JoaoJunior/formatted-java-code-APR · Datasets at Hugging Face

public final boolean isNameStartChar() { return isNameStartChar(_cur); }

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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("eql?", EQUAL, 1); context.createAlias("equal?", "=="); context.createOptional("extend", EXTEND, 1); context.create("freeze", FREEZE, 0); context.create("frozen?", FROZEN, 0); context.create("hash", HASH, 0); context.create("id", ID, 0); context.create("__id__", ID, 0); context.create("inspect", INSPECT, 0); context.createOptional("instance_eval", INSTANCE_EVAL); context.create("instance_of?", INSTANCE_OF, 1); context.create("instance_variables", INSTANCE_VARIABLES, 0); context.create("is_a?", KIND_OF, 1); context.create("kind_of?", KIND_OF, 1); context.create("method", METHOD, 1); context.create("methods", METHODS, 0); context.createOptional("method_missing", METHOD_MISSING); context.create("nil?", NIL, 0); context.create("private_methods", PRIVATE_METHODS, 0); context.create("protected_methods", PROTECTED_METHODS, 0); context.create("public_methods", METHODS, 0); context.createOptional("respond_to?", RESPOND_TO, 1); context.createOptional("send", SEND, 1); context.createOptional("__send__", SEND, 1); context.create("singleton_methods", SINGLETON_METHODS, 0); context.create("taint", TAINT, 0); context.create("tainted?", TAINTED, 0); context.create("to_a", TO_A, 0); context.create("to_s", TO_S, 0); context.create("type", TYPE, 0); context.create("untaint", UNTAINT, 0); }

protected void defineMethods(MethodContext context) { context.create("==", EQUAL, 1); context.createAlias("===", "=="); context.create("=~", MATCH, 1); context.create("class", TYPE, 0); context.create("clone", RBCLONE, 0); context.create("dup", DUP, 0); context.create("eql?", EQUAL, 1); context.createAlias("equal?", "=="); context.createOptional("extend", EXTEND, 1); context.create("freeze", FREEZE, 0); context.create("frozen?", FROZEN, 0); context.create("hash", HASH, 0); context.create("id", ID, 0); context.create("__id__", ID, 0); context.create("inspect", INSPECT, 0); context.createOptional("instance_eval", INSTANCE_EVAL); context.create("instance_of?", INSTANCE_OF, 1); context.create("instance_variables", INSTANCE_VARIABLES, 0); context.create("is_a?", KIND_OF, 1); context.create("kind_of?", KIND_OF, 1); context.create("method", METHOD, 1); context.create("methods", METHODS, 0); context.createOptional("method_missing", METHOD_MISSING); context.create("nil?", NIL, 0); context.create("private_methods", PRIVATE_METHODS, 0); context.create("protected_methods", PROTECTED_METHODS, 0); context.create("public_methods", METHODS, 0); context.createOptional("respond_to?", RESPOND_TO, 1); context.createOptional("send", SEND, 1); context.createOptional("__send__", SEND, 1); context.create("singleton_methods", SINGLETON_METHODS, 0); context.create("taint", TAINT, 0); context.create("tainted?", TAINTED, 0); context.create("to_a", TO_A, 0); context.create("to_s", TO_S, 0); context.create("type", TYPE, 0); context.create("untaint", UNTAINT, 0); }

