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ParseTool(String name, Reader inputStream) { _escaped = false; _name = name; LineNumberReader in = new LineNumberReader(inputStream); _cur = _last = _len = _pos = EOF; _buf = ""; _in = in; for (int i = 0; i < MAX_MARKS; i++) { _marks[i] = new Mark(); } read();
ParseTool(String name, InputStream in) throws IOException { this(name, new InputStreamReader(in));
ParseTool(String name, Reader inputStream) { _escaped = false; _name = name; LineNumberReader in = new LineNumberReader(inputStream); _cur = _last = _len = _pos = EOF; _buf = ""; // must be non-null or we will abort before we start _in = in; for (int i = 0; i < MAX_MARKS; i++) {...
52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/b09d2b26d0e942a7d01885758ceee8a4a6c40b05/ParseTool.java/buggy/webmacro/src/org/webmacro/engine/ParseTool.java
public final void parseUntil(StringBuffer buf, String marker) throws ParseException
public final boolean parseUntil(StringBuffer buf, char c) throws IOException
public final void parseUntil(StringBuffer buf, String marker) throws ParseException { if (marker == null) { return; } if (marker.length() < 1) { return; } char start = marker.charAt(0); int mark = DUMMY_MARK; buf.setLength(0); LOOKING: while(_cur != EO...
52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/b09d2b26d0e942a7d01885758ceee8a4a6c40b05/ParseTool.java/buggy/webmacro/src/org/webmacro/engine/ParseTool.java
if (marker == null) { return; } if (marker.length() < 1) { return; } char start = marker.charAt(0); int mark = DUMMY_MARK; buf.setLength(0); LOOKING: while(_cur != EOF) { if (_cur == start) { mark = mark(); try { for (int i = 0; i < marker.length(); i++) { if (_cur != marker.charAt(i)) { rewind(mark); buf.append((char...
boolean readSome = false; while (((_cur != c) || _escaped) && (_cur != EOF)) {
public final void parseUntil(StringBuffer buf, String marker) throws ParseException { if (marker == null) { return; } if (marker.length() < 1) { return; } char start = marker.charAt(0); int mark = DUMMY_MARK; buf.setLength(0); LOOKING: while(_cur != EO...
52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/b09d2b26d0e942a7d01885758ceee8a4a6c40b05/ParseTool.java/buggy/webmacro/src/org/webmacro/engine/ParseTool.java
clearMark(mark); throw new ParseException(this,"Expected " + marker + " but reached end of file");
return readSome;
public final void parseUntil(StringBuffer buf, String marker) throws ParseException { if (marker == null) { return; } if (marker.length() < 1) { return; } char start = marker.charAt(0); int mark = DUMMY_MARK; buf.setLength(0); LOOKING: while(_cur != EO...
52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/b09d2b26d0e942a7d01885758ceee8a4a6c40b05/ParseTool.java/buggy/webmacro/src/org/webmacro/engine/ParseTool.java
public final boolean isNameStartChar() { return isNameStartChar(_cur);
static public final boolean isNameStartChar(int c) { return ((c != '$') && (Character.isJavaIdentifierStart((char) c)));
public final boolean isNameStartChar() { return isNameStartChar(_cur); }
52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/b09d2b26d0e942a7d01885758ceee8a4a6c40b05/ParseTool.java/buggy/webmacro/src/org/webmacro/engine/ParseTool.java
context.create("clone", CLONE, 0);
context.create("clone", RBCLONE, 0);
protected void defineMethods(MethodContext context) { context.create("==", EQUAL, 1); context.createAlias("===", "=="); context.create("=~", MATCH, 1); context.create("class", TYPE, 0); context.create("clone", CLONE, 0); context.create("dup", DUP, 0); context.create(...
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/dcea3e9f2f6ecba04f862dbfb01b220d7890a706/ObjectDefinition.java/clean/src/org/jruby/internal/runtime/builtin/definitions/ObjectDefinition.java
context.create("frozen?", FROZEN, 0);
context.create("frozen?", FROZEN_P, 0);
protected void defineMethods(MethodContext context) { context.create("==", EQUAL, 1); context.createAlias("===", "=="); context.create("=~", MATCH, 1); context.create("class", TYPE, 0); context.create("clone", CLONE, 0); context.create("dup", DUP, 0); context.create(...
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/dcea3e9f2f6ecba04f862dbfb01b220d7890a706/ObjectDefinition.java/clean/src/org/jruby/internal/runtime/builtin/definitions/ObjectDefinition.java
public void bind(String name, Object obj)
public void bind(String name, Object value)
public void bind(String name, Object obj) { entriesMap.put(name, obj); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/930bc29b9720793c48424a89988a93925f544043/RegistryImpl.java/buggy/SRC/org/openmicroscopy/shoola/env/config/RegistryImpl.java
entriesMap.put(name, obj);
if (name != null) { ObjectEntry entry = new ObjectEntry(name); entry.setContent(value); entriesMap.put(name, entry); }
public void bind(String name, Object obj) { entriesMap.put(name, obj); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/930bc29b9720793c48424a89988a93925f544043/RegistryImpl.java/buggy/SRC/org/openmicroscopy/shoola/env/config/RegistryImpl.java
public static RubyModule m_new(Ruby ruby, RubyModule rubyClass) {
public static RubyModule m_new(Ruby ruby, RubyObject recv) {
public static RubyModule m_new(Ruby ruby, RubyModule rubyClass) { RubyModule mod = RubyModule.m_newModule(ruby); mod.setRubyClass(rubyClass); ruby.getModuleClass().callInit(null); return mod; }
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/a9420f23379e292698ea011ab08fb480b4decbcc/RubyModule.java/buggy/org/jruby/RubyModule.java
mod.setRubyClass(rubyClass);
mod.setRubyClass((RubyModule)recv);
public static RubyModule m_new(Ruby ruby, RubyModule rubyClass) { RubyModule mod = RubyModule.m_newModule(ruby); mod.setRubyClass(rubyClass); ruby.getModuleClass().callInit(null); return mod; }
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/a9420f23379e292698ea011ab08fb480b4decbcc/RubyModule.java/buggy/org/jruby/RubyModule.java
input.register(result);
public static RubyArray unmarshalFrom(UnmarshalStream input) throws java.io.IOException { RubyArray result = newArray(input.getRuntime()); int size = input.unmarshalInt(); for (int i = 0; i < size; i++) { result.append(input.unmarshalObject()); } return result; }
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/9db4d278a734c4fdfd9a83ed95575a45577f1e1b/RubyArray.java/clean/org/jruby/RubyArray.java
return new PDILoader(component, images);
return new PDILoader(component, ids);
protected DataLoader createHierarchyLoader() { Set ids = new HashSet(images.size()); Iterator i = images.iterator(); while (i.hasNext()) ids.add(new Integer(((ImageData) i.next()).getId())); switch (type) { case HiViewer.PDI_HIERARCHY: ret...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/64ee7ec527da3cc538fcd8d0a21183719f854676/HierarchyModel.java/buggy/SRC/org/openmicroscopy/shoola/agents/hiviewer/view/HierarchyModel.java
RubyNumeric other = numericValue(num); if (other instanceof RubyFloat) { return RubyFloat.newFloat(getRuntime(), getDoubleValue()).op_mul(other); } else if (other instanceof RubyBignum) { return RubyBignum.newBignum(getRuntime(), getLongValue()).op_mul(other); } else { long otherValue = other.getLongValue(); long resul...
