadRoot = true;
void setLeavesViews(Set nodes, TreeImageSet parent) { DefaultTreeModel dtm = (DefaultTreeModel) treeDisplay.getModel(); parent.removeAllChildren(); parent.setChildrenLoaded(Boolean.TRUE); if (nodes.size() != 0) { Iterator i = nodes.iterator(); while (i.hasNext()) parent.addChildDisplay((TreeImageDisplay) i.next()) ; buildTreeNode(parent, sorter.sort(nodes), dtm); } else buildEmptyNode(parent); dtm.reload(parent); reloadRoot = true; if (!model.isMainTree()) loadGoIntoTree(); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9e74eb87688bcf709c72b37a05e54a0314b1974e/BrowserUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java
reloadRoot = true;
void setSortedNodes(List nodes, TreeImageDisplay parentNode) { DefaultTreeModel dtm = (DefaultTreeModel) treeDisplay.getModel(); parentNode.removeAllChildren(); Iterator i = nodes.iterator(); boolean b = (parentNode.equals(dtm.getRoot())); TreeImageDisplay child; while (i.hasNext()) { child = (TreeImageDisplay) i.next(); if (b) parentNode.addChildDisplay(child); dtm.insertNodeInto(child, parentNode, parentNode.getChildCount()); } dtm.reload(parentNode); expandNode(parentNode); if (!model.isMainTree()) { i = nodes.iterator(); List copies = new ArrayList(nodes.size()); while (i.hasNext()) { copies.add(((TreeImageDisplay) i.next()).copy()); } dtm = (DefaultTreeModel) goIntoTree.getModel(); DefaultMutableTreeNode r = (DefaultMutableTreeNode) dtm.getRoot(); TreeImageDisplay d = model.getLastSelectedDisplay(); r.removeAllChildren(); TreeImageDisplay copy = d.copy(); dtm.insertNodeInto(copy, r, r.getChildCount()); buildTreeNode(copy, copies, dtm); reloadRoot = true; dtm.reload(r); if (copy.isChildrenLoaded()) expandGoIntoTreeNode(copy); scrollPane.getViewport().removeAll(); scrollPane.getViewport().add(goIntoTree); repaint(); } reloadRoot = true; }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9e74eb87688bcf709c72b37a05e54a0314b1974e/BrowserUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java
reloadRoot = true;
void setSortedNodes(List nodes, TreeImageDisplay parentNode) { DefaultTreeModel dtm = (DefaultTreeModel) treeDisplay.getModel(); parentNode.removeAllChildren(); Iterator i = nodes.iterator(); boolean b = (parentNode.equals(dtm.getRoot())); TreeImageDisplay child; while (i.hasNext()) { child = (TreeImageDisplay) i.next(); if (b) parentNode.addChildDisplay(child); dtm.insertNodeInto(child, parentNode, parentNode.getChildCount()); } dtm.reload(parentNode); expandNode(parentNode); if (!model.isMainTree()) { i = nodes.iterator(); List copies = new ArrayList(nodes.size()); while (i.hasNext()) { copies.add(((TreeImageDisplay) i.next()).copy()); } dtm = (DefaultTreeModel) goIntoTree.getModel(); DefaultMutableTreeNode r = (DefaultMutableTreeNode) dtm.getRoot(); TreeImageDisplay d = model.getLastSelectedDisplay(); r.removeAllChildren(); TreeImageDisplay copy = d.copy(); dtm.insertNodeInto(copy, r, r.getChildCount()); buildTreeNode(copy, copies, dtm); reloadRoot = true; dtm.reload(r); if (copy.isChildrenLoaded()) expandGoIntoTreeNode(copy); scrollPane.getViewport().removeAll(); scrollPane.getViewport().add(goIntoTree); repaint(); } reloadRoot = true; }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9e74eb87688bcf709c72b37a05e54a0314b1974e/BrowserUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java
void setViews(Set nodes) { DefaultTreeModel dtm = (DefaultTreeModel) treeDisplay.getModel(); TreeImageDisplay root = (TreeImageDisplay) dtm.getRoot(); root.removeAllChildren(); root.setChildrenLoaded(Boolean.TRUE); root.setExpanded(true); dtm.reload(); if (nodes.size() != 0) { Iterator i = nodes.iterator(); while (i.hasNext()) root.addChildDisplay((TreeImageDisplay) i.next()) ; buildTreeNode(root, sorter.sort(nodes), (DefaultTreeModel) treeDisplay.getModel()); //if (!reload) reload = reloadRoot; } else buildEmptyNode(root); //if (reload) dtm.reload(root); if (!model.isMainTree()) loadGoIntoTree(); reloadRoot = true; }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9e74eb87688bcf709c72b37a05e54a0314b1974e/BrowserUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java