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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("eql?", EQUAL, 1); context.createAlias("equal?", "=="); context.createOptional("extend", EXTEND, 1); context.create("freeze", FREEZE, 0); context.create("frozen?", FROZEN, 0); context.create("hash", HASH, 0); context.create("id", ID, 0); context.create("__id__", ID, 0); context.create("inspect", INSPECT, 0); context.createOptional("instance_eval", INSTANCE_EVAL); context.create("instance_of?", INSTANCE_OF, 1); context.create("instance_variables", INSTANCE_VARIABLES, 0); context.create("is_a?", KIND_OF, 1); context.create("kind_of?", KIND_OF, 1); context.create("method", METHOD, 1); context.create("methods", METHODS, 0); context.createOptional("method_missing", METHOD_MISSING); context.create("nil?", NIL, 0); context.create("private_methods", PRIVATE_METHODS, 0); context.create("protected_methods", PROTECTED_METHODS, 0); context.create("public_methods", METHODS, 0); context.createOptional("respond_to?", RESPOND_TO, 1); context.createOptional("send", SEND, 1); context.createOptional("__send__", SEND, 1); context.create("singleton_methods", SINGLETON_METHODS, 0); context.create("taint", TAINT, 0); context.create("tainted?", TAINTED, 0); context.create("to_a", TO_A, 0); context.create("to_s", TO_S, 0); context.create("type", TYPE, 0); context.create("untaint", UNTAINT, 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("eql?", EQUAL, 1); context.createAlias("equal?", "=="); context.createOptional("extend", EXTEND, 1); context.create("freeze", FREEZE, 0); context.create("frozen?", FROZEN_P, 0); context.create("hash", HASH, 0); context.create("id", ID, 0); context.create("__id__", ID, 0); context.create("inspect", INSPECT, 0); context.createOptional("instance_eval", INSTANCE_EVAL); context.create("instance_of?", INSTANCE_OF, 1); context.create("instance_variables", INSTANCE_VARIABLES, 0); context.create("is_a?", KIND_OF, 1); context.create("kind_of?", KIND_OF, 1); context.create("method", METHOD, 1); context.create("methods", METHODS, 0); context.createOptional("method_missing", METHOD_MISSING); context.create("nil?", NIL, 0); context.create("private_methods", PRIVATE_METHODS, 0); context.create("protected_methods", PROTECTED_METHODS, 0); context.create("public_methods", METHODS, 0); context.createOptional("respond_to?", RESPOND_TO, 1); context.createOptional("send", SEND, 1); context.createOptional("__send__", SEND, 1); context.create("singleton_methods", SINGLETON_METHODS, 0); context.create("taint", TAINT, 0); context.create("tainted?", TAINTED, 0); context.create("to_a", TO_A, 0); context.create("to_s", TO_S, 0); context.create("type", TYPE, 0); context.create("untaint", UNTAINT, 0); }

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public void bind(String name, Object obj) { entriesMap.put(name, obj); }

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public void bind(String name, Object obj) { entriesMap.put(name, obj); }

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public static RubyModule m_new(Ruby ruby, RubyModule rubyClass) { RubyModule mod = RubyModule.m_newModule(ruby); mod.setRubyClass(rubyClass); ruby.getModuleClass().callInit(null); return mod; }

public static RubyModule m_new(Ruby ruby, RubyObject recv) { RubyModule mod = RubyModule.m_newModule(ruby); mod.setRubyClass(rubyClass); ruby.getModuleClass().callInit(null); return mod; }

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public static RubyModule m_new(Ruby ruby, RubyModule rubyClass) { RubyModule mod = RubyModule.m_newModule(ruby); mod.setRubyClass(rubyClass); ruby.getModuleClass().callInit(null); return mod; }

public static RubyModule m_new(Ruby ruby, RubyModule rubyClass) { RubyModule mod = RubyModule.m_newModule(ruby); mod.setRubyClass((RubyModule)recv); ruby.getModuleClass().callInit(null); return mod; }

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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: return new PDILoader(component, images); case HiViewer.CGCI_HIERARCHY: return new CGCILoader(component, ids); } return null; }

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: return new PDILoader(component, ids); case HiViewer.CGCI_HIERARCHY: return new CGCILoader(component, ids); } return null; }

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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(), getLongValue()).op_mul(other); } else { long otherValue = other.getLongValue(); long result = value * otherValue; if (result > MAX || result < MIN || result / otherValue != value) { return RubyBignum.newBignum(getRuntime(), getLongValue()).op_mul(other); } else { return newFixnum(result); } } }

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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); }

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HistogramDialogManager(HistogramDialog view, QuantumPaneManager control) { this.view = view; this.control = control; inputStartKnob = false; inputEndKnob = false; boxInputStart = new Rectangle(); boxInputEnd = new Rectangle(); }