return numericValue(num).multiplyWith(this);
public RubyNumeric op_mul(IRubyObject num) { RubyNumeric other = numericValue(num); if (other instanceof RubyFloat) { return RubyFloat.newFloat(getRuntime(), getDoubleValue()).op_mul(other); } else if (other instanceof RubyBignum) { return RubyBignum.newBignum(getRuntime()...
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/a25fc494ea7daeb4b5b479e0173372332cf7d4ac/RubyFixnum.java/clean/src/org/jruby/RubyFixnum.java
JPanel p = new JPanel(); p.setLayout(new BorderLayout(0, 0)); p.add(histogramPanel, BorderLayout.CENTER); getContentPane().add(p);
getContentPane().add(histogramPanel);
void buildGUI() { JPanel p = new JPanel(); p.setLayout(new BorderLayout(0, 0)); p.add(histogramPanel, BorderLayout.CENTER); //getContentPane().add(histogramPanel); getContentPane().add(p); setSize(HistogramPanel.WIDTH, HEIGHT_WIN); setResizable(false); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/6a28b54c142c80cf786f76c45b6be256d92fd0bb/HistogramDialog.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/pane/HistogramDialog.java
{ this.view = view; this.control = control; inputStartKnob = false; inputEndKnob = false;
{ this.view = view; this.control = control; inputStartKnob = false; inputEndKnob = false;
HistogramDialogManager(HistogramDialog view, QuantumPaneManager control) { this.view = view; this.control = control; inputStartKnob = false; inputEndKnob = false; boxInputStart = new Rectangle(); boxInputEnd = new Rectangle(); }
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
}
}
HistogramDialogManager(HistogramDialog view, QuantumPaneManager control) { this.view = view; this.control = control; inputStartKnob = false; inputEndKnob = false; boxInputStart = new Rectangle(); boxInputEnd = new Rectangle(); }
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
{ lS = HistogramPanel.leftBorder+view.getHistogramPanel().getWidthStat();
{ lS = HistogramPanel.leftBorder+view.getHistogramPanel().getWidthStat();
void initRectangles(int yStart, int yEnd) { lS = HistogramPanel.leftBorder+view.getHistogramPanel().getWidthStat(); setInputStartBox(yStart); setInputEndBox(yEnd); }
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
}
}
void initRectangles(int yStart, int yEnd) { lS = HistogramPanel.leftBorder+view.getHistogramPanel().getWidthStat(); setInputStartBox(yStart); setInputEndBox(yEnd); }
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
{ view.getHistogramPanel().addMouseListener(this); view.getHistogramPanel().addMouseMotionListener(this); view.addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent we) { view.dispose(); } }); }
{ view.getHistogramPanel().addMouseListener(this); view.getHistogramPanel().addMouseMotionListener(this); view.addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent we) { view.dispose(); } }); }
void attachListeners() { view.getHistogramPanel().addMouseListener(this); view.getHistogramPanel().addMouseMotionListener(this); view.addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent we) { view.dispose(); } }); }
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
PixelsDimensions pxsDims = renderingControl.getPixelsDims();
private void handleImageLoaded(ImageLoaded response) { LoadImage request = (LoadImage) response.getACT(); renderingControl = response.getProxy(); PixelsDimensions pxsDims = renderingControl.getPixelsDims(); //TODO: REMOVE COMMENTS //control.removeProgressNotifier(); if (...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/02bc3351cbc1f2e45d28539c79317f881c2ec11b/Viewer.java/clean/SRC/org/openmicroscopy/shoola/agents/viewer/Viewer.java
if (curImageID != request.getImageID()) { if (presentation == null) buildPresentation(pxsDims);
if (curImageID != request.getImageID()) { presentationDispose(); PixelsDimensions pxsDims = renderingControl.getPixelsDims(); buildPresentation(pxsDims);
private void handleImageLoaded(ImageLoaded response) { LoadImage request = (LoadImage) response.getACT(); renderingControl = response.getProxy(); PixelsDimensions pxsDims = renderingControl.getPixelsDims(); //TODO: REMOVE COMMENTS //control.removeProgressNotifier(); if (...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/02bc3351cbc1f2e45d28539c79317f881c2ec11b/Viewer.java/clean/SRC/org/openmicroscopy/shoola/agents/viewer/Viewer.java
control.disposeDialogs(); } showPresentation();
} else presentation.deIconify();
private void handleImageLoaded(ImageLoaded response) { LoadImage request = (LoadImage) response.getACT(); renderingControl = response.getProxy(); PixelsDimensions pxsDims = renderingControl.getPixelsDims(); //TODO: REMOVE COMMENTS //control.removeProgressNotifier(); if (...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/02bc3351cbc1f2e45d28539c79317f881c2ec11b/Viewer.java/clean/SRC/org/openmicroscopy/shoola/agents/viewer/Viewer.java
curImage = null;
private void handleImageRendered(ImageRendered response) { curImage = null; curImage = response.getRenderedImage(); presentation.setImage(curImage); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/02bc3351cbc1f2e45d28539c79317f881c2ec11b/Viewer.java/clean/SRC/org/openmicroscopy/shoola/agents/viewer/Viewer.java
if (!display) presentation.setOnScreen();
private void handleImageRendered(ImageRendered response) { curImage = null; curImage = response.getRenderedImage(); presentation.setImage(curImage); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/02bc3351cbc1f2e45d28539c79317f881c2ec11b/Viewer.java/clean/SRC/org/openmicroscopy/shoola/agents/viewer/Viewer.java
boolean active)
boolean b)
private void initPresentation(String imageName, PixelsDimensions pxsDims, boolean active) { curImageName = imageName; presentation.setDefaultZT(getDefaultT(), getDefaultZ(), pxsDims.sizeT, pxsDims.sizeZ); presentation.setImageNa...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/02bc3351cbc1f2e45d28539c79317f881c2ec11b/Viewer.java/clean/SRC/org/openmicroscopy/shoola/agents/viewer/Viewer.java
presentation.setActive(active);
presentation.setImageDisplay(b);
private void initPresentation(String imageName, PixelsDimensions pxsDims, boolean active) { curImageName = imageName; presentation.setDefaultZT(getDefaultT(), getDefaultZ(), pxsDims.sizeT, pxsDims.sizeZ); presentation.setImageNa...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/02bc3351cbc1f2e45d28539c79317f881c2ec11b/Viewer.java/clean/SRC/org/openmicroscopy/shoola/agents/viewer/Viewer.java
if (moviePlayer != null) moviePlayer.dispose();
if (moviePlayer != null) moviePlayer.close();