void setViews(Set nodes) { DefaultTreeModel dtm = (DefaultTreeModel) treeDisplay.getModel(); TreeImageDisplay root = (TreeImageDisplay) dtm.getRoot(); root.removeAllChildren(); root.setChildrenLoaded(Boolean.TRUE); root.setExpanded(true); dtm.reload(); if (nodes.size() != 0) { Iterator i = nodes.iterator(); while (i.hasNext()) root.addChildDisplay((TreeImageDisplay) i.next()) ; buildTreeNode(root, sorter.sort(nodes), (DefaultTreeModel) treeDisplay.getModel()); //if (!reload) reload = reloadRoot; } else buildEmptyNode(root); //if (reload) dtm.reload(root); if (!model.isMainTree()) loadGoIntoTree(); reloadRoot = true; }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9e74eb87688bcf709c72b37a05e54a0314b1974e/BrowserUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java
void setViews(Set nodes) { DefaultTreeModel dtm = (DefaultTreeModel) treeDisplay.getModel(); TreeImageDisplay root = (TreeImageDisplay) dtm.getRoot(); root.removeAllChildren(); root.setChildrenLoaded(Boolean.TRUE); root.setExpanded(true); dtm.reload(); if (nodes.size() != 0) { Iterator i = nodes.iterator(); while (i.hasNext()) root.addChildDisplay((TreeImageDisplay) i.next()) ; buildTreeNode(root, sorter.sort(nodes), (DefaultTreeModel) treeDisplay.getModel()); //if (!reload) reload = reloadRoot; } else buildEmptyNode(root); //if (reload) dtm.reload(root); if (!model.isMainTree()) loadGoIntoTree(); reloadRoot = true; }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9e74eb87688bcf709c72b37a05e54a0314b1974e/BrowserUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java
reloadRoot = true;
Iterator j = nodesToReset.iterator(); while (j.hasNext()) { setExpandedParent((TreeImageDisplay) j.next(), true); }
void setViews(Set nodes) { DefaultTreeModel dtm = (DefaultTreeModel) treeDisplay.getModel(); TreeImageDisplay root = (TreeImageDisplay) dtm.getRoot(); root.removeAllChildren(); root.setChildrenLoaded(Boolean.TRUE); root.setExpanded(true); dtm.reload(); if (nodes.size() != 0) { Iterator i = nodes.iterator(); while (i.hasNext()) root.addChildDisplay((TreeImageDisplay) i.next()) ; buildTreeNode(root, sorter.sort(nodes), (DefaultTreeModel) treeDisplay.getModel()); //if (!reload) reload = reloadRoot; } else buildEmptyNode(root); //if (reload) dtm.reload(root); if (!model.isMainTree()) loadGoIntoTree(); reloadRoot = true; }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9e74eb87688bcf709c72b37a05e54a0314b1974e/BrowserUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java
boolean reload = false;
void sortNodes(int type) { sorter.setByDate(type == Browser.SORT_NODES_BY_DATE); DefaultTreeModel dtm = (DefaultTreeModel) treeDisplay.getModel(); TreeImageDisplay root = (TreeImageDisplay) dtm.getRoot(); boolean reload = false; Set children = root.getChildrenDisplay(); root.removeAllChildren(); dtm.reload(root); if (children.size() != 0) { buildTreeNode(root, sorter.sort(children), dtm); if (!reload) reload = reloadRoot; } else buildEmptyNode(root); //if (reload) dtm.reload(root); if (!model.isMainTree()) loadGoIntoTree(); reloadRoot = true; }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9e74eb87688bcf709c72b37a05e54a0314b1974e/BrowserUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java
if (!reload) reload = reloadRoot;
void sortNodes(int type) { sorter.setByDate(type == Browser.SORT_NODES_BY_DATE); DefaultTreeModel dtm = (DefaultTreeModel) treeDisplay.getModel(); TreeImageDisplay root = (TreeImageDisplay) dtm.getRoot(); boolean reload = false; Set children = root.getChildrenDisplay(); root.removeAllChildren(); dtm.reload(root); if (children.size() != 0) { buildTreeNode(root, sorter.sort(children), dtm); if (!reload) reload = reloadRoot; } else buildEmptyNode(root); //if (reload) dtm.reload(root); if (!model.isMainTree()) loadGoIntoTree(); reloadRoot = true; }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9e74eb87688bcf709c72b37a05e54a0314b1974e/BrowserUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java