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HistogramDialogManager(HistogramDialog view, QuantumPaneManager control) { this.view = view; this.control = control; inputStartKnob = false; inputEndKnob = false; boxInputStart = new Rectangle(); boxInputEnd = new Rectangle(); }

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void initRectangles(int yStart, int yEnd) { lS = HistogramPanel.leftBorder+view.getHistogramPanel().getWidthStat(); setInputStartBox(yStart); setInputEndBox(yEnd); }

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void initRectangles(int yStart, int yEnd) { lS = HistogramPanel.leftBorder+view.getHistogramPanel().getWidthStat(); setInputStartBox(yStart); setInputEndBox(yEnd); }

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void attachListeners() { view.getHistogramPanel().addMouseListener(this); view.getHistogramPanel().addMouseMotionListener(this); view.addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent we) { view.dispose(); } }); }

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private void handleImageLoaded(ImageLoaded response) { LoadImage request = (LoadImage) response.getACT(); renderingControl = response.getProxy(); PixelsDimensions pxsDims = renderingControl.getPixelsDims(); //TODO: REMOVE COMMENTS //control.removeProgressNotifier(); if (curImageID != request.getImageID()) { if (presentation == null) buildPresentation(pxsDims); initPresentation(request.getImageName(), pxsDims, false); curImageID = request.getImageID(); curPixelsID = request.getPixelsID(); registry.getEventBus().post(new RenderImage(curPixelsID)); // have to dispose all windows linked control.disposeDialogs(); } showPresentation(); }

private void handleImageLoaded(ImageLoaded response) { LoadImage request = (LoadImage) response.getACT(); renderingControl = response.getProxy(); //TODO: REMOVE COMMENTS //control.removeProgressNotifier(); if (curImageID != request.getImageID()) { if (presentation == null) buildPresentation(pxsDims); initPresentation(request.getImageName(), pxsDims, false); curImageID = request.getImageID(); curPixelsID = request.getPixelsID(); registry.getEventBus().post(new RenderImage(curPixelsID)); // have to dispose all windows linked control.disposeDialogs(); } showPresentation(); }

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private void handleImageLoaded(ImageLoaded response) { LoadImage request = (LoadImage) response.getACT(); renderingControl = response.getProxy(); PixelsDimensions pxsDims = renderingControl.getPixelsDims(); //TODO: REMOVE COMMENTS //control.removeProgressNotifier(); if (curImageID != request.getImageID()) { if (presentation == null) buildPresentation(pxsDims); initPresentation(request.getImageName(), pxsDims, false); curImageID = request.getImageID(); curPixelsID = request.getPixelsID(); registry.getEventBus().post(new RenderImage(curPixelsID)); // have to dispose all windows linked control.disposeDialogs(); } showPresentation(); }

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private void handleImageLoaded(ImageLoaded response) { LoadImage request = (LoadImage) response.getACT(); renderingControl = response.getProxy(); PixelsDimensions pxsDims = renderingControl.getPixelsDims(); //TODO: REMOVE COMMENTS //control.removeProgressNotifier(); if (curImageID != request.getImageID()) { if (presentation == null) buildPresentation(pxsDims); initPresentation(request.getImageName(), pxsDims, false); curImageID = request.getImageID(); curPixelsID = request.getPixelsID(); registry.getEventBus().post(new RenderImage(curPixelsID)); // have to dispose all windows linked control.disposeDialogs(); } showPresentation(); }

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private void handleImageRendered(ImageRendered response) { curImage = null; curImage = response.getRenderedImage(); presentation.setImage(curImage); }

private void handleImageRendered(ImageRendered response) { curImage = response.getRenderedImage(); presentation.setImage(curImage); }