void disposeDialogs() { if (moviePlayer != null) moviePlayer.dispose(); if (imageInspector != null) imageInspector.dispose(); roiOnOff = false; presentation.removeCanvasFromLayer(presentation.getDrawingCanvas()); presentation.getBottomBar().resetMessage(BottomBar.LENS); ...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0a711d50cfe02a185f8d314b378ca4c49e92ab2f/ViewerCtrl.java/buggy/SRC/org/openmicroscopy/shoola/agents/viewer/ViewerCtrl.java
PojosQP.ids(c.getIds(key)), PojosQP.String("field",key)
PojosQP.String("field",key), PojosQP.ids(c.getIds(key))
private void collectCounts(Collection queryResults, PojoOptions po) { if (po.hasCountFields() && po.isCounts()) { CountCollector c = new CountCollector(po.countFields()); c.collect(queryResults); for (String key : po.countFields()) { Query ...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
@NotNull @Validate(Integer.class) Set rootNodeIds, @Validate(Integer.class) Set annotatorIds, Map options) {
@NotNull @Validate(Long.class) Set rootNodeIds, @Validate(Long.class) Set annotatorIds, Map options) {
public Map findAnnotations(Class rootNodeType, @NotNull @Validate(Integer.class) Set rootNodeIds, @Validate(Integer.class) Set annotatorIds, Map options) { if (rootNodeIds.size()==0) return new HashMap(); PojoOptions po = new PojoOptions(options); Query q = queryFa...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
"ome.servics.query.FindAnnotationsQueryDefinition",
PojosFindAnnotationsQueryDefinition.class.getName(),
public Map findAnnotations(Class rootNodeType, @NotNull @Validate(Integer.class) Set rootNodeIds, @Validate(Integer.class) Set annotatorIds, Map options) { if (rootNodeIds.size()==0) return new HashMap(); PojoOptions po = new PojoOptions(options); Query q = queryFa...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
for (Object object : l) { iQuery.evict(object); }
public Map findAnnotations(Class rootNodeType, @NotNull @Validate(Integer.class) Set rootNodeIds, @Validate(Integer.class) Set annotatorIds, Map options) { if (rootNodeIds.size()==0) return new HashMap(); PojoOptions po = new PojoOptions(options); Query q = queryFa...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
public Set findCGCPaths(@NotNull @Validate(Integer.class) Set imgIds,
public Set findCGCPaths(@NotNull @Validate(Long.class) Set imgIds,
public Set findCGCPaths(@NotNull @Validate(Integer.class) Set imgIds, String algorithm, Map options) { if (imgIds.size()==0){ return new HashSet(); } if (! IPojos.ALGORITHMS.contains(algorithm)) { throw new IllegalArgumentException( "No such algorithm known:"+algorithm); } PojoOptions po = n...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
"ome.servics.query.FindCGCPathsQueryDefinition",
PojosCGCPathsQueryDefinition.class.getName(),
public Set findCGCPaths(@NotNull @Validate(Integer.class) Set imgIds, String algorithm, Map options) { if (imgIds.size()==0){ return new HashSet(); } if (! IPojos.ALGORITHMS.contains(algorithm)) { throw new IllegalArgumentException( "No such algorithm known:"+algorithm); } PojoOptions po = n...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
public Set findCGCPaths(@NotNull @Validate(Integer.class) Set imgIds, String algorithm, Map options) { if (imgIds.size()==0){ return new HashSet(); } if (! IPojos.ALGORITHMS.contains(algorithm)) { throw new IllegalArgumentException( "No such algorithm known:"+algorithm); } PojoOptions po = n...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
public Set findCGCPaths(@NotNull @Validate(Integer.class) Set imgIds, String algorithm, Map options) { if (imgIds.size()==0){ return new HashSet(); } if (! IPojos.ALGORITHMS.contains(algorithm)) { throw new IllegalArgumentException( "No such algorithm known:"+algorithm); } PojoOptions po = n...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
@NotNull @Validate(Integer.class) Set imageIds, Map options) {
@NotNull @Validate(Long.class) Set imageIds, Map options) {
public Set findContainerHierarchies(@NotNull Class rootNodeType, @NotNull @Validate(Integer.class) Set imageIds, Map options) { PojoOptions po = new PojoOptions(options); Query q = queryFactory.lookup( PojosFindHierarchiesQueryDefinition.class.getName(), Pojo...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
for (Object object : l) { iQuery.evict(object); }
public Set findContainerHierarchies(@NotNull Class rootNodeType, @NotNull @Validate(Integer.class) Set imageIds, Map options) { PojoOptions po = new PojoOptions(options); Query q = queryFactory.lookup( PojosFindHierarchiesQueryDefinition.class.getName(), Pojo...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
public Set findContainerHierarchies(@NotNull Class rootNodeType, @NotNull @Validate(Integer.class) Set imageIds, Map options) { PojoOptions po = new PojoOptions(options); Query q = queryFactory.lookup( PojosFindHierarchiesQueryDefinition.class.getName(), Pojo...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
@NotNull @Validate(Integer.class) Set ids, Map options)
@NotNull @Validate(Long.class) Set ids, Map options)
public Map getCollectionCount(@NotNull String type, @NotNull String property, @NotNull @Validate(Integer.class) Set ids, Map options) { Map results = new HashMap(); String alphaNumeric = "^\\w+$"; String alphaNumericDotted = "^\\w[.\\w]+$"; // TODO annotations ...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
Map results = new HashMap(); String alphaNumeric = "^\\w+$"; String alphaNumericDotted = "^\\w[.\\w]+$";
String parsedProperty = LsidUtils.parseField(property);
public Map getCollectionCount(@NotNull String type, @NotNull String property, @NotNull @Validate(Integer.class) Set ids, Map options) { Map results = new HashMap(); String alphaNumeric = "^\\w+$"; String alphaNumericDotted = "^\\w[.\\w]+$"; // TODO annotations ...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
if (!type.matches(alphaNumericDotted)) { throw new IllegalArgumentException("Type argument to getCollectionCount may ONLY be alpha-numeric with dots ("+alphaNumericDotted+")"); }
checkType(type); checkProperty(type,parsedProperty);
public Map getCollectionCount(@NotNull String type, @NotNull String property, @NotNull @Validate(Integer.class) Set ids, Map options) { Map results = new HashMap(); String alphaNumeric = "^\\w+$"; String alphaNumericDotted = "^\\w[.\\w]+$"; // TODO annotations ...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
if (!property.matches(alphaNumeric)) { throw new IllegalArgumentException("Property argument to getCollectionCount may ONLY be alpha-numeric ("+alphaNumeric+")"); } if (iQuery.checkType(type)) { throw new IllegalArgumentException(type+"."+property+" is an unknown type."); } if (iQuery.checkProperty(type,property)) { ...