void sortNodes(int type) { sorter.setByDate(type == Browser.SORT_NODES_BY_DATE); DefaultTreeModel dtm = (DefaultTreeModel) treeDisplay.getModel(); TreeImageDisplay root = (TreeImageDisplay) dtm.getRoot(); boolean reload = false; Set children = root.getChildrenDisplay(); root.removeAllChildren(); dtm.reload(root); if (children.size() != 0) { buildTreeNode(root, sorter.sort(children), dtm); if (!reload) reload = reloadRoot; } else buildEmptyNode(root); //if (reload) dtm.reload(root); if (!model.isMainTree()) loadGoIntoTree(); reloadRoot = true; }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9e74eb87688bcf709c72b37a05e54a0314b1974e/BrowserUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java
reloadRoot = true;
Iterator j = nodesToReset.iterator(); while (j.hasNext()) { setExpandedParent((TreeImageDisplay) j.next(), true); }
void sortNodes(int type) { sorter.setByDate(type == Browser.SORT_NODES_BY_DATE); DefaultTreeModel dtm = (DefaultTreeModel) treeDisplay.getModel(); TreeImageDisplay root = (TreeImageDisplay) dtm.getRoot(); boolean reload = false; Set children = root.getChildrenDisplay(); root.removeAllChildren(); dtm.reload(root); if (children.size() != 0) { buildTreeNode(root, sorter.sort(children), dtm); if (!reload) reload = reloadRoot; } else buildEmptyNode(root); //if (reload) dtm.reload(root); if (!model.isMainTree()) loadGoIntoTree(); reloadRoot = true; }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9e74eb87688bcf709c72b37a05e54a0314b1974e/BrowserUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java
showGraphicSelection(); break;
mng.showGraphicSelection(); break;
public void actionPerformed(ActionEvent e) { int index = Integer.parseInt(e.getActionCommand()); try { switch (index) { case SAVE: mng.saveResult(); break; case GRAPHIC: showGraphicSelection(); break; case BACK_TO_TABLE: mng.backToTable(); break; case BACK_TO_GRAPHIC: mng.backToGraphic(); break; case BACKGROUND: showROISelector(StatsResultsPaneMng.TABLE_BACKGROUND, "Background"); break; case RATIO: showROISelector(StatsResultsPaneMng.TABLE_RATIO, "Ratio"); break; case INITIAL: view.setEnabledMoveButtons(false); mng.displayInitialData(); break; } } catch(NumberFormatException nfe) { throw new Error("Invalid Action ID "+index, nfe); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3db37517e6873d11567ee5822e769ab058e1abed/BottomBarMng.java/buggy/SRC/org/openmicroscopy/shoola/agents/roi/results/stats/BottomBarMng.java
return Collections.EMPTY_LIST;
return EMPTY_LIST;
public List childNodes() { return Collections.EMPTY_LIST; }
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/b1293eda8454686e846e2a9837b348e2983bb423/LocalVarNode.java/clean/src/org/jruby/ast/LocalVarNode.java
RubyMatchData result = (RubyMatchData)matcher.search(getRuby(), str, pos);
RubyObject result = matcher.search(getRuby(), str, pos);
public int m_search(RubyObject target, int pos) {// RubyString str = RubyString.m_as_str(target); String str = ((RubyString)target).getValue(); if (pos >= str.length()) { return -1; } recompileIfNeeded(); RubyMatchData result = (RubyMatchData)matcher.search(getRuby(), str, pos); getRuby().setBackRef(result); return result.matchStartPosition(); }
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/896113b9a8117e7c4e8677cee39ccc8ad730fdcf/RubyRegexp.java/clean/org/jruby/RubyRegexp.java
return result.matchStartPosition();
return result instanceof RubyMatchData ? ((RubyMatchData)result).matchStartPosition() : -1;
public int m_search(RubyObject target, int pos) {// RubyString str = RubyString.m_as_str(target); String str = ((RubyString)target).getValue(); if (pos >= str.length()) { return -1; } recompileIfNeeded(); RubyMatchData result = (RubyMatchData)matcher.search(getRuby(), str, pos); getRuby().setBackRef(result); return result.matchStartPosition(); }
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/896113b9a8117e7c4e8677cee39ccc8ad730fdcf/RubyRegexp.java/clean/org/jruby/RubyRegexp.java
private void buildPresentation(String imageName)
private void buildPresentation()