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private void initPresentation(String imageName, PixelsDimensions pxsDims, boolean active) { curImageName = imageName; presentation.setDefaultZT(getDefaultT(), getDefaultZ(), pxsDims.sizeT, pxsDims.sizeZ); presentation.setImageName(imageName); presentation.setActive(active); presentation.resetMagFactor(); presentation.setUnitBarSize(pxsDims.pixelSizeX); }

private void initPresentation(String imageName, PixelsDimensions pxsDims, boolean b) { curImageName = imageName; presentation.setDefaultZT(getDefaultT(), getDefaultZ(), pxsDims.sizeT, pxsDims.sizeZ); presentation.setImageName(imageName); presentation.setActive(active); presentation.resetMagFactor(); presentation.setUnitBarSize(pxsDims.pixelSizeX); }

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private void initPresentation(String imageName, PixelsDimensions pxsDims, boolean active) { curImageName = imageName; presentation.setDefaultZT(getDefaultT(), getDefaultZ(), pxsDims.sizeT, pxsDims.sizeZ); presentation.setImageName(imageName); presentation.setActive(active); presentation.resetMagFactor(); presentation.setUnitBarSize(pxsDims.pixelSizeX); }

private void initPresentation(String imageName, PixelsDimensions pxsDims, boolean active) { curImageName = imageName; presentation.setDefaultZT(getDefaultT(), getDefaultZ(), pxsDims.sizeT, pxsDims.sizeZ); presentation.setImageName(imageName); presentation.setImageDisplay(b); presentation.resetMagFactor(); presentation.setUnitBarSize(pxsDims.pixelSizeX); }

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void disposeDialogs() { if (moviePlayer != null) moviePlayer.dispose(); if (imageInspector != null) imageInspector.dispose(); roiOnOff = false; presentation.removeCanvasFromLayer(presentation.getDrawingCanvas()); presentation.getBottomBar().resetMessage(BottomBar.LENS); presentation.getDrawingCanvas().setOnOff(true); moviePlayer = null; imageInspector = null; movieSettings = null; iat.setMagFactor(ImageInspector.ZOOM_DEFAULT); //Need to remove the drawing canvas. and erase all color. // will post an even to kill the ROIAgt. }

void disposeDialogs() { if (moviePlayer != null) moviePlayer.close(); if (imageInspector != null) imageInspector.dispose(); roiOnOff = false; presentation.removeCanvasFromLayer(presentation.getDrawingCanvas()); presentation.getBottomBar().resetMessage(BottomBar.LENS); presentation.getDrawingCanvas().setOnOff(true); moviePlayer = null; imageInspector = null; movieSettings = null; iat.setMagFactor(ImageInspector.ZOOM_DEFAULT); //Need to remove the drawing canvas. and erase all color. // will post an even to kill the ROIAgt. }

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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 q_c = queryFactory.lookup( /* TODO po.map() here */ CollectionCountQueryDefinition.class.getName(), PojosQP.ids(c.getIds(key)), PojosQP.String("field",key) ); List l_c = (List) iQuery.execute(q_c); for (Object o : l_c) { Object[] results = (Object[]) o; Long id = (Long) results[0]; Integer count = (Integer) results[1]; c.addCounts(key,id,count); } } } }

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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 = queryFactory.lookup( "ome.servics.query.FindAnnotationsQueryDefinition", PojosQP.klass(rootNodeType), PojosQP.ids(rootNodeIds), PojosQP.Set("annotatorIds",annotatorIds), PojosQP.options(po.map())); List l = (List) iQuery.execute(q); // no count collection if (Dataset.class.equals(rootNodeType)){ return AnnotationTransformations.sortDatasetAnnotatiosn(new HashSet(l)); } else if (Image.class.equals(rootNodeType)){ return AnnotationTransformations.sortImageAnnotatiosn(new HashSet(l)); } else { throw new IllegalArgumentException( "Class parameter for findAnnotation() must be in " + "{Dataset,Image}, not "+ rootNodeType); } }

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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 = queryFactory.lookup( "ome.servics.query.FindAnnotationsQueryDefinition", PojosQP.klass(rootNodeType), PojosQP.ids(rootNodeIds), PojosQP.Set("annotatorIds",annotatorIds), PojosQP.options(po.map())); List l = (List) iQuery.execute(q); // no count collection if (Dataset.class.equals(rootNodeType)){ return AnnotationTransformations.sortDatasetAnnotatiosn(new HashSet(l)); } else if (Image.class.equals(rootNodeType)){ return AnnotationTransformations.sortImageAnnotatiosn(new HashSet(l)); } else { throw new IllegalArgumentException( "Class parameter for findAnnotation() must be in " + "{Dataset,Image}, not "+ rootNodeType); } }