String query = "select size(table."+parsedProperty+") from "+type+" table where table.id = ?";
public Map getCollectionCount(@NotNull String type, @NotNull String property, @NotNull @Validate(Integer.class) Set ids, Map options) { Map results = new HashMap(); String alphaNumeric = "^\\w+$"; String alphaNumericDotted = "^\\w[.\\w]+$"; // TODO annotations ...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
Integer id = (Integer) iter.next();
Long id = (Long) iter.next();
public Map getCollectionCount(@NotNull String type, @NotNull String property, @NotNull @Validate(Integer.class) Set ids, Map options) { Map results = new HashMap(); String alphaNumeric = "^\\w+$"; String alphaNumericDotted = "^\\w[.\\w]+$"; // TODO annotations ...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
@NotNull @Validate(Integer.class) Set rootNodeIds, Map options) {
@NotNull @Validate(Long.class) Set rootNodeIds, Map options) {
public Set getImages(@NotNull Class rootNodeType, @NotNull @Validate(Integer.class) Set rootNodeIds, Map options) { if (rootNodeIds.size()==0){ return new HashSet(); } PojoOptions po = new PojoOptions(options); Query q = queryFactory.lookup( "ome.servics.query.GetImagesQueryDef...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
"ome.servics.query.GetImagesQueryDefinition",
PojosGetImagesQueryDefinition.class.getName(),
public Set getImages(@NotNull Class rootNodeType, @NotNull @Validate(Integer.class) Set rootNodeIds, Map options) { if (rootNodeIds.size()==0){ return new HashSet(); } PojoOptions po = new PojoOptions(options); Query q = queryFactory.lookup( "ome.servics.query.GetImagesQueryDef...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
"left outer join fetch e.group " + "left outer join fetch e.groups " +
"left outer join fetch e.groupExperimenterMap gs " + "left outer join fetch gs.child g " +
public Map getUserDetails(@NotNull @Validate(String.class) Set names, Map options) { List results; Map<String, Experimenter> map = new HashMap<String, Experimenter>(); /* query only if we have some ids */ if (names.size() > 0) { Map<String...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
Query q = queryFactory.lookup( "ome.servics.query.GetImagesQueryDefinition", PojosQP.options(po.map()));
Query q = queryFactory.lookup(" select i from Image i " + "where i.details.owner.id = :id ", PojosQP.Long("id",po.getExperimenter()));
public Set getUserImages(Map options) { PojoOptions po = new PojoOptions(options); if (!po.isExperimenter() ) { // FIXME && !po.isGroup()){ throw new IllegalArgumentException( "experimenter or group option " + "is required for getUserImages()."); } Query q = queryFactory.lookup(...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
@Validate(Integer.class) Set rootNodeIds, Map options) {
@Validate(Long.class) Set rootNodeIds, Map options) {
public Set loadContainerHierarchy(Class rootNodeType, @Validate(Integer.class) Set rootNodeIds, Map options) { PojoOptions po = new PojoOptions(options); if (null==rootNodeIds && !po.isExperimenter()) throw new IllegalArgumentException( "Set of ids for lo...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
return (Collection) context.retrieve(arg1);
Collection c = (Collection) context.retrieve(arg1); iQuery.initialize(c); return c;
public Collection retrieveCollection(IObject arg0, String arg1, Map arg2) { IObject context = (IObject) iQuery.getById(arg0.getClass(),arg0.getId()); return (Collection) context.retrieve(arg1); // FIXME not type.o.null safe }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/PojosImpl.java/clean/components/server/src/ome/logic/PojosImpl.java
} else
} else {
private void datasetNodeNavigation(DatasetData d, DefaultMutableTreeNode node, boolean isExpanding) { DefaultTreeModel treeModel = (DefaultTreeModel) view.tree.getModel(); Integer datasetID = new Integer(d.getId()); ...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/5d253e1d8b8b563bd79074b962fe0a01fca0a091/ExplorerPaneManager.java/clean/SRC/org/openmicroscopy/shoola/agents/datamng/ExplorerPaneManager.java
node, node.getChildCount());
node, node.getChildCount()); }
private void datasetNodeNavigation(DatasetData d, DefaultMutableTreeNode node, boolean isExpanding) { DefaultTreeModel treeModel = (DefaultTreeModel) view.tree.getModel(); Integer datasetID = new Integer(d.getId()); ...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/5d253e1d8b8b563bd79074b962fe0a01fca0a091/ExplorerPaneManager.java/clean/SRC/org/openmicroscopy/shoola/agents/datamng/ExplorerPaneManager.java
recv.getRuntime().getRuntime().setTraceFunction((RubyProc) trace_func);
public static IRubyObject set_trace_func(IRubyObject recv, IRubyObject trace_func) { if (trace_func.isNil()) { recv.getRuntime().getRuntime().setTraceFunction(null); } else if (!(trace_func instanceof RubyProc)) { throw new TypeError(recv.getRuntime(), "trace_func needs to be Pro...
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/7b41d102019836c9a5ec6884b2d9b9380f9853a7/KernelModule.java/clean/org/jruby/KernelModule.java
blockArg = runtime.newProc(); blockArg.getBlock().isLambda = context.getCurrentBlock().isLambda;
public IRubyObject internalCall(ThreadContext context, IRubyObject receiver, RubyModule lastClass, String name, IRubyObject[] args, boolean noSuper) { assert args != null; IRuby runtime = context.getRuntime(); RubyProc blockArg = null; if (argsNode.getBlockArgNode() != null && context.isBlo...
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/048e5b9179a657d1e786630b4cb43ae2bfdfbe4a/DefaultMethod.java/buggy/src/org/jruby/internal/runtime/methods/DefaultMethod.java
RubyObject[] args = ArgsUtil.setupArgs(ruby, self, getArgsNode().getNextNode()); RubyList argsList = new RubyList(args); argsList.remove(args.length - 1); RubyObject val = recv.funcall(ruby.intern("[]"), argsList.toRubyArray());
RubyPointer args = ArgsUtil.setupArgs(ruby, self, getArgsNode().getNextNode()); args.remove(args.size() - 1); RubyObject val = recv.funcall(ruby.intern("[]"), args);
public RubyObject eval(Ruby ruby, RubyObject self) { // TMP_PROTECT; RubyObject recv = getRecvNode().eval(ruby, self); Node rval = getArgsNode().getHeadNode(); RubyObject[] args = ArgsUtil.setupArgs(ruby, self, getArgsNode().getNextNode()); RubyList argsList = new ...