private void buildPresentation(String imageName) { control = new RenderingAgtCtrl(this); presentation = new RenderingAgtUIF(control, registry, imageName); control.setPresentation(presentation); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8a4d5e12d87798c81c0e8de88f3ca3fd97e8a6cc/RenderingAgt.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/RenderingAgt.java
control = new RenderingAgtCtrl(this); presentation = new RenderingAgtUIF(control, registry, imageName);
presentation = new RenderingAgtUIF(control, registry, curImageName);
private void buildPresentation(String imageName) { control = new RenderingAgtCtrl(this); presentation = new RenderingAgtUIF(control, registry, imageName); control.setPresentation(presentation); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8a4d5e12d87798c81c0e8de88f3ca3fd97e8a6cc/RenderingAgt.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/RenderingAgt.java
if (presentation != null) presentation.deIconify();
if (presentation == null) { initChannelData(); buildPresentation(); } presentation.deIconify();
private void handleDisplayViewerRelatedAgents(DisplayViewerRelatedAgent response) { if (response.isOnOff()) { if (presentation != null) presentation.deIconify(); } else { if (presentation != null) removePresentation(); } }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8a4d5e12d87798c81c0e8de88f3ca3fd97e8a6cc/RenderingAgt.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/RenderingAgt.java
initChannelData();
curImageName = request.getImageName();
private void handleImageLoaded(ImageLoaded response) { LoadImage request = (LoadImage) response.getACT(); renderingControl = response.getProxy(); pxsDims = renderingControl.getPixelsDims(); pxsStats = renderingControl.getPixelsStats(); curImageID = request.getImageID(); curPixelsID = request.getPixelsID(); initChannelData(); if (presentation != null) removePresentation(); buildPresentation(request.getImageName()); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8a4d5e12d87798c81c0e8de88f3ca3fd97e8a6cc/RenderingAgt.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/RenderingAgt.java
buildPresentation(request.getImageName());
private void handleImageLoaded(ImageLoaded response) { LoadImage request = (LoadImage) response.getACT(); renderingControl = response.getProxy(); pxsDims = renderingControl.getPixelsDims(); pxsStats = renderingControl.getPixelsStats(); curImageID = request.getImageID(); curPixelsID = request.getPixelsID(); initChannelData(); if (presentation != null) removePresentation(); buildPresentation(request.getImageName()); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8a4d5e12d87798c81c0e8de88f3ca3fd97e8a6cc/RenderingAgt.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/RenderingAgt.java
RenderImage event = new RenderImage(curPixelsID); registry.getEventBus().post(event);
registry.getEventBus().post(new RenderImage(curPixelsID));
private void refreshImage() { RenderImage event = new RenderImage(curPixelsID); registry.getEventBus().post(event); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8a4d5e12d87798c81c0e8de88f3ca3fd97e8a6cc/RenderingAgt.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/RenderingAgt.java
control = null;
private void removePresentation() { control.disposeDialogs(); presentation.dispose(); control = null; presentation = null; }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8a4d5e12d87798c81c0e8de88f3ca3fd97e8a6cc/RenderingAgt.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/RenderingAgt.java
control = new RenderingAgtCtrl(this);
public void setContext(Registry ctx) { registry = ctx; canUpdate = true; EventBus bus = registry.getEventBus(); bus.register(this, ImageLoaded.class); bus.register(this, DisplayViewerRelatedAgent.class); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8a4d5e12d87798c81c0e8de88f3ca3fd97e8a6cc/RenderingAgt.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/RenderingAgt.java
public boolean isAutoloadDefined(String id) {
public boolean isAutoloadDefined(String name) {
public boolean isAutoloadDefined(String id) { return false; }
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/fe5b7835d80b52a0683d503660a7f722b7af69b1/Ruby.java/clean/org/jruby/Ruby.java