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 = queryFactory.lookup( PojosFindAnnotationsQueryDefinition.class.getName(), PojosQP.klass(rootNodeType), PojosQP.ids(rootNodeIds), PojosQP.Set("annotatorIds",annotatorIds), PojosQP.options(po.map())); List l = (List) iQuery.execute(q); // no count collection if (Dataset.class.equals(rootNodeType)){ return AnnotationTransformations.sortDatasetAnnotatiosn(new HashSet(l)); } else if (Image.class.equals(rootNodeType)){ return AnnotationTransformations.sortImageAnnotatiosn(new HashSet(l)); } else { throw new IllegalArgumentException( "Class parameter for findAnnotation() must be in " + "{Dataset,Image}, not "+ rootNodeType); } }

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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 = new PojoOptions(options); Query q = queryFactory.lookup( "ome.servics.query.FindCGCPathsQueryDefinition", PojosQP.ids(imgIds), PojosQP.String("algorithm",algorithm), PojosQP.options(po.map())); List<List> result_set = (List) iQuery.execute(q); Map<CategoryGroup,Set<Category>> map = new HashMap<CategoryGroup,Set<Category>>(); Set<CategoryGroup> returnValues = new HashSet<CategoryGroup>(); // Parse for (List result_row : result_set) { CategoryGroup cg = (CategoryGroup) result_row.get(0); Category c = (Category) result_row.get(1); if (!map.containsKey(cg)) map.put(cg,new HashSet<Category>()); map.get(cg).add(c); } for (CategoryGroup cg : map.keySet()) { for (Category c : map.get(cg)) { iQuery.evict(cg); // FIXME does this suffice? cg.addCategory(c); } returnValues.add(cg); } collectCounts(returnValues,po); return returnValues; }

public Set findCGCPaths(@NotNull @Validate(Long.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 = new PojoOptions(options); Query q = queryFactory.lookup( "ome.servics.query.FindCGCPathsQueryDefinition", PojosQP.ids(imgIds), PojosQP.String("algorithm",algorithm), PojosQP.options(po.map())); List<List> result_set = (List) iQuery.execute(q); Map<CategoryGroup,Set<Category>> map = new HashMap<CategoryGroup,Set<Category>>(); Set<CategoryGroup> returnValues = new HashSet<CategoryGroup>(); // Parse for (List result_row : result_set) { CategoryGroup cg = (CategoryGroup) result_row.get(0); Category c = (Category) result_row.get(1); if (!map.containsKey(cg)) map.put(cg,new HashSet<Category>()); map.get(cg).add(c); } for (CategoryGroup cg : map.keySet()) { for (Category c : map.get(cg)) { iQuery.evict(cg); // FIXME does this suffice? cg.addCategory(c); } returnValues.add(cg); } collectCounts(returnValues,po); return returnValues; }

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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 = new PojoOptions(options); Query q = queryFactory.lookup( "ome.servics.query.FindCGCPathsQueryDefinition", PojosQP.ids(imgIds), PojosQP.String("algorithm",algorithm), PojosQP.options(po.map())); List<List> result_set = (List) iQuery.execute(q); Map<CategoryGroup,Set<Category>> map = new HashMap<CategoryGroup,Set<Category>>(); Set<CategoryGroup> returnValues = new HashSet<CategoryGroup>(); // Parse for (List result_row : result_set) { CategoryGroup cg = (CategoryGroup) result_row.get(0); Category c = (Category) result_row.get(1); if (!map.containsKey(cg)) map.put(cg,new HashSet<Category>()); map.get(cg).add(c); } for (CategoryGroup cg : map.keySet()) { for (Category c : map.get(cg)) { iQuery.evict(cg); // FIXME does this suffice? cg.addCategory(c); } returnValues.add(cg); } collectCounts(returnValues,po); return returnValues; }