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/f629550c5947df9c1dbe414645f3dc76bcb70df4/OpAsgn1Node.java/buggy/org/jruby/nodes/OpAsgn1Node.java
args[args.length - 1] = val;
args.set(args.size() - 1, val);
public RubyObject eval(Ruby ruby, RubyObject self) { // TMP_PROTECT; RubyObject recv = getRecvNode().eval(ruby, self); Node rval = getArgsNode().getHeadNode(); RubyObject[] args = ArgsUtil.setupArgs(ruby, self, getArgsNode().getNextNode()); RubyList argsList = new ...
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/f629550c5947df9c1dbe414645f3dc76bcb70df4/OpAsgn1Node.java/buggy/org/jruby/nodes/OpAsgn1Node.java
int index = view.getSearchType(); String regEx = view.getSearchValue(); FindRegExCmd cmd = new FindRegExCmd(view.model.getParentModel(), regEx, index); cmd.execute();
try { int index = view.getSearchType(); String regEx = view.getSearchValue(); Pattern p = RegExFactory.createCaseInsensitivePattern(regEx); FindRegExCmd cmd = new FindRegExCmd(view.model.getParentModel(), p, index); cmd.execute(); } catch (PatternSyntaxException pse) { UserNotifier un = HiViewerAgent.getRegistry().getU...
private void performSearch() { int index = view.getSearchType(); String regEx = view.getSearchValue(); FindRegExCmd cmd = new FindRegExCmd(view.model.getParentModel(), regEx, index); cmd.execute(); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0c7517f5d0ece413452f58f3f0a071be2ccbee2e/CBSearchTabViewMng.java/clean/SRC/org/openmicroscopy/shoola/agents/hiviewer/clipboard/CBSearchTabViewMng.java
registry.getUserNotifier().notifyInfo("Data Saving Cancellation", info);
public void handleCancellation() { String info = "The data saving has been cancelled."; registry.getLogger().info(this, info); registry.getUserNotifier().notifyInfo("Data Saving Cancellation", info); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/ea7509babe2344eb702969105eb77096cc5b6bcf/EditorLoader.java/clean/SRC/org/openmicroscopy/shoola/agents/treeviewer/EditorLoader.java
e.printStackTrace();
public final Template handle(WebContext wc) throws HandlerException { String pageName = null; WikiPage wikiPage = null; // who is trying to do something? WikiUser user = getUser (wc); // which action wants to respond to this request? PageAction action = _actionManag...
52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/76bb847e1a32516a74762100398ded03f39feec8/WikiServlet.java/buggy/wiki/src/org/tcdi/opensource/wiki/servlet/WikiServlet.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/ClassVarNode.java/clean/src/org/jruby/ast/ClassVarNode.java
public static RubyObject[] setupArgs(Ruby ruby, RubyObject self, ArrayNode node) {
public static RubyPointer setupArgs(Ruby ruby, RubyObject self, ArrayNode node) {
public static RubyObject[] setupArgs(Ruby ruby, RubyObject self, ArrayNode node) { String file = ruby.getSourceFile(); int line = ruby.getSourceLine(); RubyObject[] args = node.getArray(ruby, self); ruby.setSourceFile(file); ruby.setSourceLine(line); ...
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/f629550c5947df9c1dbe414645f3dc76bcb70df4/ArgsUtil.java/buggy/org/jruby/nodes/util/ArgsUtil.java
RubyObject[] args = node.getArray(ruby, self);
RubyPointer args = new RubyPointer(node.getArrayList(ruby, self));
public static RubyObject[] setupArgs(Ruby ruby, RubyObject self, ArrayNode node) { String file = ruby.getSourceFile(); int line = ruby.getSourceLine(); RubyObject[] args = node.getArray(ruby, self); ruby.setSourceFile(file); ruby.setSourceLine(line); ...
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/f629550c5947df9c1dbe414645f3dc76bcb70df4/ArgsUtil.java/buggy/org/jruby/nodes/util/ArgsUtil.java
return super.filter(fieldId,f);
return result;
public Filterable filter(String fieldId, Filterable f) { /* TODO here's where we could use a single call back for each filter method. (onFilter) also (onFilterX) beforeFilter / afterFilter etc. */ addIfHit(fieldId); return super.filter(fieldId,f); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/5455b73a435a252c2c058cc4c625f039b667cd2f/CountCollector.java/clean/components/server/src/ome/services/util/CountCollector.java
DumpVisitor lVisitor = new DumpVisitor(); lScript.accept(lVisitor); ruby.getRuntime().getOutputStream().println(lVisitor.dump());
protected static void runInterpreter(Reader iReader2Eval, String iFileName, String[] args) { // Initialize Runtime Ruby ruby = Ruby.getDefaultInstance(sRegexpAdapter); // Parse and interpret file IRubyObject lArgv = JavaUtil.convertJavaToRuby(ruby, args); ruby.setVerbose(warning);...
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/615c030e9e2e4f7129fe3e92d877dd15dd313c3d/Main.java/buggy/org/jruby/Main.java
|| textFound.startsWith("https:
|| textFound.startsWith("https:
private String filterBody(String text) { EmoticonManager emoticonManager = EmoticonManager.getInstance(); StringBuilder builder = new StringBuilder(); final StringTokenizer tokenizer = new StringTokenizer(text, " \n \t", true); while (tokenizer.hasMoreTokens()) { String textFo...