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 = new PojoOptions(options); Query q = queryFactory.lookup( PojosCGCPathsQueryDefinition.class.getName(), PojosQP.ids(imgIds), PojosQP.String("algorithm",algorithm), PojosQP.options(po.map())); List<List> result_set = (List) iQuery.execute(q); Map<CategoryGroup,Set<Category>> map = new HashMap<CategoryGroup,Set<Category>>(); Set<CategoryGroup> returnValues = new HashSet<CategoryGroup>(); // Parse for (List result_row : result_set) { CategoryGroup cg = (CategoryGroup) result_row.get(0); Category c = (Category) result_row.get(1); if (!map.containsKey(cg)) map.put(cg,new HashSet<Category>()); map.get(cg).add(c); } for (CategoryGroup cg : map.keySet()) { for (Category c : map.get(cg)) { iQuery.evict(cg); // FIXME does this suffice? cg.addCategory(c); } returnValues.add(cg); } collectCounts(returnValues,po); return returnValues; }

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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 = new PojoOptions(options); Query q = queryFactory.lookup( "ome.servics.query.FindCGCPathsQueryDefinition", PojosQP.ids(imgIds), PojosQP.String("algorithm",algorithm), PojosQP.options(po.map())); List<List> result_set = (List) iQuery.execute(q); Map<CategoryGroup,Set<Category>> map = new HashMap<CategoryGroup,Set<Category>>(); Set<CategoryGroup> returnValues = new HashSet<CategoryGroup>(); // Parse for (List result_row : result_set) { CategoryGroup cg = (CategoryGroup) result_row.get(0); Category c = (Category) result_row.get(1); if (!map.containsKey(cg)) map.put(cg,new HashSet<Category>()); map.get(cg).add(c); } for (CategoryGroup cg : map.keySet()) { for (Category c : map.get(cg)) { iQuery.evict(cg); // FIXME does this suffice? cg.addCategory(c); } returnValues.add(cg); } collectCounts(returnValues,po); return returnValues; }

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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(), PojosQP.klass(rootNodeType), PojosQP.ids(imageIds), PojosQP.options(po.map())); List l = (List) iQuery.execute(q); collectCounts(l,po); // TODO; this if-else statement could be removed if Transformations // did their own dispatching // TODO: logging, null checking. daos should never return null // TODO then size! if (Project.class.equals(rootNodeType)) { if (imageIds.size()==0){ return new HashSet(); } return HierarchyTransformations.invertPDI(new HashSet(l)); } else if (CategoryGroup.class.equals(rootNodeType)){ if (imageIds.size()==0){ return new HashSet(); } return HierarchyTransformations.invertCGCI(new HashSet(l)); } else {throw new IllegalArgumentException( "Class parameter for findContainerHierarchies() must be" + " in {Project,CategoryGroup}, not " + rootNodeType); } }

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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(), PojosQP.klass(rootNodeType), PojosQP.ids(imageIds), PojosQP.options(po.map())); List l = (List) iQuery.execute(q); collectCounts(l,po); // TODO; this if-else statement could be removed if Transformations // did their own dispatching // TODO: logging, null checking. daos should never return null // TODO then size! if (Project.class.equals(rootNodeType)) { if (imageIds.size()==0){ return new HashSet(); } return HierarchyTransformations.invertPDI(new HashSet(l)); } else if (CategoryGroup.class.equals(rootNodeType)){ if (imageIds.size()==0){ return new HashSet(); } return HierarchyTransformations.invertCGCI(new HashSet(l)); } else {throw new IllegalArgumentException( "Class parameter for findContainerHierarchies() must be" + " in {Project,CategoryGroup}, not " + rootNodeType); } }