52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/ad8343da83861b145373d811238d8e2939352153/TranscriptWindow.java/clean/src/java/org/jivesoftware/spark/ui/TranscriptWindow.java
} throw new IllegalArgumentException("DataObject not supported.");
} else throw new IllegalArgumentException("Child and parent are not" + " compatible.");
public static IObject createIObject(DataObject child, DataObject parent) { if (child instanceof ProjectData) { ProjectData data = (ProjectData) child; Project model = new Project(); model.setName(data.getName()); model.setDescription(data.getDescription()); ...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/557c1489203604f61421342df46753983ef62091/ModelMapper.java/buggy/SRC/org/openmicroscopy/shoola/env/data/util/ModelMapper.java
} throw new IllegalArgumentException("DataObject not supported.");
} else throw new IllegalArgumentException("DataObject not supported.");
public static void linkParentToChild(IObject child, IObject parent) { if (parent == null) return; if (child == null) throw new IllegalArgumentException("Child cannot" + "be null."); if (parent instanceof Project) { if (!(child instanceof Dataset)) ...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/557c1489203604f61421342df46753983ef62091/ModelMapper.java/buggy/SRC/org/openmicroscopy/shoola/env/data/util/ModelMapper.java
public MockServiceFactory() throws NullPointerException {
private MockServiceFactory() throws NullPointerException {
public MockServiceFactory() throws NullPointerException { super(SERVICE); }
52533 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52533/2ea7b1ef6a6941dce6f02e1ac520e7e82d2bc346/StandardKernelTest.java/clean/kernel/src/test/org/gbean/kernel/standard/StandardKernelTest.java
public ISourcePosition getPosition(ISourcePosition startPosition) { return src.getPosition(startPosition);
public ISourcePosition getPosition() { return currentPos;
public ISourcePosition getPosition(ISourcePosition startPosition) { return src.getPosition(startPosition); }
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/1d8ec540dc793b2d5ad5084d2cb6b204087302b7/RubyYaccLexer.java/buggy/src/org/jruby/lexer/yacc/RubyYaccLexer.java
int r = i1.getInserted().compareTo(i2.getInserted());
Timestamp t1 = i1.getInserted(); Timestamp t2 = i2.getInserted(); if (t1 == null) t1 = TreeViewerTranslator.getDefaultTimestamp(); if (t2 == null) t2 = TreeViewerTranslator.getDefaultTimestamp(); int r = t1.compareTo(t2);
private List sort(List nodes, final boolean ascending) { Comparator c; switch (sortType) { case Browser.SORT_NODES_BY_DATE: c = new Comparator() { public int compare(Object o1, Object o2) { ImageData i1 = (ImageD...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/5cd0be53036d59904eb6332d7e2a1c1e964bdc06/SortCmd.java/clean/SRC/org/openmicroscopy/shoola/agents/treeviewer/cmd/SortCmd.java
int r = i1.getInserted().compareTo(i2.getInserted());
Timestamp t1 = i1.getInserted(); Timestamp t2 = i2.getInserted(); if (t1 == null) t1 = TreeViewerTranslator.getDefaultTimestamp(); if (t2 == null) t2 = TreeViewerTranslator.getDefaultTimestamp(); int r = t1.compareTo(t2);
public int compare(Object o1, Object o2) { ImageData i1 = (ImageData) (((TreeImageDisplay) o1).getUserObject()); ImageData i2 = (ImageData) (((TreeImageDisplay) ...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/5cd0be53036d59904eb6332d7e2a1c1e964bdc06/SortCmd.java/clean/SRC/org/openmicroscopy/shoola/agents/treeviewer/cmd/SortCmd.java
saveSettings(); break; case SAVE:
public void actionPerformed(ActionEvent e) { String s = (String) e.getActionCommand(); try { int index = Integer.parseInt(s); switch (index) { case APPLY: applySettings(); break; case CANCEL: saveSettings(); break; case SAVE: cancel(); break; case R_AREA: checkFieldVa...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0c2418384f5c30e274953927e006a71647a24f1b/ColorChooserManager.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/model/ColorChooserManager.java
String valRed = view.getRArea().getText(), red = ""+colorSelected.getRed(); String valGreen = view.getGArea().getText(), green = ""+colorSelected.getGreen(); String valBlue = view.getBArea().getText(), blue = ""+colorSelected.getBlue();
String valRed = view.getRArea().getText(), red = ""+colorSelected.getRed(); String valGreen = view.getGArea().getText(), green = ""+colorSelected.getGreen(); String valBlue = view.getBArea().getText(), blue = ""+colorSelected.getBlue();
public void focusLost(FocusEvent e) { String valRed = view.getRArea().getText(), red = ""+colorSelected.getRed(); String valGreen = view.getGArea().getText(), green = ""+colorSelected.getGreen(); String valBlue = view.getBArea().getText(), blue = ""+colorSelected.getBlue(); ...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0c2418384f5c30e274953927e006a71647a24f1b/ColorChooserManager.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/model/ColorChooserManager.java
preferences.showDatesInChat(showTime); return preferences;
return pref;
public Object getData() { LocalPreferences pref = SettingsManager.getLocalPreferences(); String nickname = pref.getDefaultNickname(); if (nickname == null) { nickname = SparkManager.getSessionManager().getUsername(); } boolean showTime = pref.isTimeDisplayedInChat(); ...
52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/f678f06c6fbc4a84079c230a0a7461759cb20755/ChatPreference.java/buggy/src/java/org/jivesoftware/sparkimpl/preference/chat/ChatPreference.java
return new XmlDataSet(new FileInputStream("sql/db-export.xml"));
URL file = this.getClass().getClassLoader().getResource("db-export.xml"); return new XmlDataSet(new FileInputStream(file.getFile()));
public IDataSet getData() throws Exception { return new XmlDataSet(new FileInputStream("sql/db-export.xml")); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9cc885fa28a62ed7b7bf1dbcf110c443345339d1/HierarchyBrowsingDbUnitTest.java/buggy/components/server/test/org/openmicroscopy/omero/server/utests/HierarchyBrowsingDbUnitTest.java
protected void setUp() throws Exception { ctx = getContext(getConfigLocations()); if (null == cdao || null == adao || null == ds) { cdao = (ContainerDao) ctx.getBean("containerDao"); adao = (AnnotationDao) ctx.getBean("annotationDao"); ds = (DataSource) ctx.getBea...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9cc885fa28a62ed7b7bf1dbcf110c443345339d1/HierarchyBrowsingDbUnitTest.java/buggy/components/server/test/org/openmicroscopy/omero/server/utests/HierarchyBrowsingDbUnitTest.java
c = new DatabaseConnection(ds.getConnection()); DatabaseOperation.CLEAN_INSERT.execute(c,getData());
try { c = new DatabaseConnection(ds.getConnection()); DatabaseOperation.CLEAN_INSERT.execute(c,getData()); } catch (Exception e){ c = null; throw e; }
protected void setUp() throws Exception { ctx = getContext(getConfigLocations()); if (null == cdao || null == adao || null == ds) { cdao = (ContainerDao) ctx.getBean("containerDao"); adao = (AnnotationDao) ctx.getBean("annotationDao"); ds = (DataSource) ctx.getBea...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9cc885fa28a62ed7b7bf1dbcf110c443345339d1/HierarchyBrowsingDbUnitTest.java/buggy/components/server/test/org/openmicroscopy/omero/server/utests/HierarchyBrowsingDbUnitTest.java
List result = cdao.findPDIHierarchies(set); assertTrue("Should have found all the images but Zero", result.size()==set.size()+1);
List tmp = cdao.findPDIHierarchies(set); Set result = new HashSet(tmp); assertTrue("Should have found all the images but Zero but found "+result.size(), result.size()+1==set.size());
public void testFindPDIHierarchies(){ Set set = getSetFromInt(new int[]{1,5,6,7,8,9,0}); List result = cdao.findPDIHierarchies(set); assertTrue("Should have found all the images but Zero", result.size()==set.size()+1); for (Iterator i = result.iterator(); i.hasNext();) { Image...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9cc885fa28a62ed7b7bf1dbcf110c443345339d1/HierarchyBrowsingDbUnitTest.java/buggy/components/server/test/org/openmicroscopy/omero/server/utests/HierarchyBrowsingDbUnitTest.java
assertTrue("Fully initialized",Hibernate.isInitialized(img.getDatasets()));
Set ds = img.getDatasets(); assertTrue("Fully initialized datasets",Hibernate.isInitialized(ds)); for (Iterator j = ds.iterator(); j.hasNext();) { Dataset d = (Dataset) j.next(); assertTrue("Fully initialized projects",Hibernate.isInitialized(d.getProjects())); }
public void testFindPDIHierarchies(){ Set set = getSetFromInt(new int[]{1,5,6,7,8,9,0}); List result = cdao.findPDIHierarchies(set); assertTrue("Should have found all the images but Zero", result.size()==set.size()+1); for (Iterator i = result.iterator(); i.hasNext();) { Image...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/9cc885fa28a62ed7b7bf1dbcf110c443345339d1/HierarchyBrowsingDbUnitTest.java/buggy/components/server/test/org/openmicroscopy/omero/server/utests/HierarchyBrowsingDbUnitTest.java
getParent().removeChild(this);
if(getParent() != null) getParent().removeChild(this);
public void respondMouseClick(PInputEvent event) { getParent().removeChild(this); t.respondMouseClick(pushParentNode(event,t)); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/07357b3d8cbf047af1ecb7b0a4514d2c06b4b04f/ImageNameNode.java/buggy/SRC/org/openmicroscopy/shoola/agents/browser/ui/ImageNameNode.java
getParent().removeChild(this);
if(getParent() != null) getParent().removeChild(this);
public void respondMouseDoubleClick(PInputEvent event) { getParent().removeChild(this); t.respondMouseDoubleClick(pushParentNode(event,t)); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/07357b3d8cbf047af1ecb7b0a4514d2c06b4b04f/ImageNameNode.java/buggy/SRC/org/openmicroscopy/shoola/agents/browser/ui/ImageNameNode.java
getParent().removeChild(this);
if(getParent() != null) getParent().removeChild(this);
public void respondMousePress(PInputEvent event) { getParent().removeChild(this); t.respondMousePress(pushParentNode(event,t)); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/07357b3d8cbf047af1ecb7b0a4514d2c06b4b04f/ImageNameNode.java/buggy/SRC/org/openmicroscopy/shoola/agents/browser/ui/ImageNameNode.java
getParent().removeChild(this);
if(getParent() != null) getParent().removeChild(this);
public void respondMouseRelease(PInputEvent event) { getParent().removeChild(this); t.respondMouseRelease(pushParentNode(event,t)); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/07357b3d8cbf047af1ecb7b0a4514d2c06b4b04f/ImageNameNode.java/buggy/SRC/org/openmicroscopy/shoola/agents/browser/ui/ImageNameNode.java
*/
public void actionPerformed(ActionEvent ae) { Rectangle oldBounds = model.getUI().getBounds(); HiViewer newOne = HiViewerFactory.reinstantiate(model); model.discard(); newOne.activate(oldBounds); }
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/fb3743d6f75abbf12f788b3b2925f4a6f4606dd6/RefreshAction.java/clean/SRC/org/openmicroscopy/shoola/agents/hiviewer/actions/RefreshAction.java
Object o = enum.nextElement(); hasNext = enum.hasMoreElements();
Object o = enumeration.nextElement(); hasNext = enumeration.hasMoreElements();
final public Object next () throws NoSuchElementException { if (!hasNext) { throw new NoSuchElementException("advanced past end of list"); } Object o = enum.nextElement(); hasNext = enum.hasMoreElements(); return o; }
52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/66b6fa23bd4cbc41e75a36f1705ebb0db3d2f013/EnumIterator.java/buggy/webmacro/src/org/webmacro/util/EnumIterator.java
p.linkDataset( d1 ); p.linkDataset( d2 ); p.linkDataset( d3 ); d1.linkImage( i1 ); d1.linkImage( i2 ); d1.linkImage( i3 );
protected void setUp() throws Exception { mapper=new Model2PojosMapper(); p = new Project(new Long(1)); d1 = new Dataset(new Long(2)); d2 = new Dataset(new Long(3)); d3 = new Dataset(new Long(4)); i1 = new Image(new Long(5)); i2 = new Image(new Long(6)); i3 = new Image(new Long(7));// p.setDatasets(new HashS...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/5f68082026bcb57849846aaa0e4de7e32b6ebf72/Model2PojosMapperTest.java/buggy/components/shoola-adapter/test/ome/adapters/pojos/utests/Model2PojosMapperTest.java
for (DisplayedNote removeMe : dd.getTree().getSelectedNotes()) {
while (dd.getTree().getSelectedNotes().size() > 0) { DisplayedNote removeMe = dd.getTree().getSelectedNotes().get(0);
public void removeNotes(Event e) { for (DisplayedNote removeMe : dd.getTree().getSelectedNotes()) { removeMe.deleteSelfAndChildren(); } }
57508 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57508/7ad283aaa04b8b53a82e0693b22ac284bcd6637b/NoteMenuController.java/buggy/trunk/src/de/berlios/koalanotes/display/menus/NoteMenuController.java
String table = null; Class klass = parent.getClass(); if (klass.equals(Category.class)) table = "CategoryImageLink"; else if (klass.equals(Dataset.class)) table = "DatasetImageLink"; else if (klass.equals(Project.class)) table = "ProjectDatasetLink"; else if (klass.equals(CategoryGroup.class)) table = "CategoryGroupCat...
String table = getTableForLink(parent.getClass());
IObject findLink(IObject parent, IObject child) throws DSOutOfServiceException, DSAccessException { try { String table = null; Class klass = parent.getClass(); if (klass.equals(Category.class)) table = "CategoryImageLink"; else if (klass.equals(Dataset.cl...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/87f0144809415c3236dabaa1afd6162d13a14ebe/OMEROGateway.java/clean/SRC/org/openmicroscopy/shoola/env/data/OMEROGateway.java
String table = null; Class klass = parent.getClass(); if (klass.equals(Category.class)) table = "CategoryImageLink"; else if (klass.equals(Dataset.class)) table = "DatasetImageLink"; else if (klass.equals(Project.class)) table = "ProjectDatasetLink"; else if (klass.equals(CategoryGroup.class)) table = "CategoryGroupCat...
String table = getTableForLink(parent.getClass());
List findLinks(IObject parent, List children) throws DSOutOfServiceException, DSAccessException { try { String table = null; Class klass = parent.getClass(); if (klass.equals(Category.class)) table = "CategoryImageLink"; else if (klass.equals(Dataset.clas...