public for (Object object : l) { iQuery.evict(object); } Set for (Object object : l) { iQuery.evict(object); } findContainerHierarchies(@NotNull for (Object object : l) { iQuery.evict(object); } Class for (Object object : l) { iQuery.evict(object); } rootNodeType, for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } @NotNull for (Object object : l) { iQuery.evict(object); } @Validate(Integer.class) for (Object object : l) { iQuery.evict(object); } Set for (Object object : l) { iQuery.evict(object); } imageIds, for (Object object : l) { iQuery.evict(object); } Map for (Object object : l) { iQuery.evict(object); } options) for (Object object : l) { iQuery.evict(object); } { PojoOptions for (Object object : l) { iQuery.evict(object); } po for (Object object : l) { iQuery.evict(object); } = for (Object object : l) { iQuery.evict(object); } new for (Object object : l) { iQuery.evict(object); } PojoOptions(options); for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } Query for (Object object : l) { iQuery.evict(object); } q for (Object object : l) { iQuery.evict(object); } = for (Object object : l) { iQuery.evict(object); } queryFactory.lookup( for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } PojosFindHierarchiesQueryDefinition.class.getName(), for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } PojosQP.klass(rootNodeType), for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } PojosQP.ids(imageIds), for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } PojosQP.options(po.map())); for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } List for (Object object : l) { iQuery.evict(object); } l for (Object object : l) { iQuery.evict(object); } = for (Object object : l) { iQuery.evict(object); } (List) for (Object object : l) { iQuery.evict(object); } iQuery.execute(q); for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } collectCounts(l,po); for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } // for (Object object : l) { iQuery.evict(object); } TODO; for (Object object : l) { iQuery.evict(object); } this for (Object object : l) { iQuery.evict(object); } if-else for (Object object : l) { iQuery.evict(object); } statement for (Object object : l) { iQuery.evict(object); } could for (Object object : l) { iQuery.evict(object); } be for (Object object : l) { iQuery.evict(object); } removed for (Object object : l) { iQuery.evict(object); } if for (Object object : l) { iQuery.evict(object); } Transformations for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } // for (Object object : l) { iQuery.evict(object); } did for (Object object : l) { iQuery.evict(object); } their for (Object object : l) { iQuery.evict(object); } own for (Object object : l) { iQuery.evict(object); } dispatching for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } // for (Object object : l) { iQuery.evict(object); } TODO: for (Object object : l) { iQuery.evict(object); } logging, for (Object object : l) { iQuery.evict(object); } null for (Object object : l) { iQuery.evict(object); } checking. for (Object object : l) { iQuery.evict(object); } daos for (Object object : l) { iQuery.evict(object); } should for (Object object : l) { iQuery.evict(object); } never for (Object object : l) { iQuery.evict(object); } return for (Object object : l) { iQuery.evict(object); } null for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } // for (Object object : l) { iQuery.evict(object); } TODO for (Object object : l) { iQuery.evict(object); } then for (Object object : l) { iQuery.evict(object); } size! if for (Object object : l) { iQuery.evict(object); } (Project.class.equals(rootNodeType)) for (Object object : l) { iQuery.evict(object); } { if for (Object object : l) { iQuery.evict(object); } (imageIds.size()==0){ return for (Object object : l) { iQuery.evict(object); } new for (Object object : l) { iQuery.evict(object); } HashSet(); } return for (Object object : l) { iQuery.evict(object); } HierarchyTransformations.invertPDI(new for (Object object : l) { iQuery.evict(object); } HashSet(l)); for (Object object : l) { iQuery.evict(object); } } else for (Object object : l) { iQuery.evict(object); } if for (Object object : l) { iQuery.evict(object); } (CategoryGroup.class.equals(rootNodeType)){ if for (Object object : l) { iQuery.evict(object); } (imageIds.size()==0){ return for (Object object : l) { iQuery.evict(object); } new for (Object object : l) { iQuery.evict(object); } HashSet(); } return for (Object object : l) { iQuery.evict(object); } HierarchyTransformations.invertCGCI(new for (Object object : l) { iQuery.evict(object); } HashSet(l)); for (Object object : l) { iQuery.evict(object); } } else for (Object object : l) { iQuery.evict(object); } {throw for (Object object : l) { iQuery.evict(object); } new for (Object object : l) { iQuery.evict(object); } IllegalArgumentException( for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } "Class for (Object object : l) { iQuery.evict(object); } parameter for (Object object : l) { iQuery.evict(object); } for for (Object object : l) { iQuery.evict(object); } findContainerHierarchies() for (Object object : l) { iQuery.evict(object); } must for (Object object : l) { iQuery.evict(object); } be" for (Object object : l) { iQuery.evict(object); } + for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } for (Object object : l) { iQuery.evict(object); } " for (Object object : l) { iQuery.evict(object); } in for (Object object : l) { iQuery.evict(object); } {Project,CategoryGroup}, for (Object object : l) { iQuery.evict(object); } not for (Object object : l) { iQuery.evict(object); } " for (Object object : l) { iQuery.evict(object); } + for (Object object : l) { iQuery.evict(object); } rootNodeType); } }