54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/87f0144809415c3236dabaa1afd6162d13a14ebe/OMEROGateway.java/clean/SRC/org/openmicroscopy/shoola/env/data/OMEROGateway.java
tmpl = "#if (true)\n { pass\n }\n #else\n { fail\n }"; assertStringTemplateEquals (tmpl, " pass\n ");
public void testBeginEnd () throws Exception { String tmpl = "#if (true) #begin pass #end #else #begin fail #end"; assertStringTemplateEquals (tmpl, "pass"); tmpl = "#if (true)\n #begin pass\n #end\n #else\n #begin fail\n #end"; assertStringTemplateEquals (tmpl, "pass\n"); }
52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/4e88c3a52c24e9e3115286b7b792ccb08ca7a24a/TestBlocks.java/clean/webmacro/test/unit/org/webmacro/template/TestBlocks.java
public RubyRegexpException(String msg) { super(msg);
public RubyRegexpException() {
public RubyRegexpException(String msg) { super(msg); }
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/9a05f18f2b6207bf93455d756436fe8f0002b542/RubyRegexpException.java/buggy/org/jruby/exceptions/RubyRegexpException.java
ruby.getRubyParser().compileString(sb.toString(), fname, 0);
ruby.getRubyParser().compileString(fname.getValue(), RubyString.m_newString(ruby, sb.toString()), 0);
public void load(RubyString fname, boolean wrap) { RubyObject self = ruby.getRubyTopSelf(); NODE savedCRef = ruby.getRubyCRef(); // TMP_PROTECT; if (wrap && ruby.getSecurityLevel() >= 4) { // Check_Type(fname, T_STRING); } else { // Check_SafeStr(...
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/a6fb3288b71aaedfe3a7b5e8d1e561e0bc249dc6/RubyInterpreter.java/clean/org/jruby/interpreter/RubyInterpreter.java
eval(self, ruby.getParserHelper().getEvalTree()); } catch (RubyException excptn) {
if (ruby.getParserHelper().getEvalTreeBegin() != null) { System.out.println("EvalTreeBegin"); eval(self, ruby.getParserHelper().getEvalTreeBegin()); ruby.getParserHelper().setEvalTreeBegin(null); } if (ruby.getParserHelper().getEvalTree() != null) { System.out.println("EvalTree"); eval(self, ruby.getParserHelper().ge...
public void load(RubyString fname, boolean wrap) { RubyObject self = ruby.getRubyTopSelf(); NODE savedCRef = ruby.getRubyCRef(); // TMP_PROTECT; if (wrap && ruby.getSecurityLevel() >= 4) { // Check_Type(fname, T_STRING); } else { // Check_SafeStr(...
50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/a6fb3288b71aaedfe3a7b5e8d1e561e0bc249dc6/RubyInterpreter.java/clean/org/jruby/interpreter/RubyInterpreter.java
if (!name.startsWith("/")) name = "/" + name; URL u = _servletContext.getResource(name);
String contextName = name; if (name.startsWith("/")) { name = name.substring(1); } else { StringBuffer b = new StringBuffer(name.length()+1); b.append("/"); b.append(name); contextName = b.toString(); } URL u = _servletContext.getResource(contextName);
public URL getResource(String name) { try { // NOTE: Tomcat4 needs a leading '/'. // If this doesn't work with your 2.2+ container, try commenting out the following line if (!name.startsWith("/")) name = "/" + name; URL u = _servletContext.getResource(name); if (u != null...
52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/8fa9b52e736aaea7b8b1845ed47dba457c9a7c94/Servlet22Broker.java/clean/webmacro/src/org/webmacro/servlet/Servlet22Broker.java
File f = new File(u.getFile()); if (!f.exists()) u = null;
File f = new File(u.getFile()); if (!f.exists()) u = null;
public URL getResource(String name) { try { // NOTE: Tomcat4 needs a leading '/'. // If this doesn't work with your 2.2+ container, try commenting out the following line if (!name.startsWith("/")) name = "/" + name; URL u = _servletContext.getResource(name); if (u != null...
52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/8fa9b52e736aaea7b8b1845ed47dba457c9a7c94/Servlet22Broker.java/clean/webmacro/src/org/webmacro/servlet/Servlet22Broker.java
if (u == null)
if (u == null) {
public URL getResource(String name) { try { // NOTE: Tomcat4 needs a leading '/'. // If this doesn't work with your 2.2+ container, try commenting out the following line if (!name.startsWith("/")) name = "/" + name; URL u = _servletContext.getResource(name); if (u != null...
52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/8fa9b52e736aaea7b8b1845ed47dba457c9a7c94/Servlet22Broker.java/clean/webmacro/src/org/webmacro/servlet/Servlet22Broker.java
if (u == null)
} if (u == null)
public URL getResource(String name) { try { // NOTE: Tomcat4 needs a leading '/'. // If this doesn't work with your 2.2+ container, try commenting out the following line if (!name.startsWith("/")) name = "/" + name; URL u = _servletContext.getResource(name); if (u != null...
52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/8fa9b52e736aaea7b8b1845ed47dba457c9a7c94/Servlet22Broker.java/clean/webmacro/src/org/webmacro/servlet/Servlet22Broker.java
public void actionPerformed(ActionEvent e) { long now = System.currentTimeMillis(); if (now - lastTypedCharTime > 2000) { if (!sendNotification) { // send cancel SparkManager.getMessageEventManager().sendCancelled...
52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/0bc7db8cc68c7433cd601f93a8d06f275e576e91/ChatRoomImpl.java/buggy/src/java/org/jivesoftware/spark/ui/rooms/ChatRoomImpl.java
SparkManager.getMessageEventManager().removeMessageEventRequestListener(messageEventRequestListener);
public void closeChatRoom() { super.closeChatRoom(); SparkManager.getMessageEventManager().removeMessageEventRequestListener(messageEventRequestListener); SparkManager.getChatManager().removeChat(this); SparkManager.getConnection().removePacketListener(this); }
52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/0bc7db8cc68c7433cd601f93a8d06f275e576e91/ChatRoomImpl.java/buggy/src/java/org/jivesoftware/spark/ui/rooms/ChatRoomImpl.java
typingTimer.stop();
public void closeChatRoom() { super.closeChatRoom(); SparkManager.getMessageEventManager().removeMessageEventRequestListener(messageEventRequestListener); SparkManager.getChatManager().removeChat(this); SparkManager.getConnection().removePacketListener(this); }
52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/0bc7db8cc68c7433cd601f93a8d06f275e576e91/ChatRoomImpl.java/buggy/src/java/org/jivesoftware/spark/ui/rooms/ChatRoomImpl.java