3,235,637

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(), PojosQP.klass(rootNodeType), PojosQP.ids(imageIds), PojosQP.options(po.map())); List l = (List) iQuery.execute(q); collectCounts(l,po); // TODO; this if-else statement could be removed if Transformations // did their own dispatching // TODO: logging, null checking. daos should never return null // TODO then size! if (Project.class.equals(rootNodeType)) { if (imageIds.size()==0){ return new HashSet(); } return HierarchyTransformations.invertPDI(new HashSet(l)); } else if (CategoryGroup.class.equals(rootNodeType)){ if (imageIds.size()==0){ return new HashSet(); } return HierarchyTransformations.invertCGCI(new HashSet(l)); } else {throw new IllegalArgumentException( "Class parameter for findContainerHierarchies() must be" + " in {Project,CategoryGroup}, not " + rootNodeType); } }

3,235,638

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 if (!type.matches(alphaNumericDotted)) { throw new IllegalArgumentException("Type argument to getCollectionCount may ONLY be alpha-numeric with dots ("+alphaNumericDotted+")"); } 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)) { throw new IllegalArgumentException(type+"."+property+" is an unknown property on type "+type); } String query = "select size(table."+property+") from "+type+" table where table.id = ?"; // FIXME: optimize by doing new list(id,size(table.property)) ... group by id for (Iterator iter = ids.iterator(); iter.hasNext();) { Integer id = (Integer) iter.next(); Integer count = (Integer) iQuery.queryUnique(query,new Object[]{id}); results.put(id,count); } return results; }

public Map getCollectionCount(@NotNull String type, @NotNull String property, @NotNull @Validate(Long.class) Set ids, Map options) { Map results = new HashMap(); String alphaNumeric = "^\\w+$"; String alphaNumericDotted = "^\\w[.\\w]+$"; // TODO annotations if (!type.matches(alphaNumericDotted)) { throw new IllegalArgumentException("Type argument to getCollectionCount may ONLY be alpha-numeric with dots ("+alphaNumericDotted+")"); } 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)) { throw new IllegalArgumentException(type+"."+property+" is an unknown property on type "+type); } String query = "select size(table."+property+") from "+type+" table where table.id = ?"; // FIXME: optimize by doing new list(id,size(table.property)) ... group by id for (Iterator iter = ids.iterator(); iter.hasNext();) { Integer id = (Integer) iter.next(); Integer count = (Integer) iQuery.queryUnique(query,new Object[]{id}); results.put(id,count); } return results; }

3,235,639

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 if (!type.matches(alphaNumericDotted)) { throw new IllegalArgumentException("Type argument to getCollectionCount may ONLY be alpha-numeric with dots ("+alphaNumericDotted+")"); } 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)) { throw new IllegalArgumentException(type+"."+property+" is an unknown property on type "+type); } String query = "select size(table."+property+") from "+type+" table where table.id = ?"; // FIXME: optimize by doing new list(id,size(table.property)) ... group by id for (Iterator iter = ids.iterator(); iter.hasNext();) { Integer id = (Integer) iter.next(); Integer count = (Integer) iQuery.queryUnique(query,new Object[]{id}); results.put(id,count); } return results; }

3,235,640

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 if (!type.matches(alphaNumericDotted)) { throw new IllegalArgumentException("Type argument to getCollectionCount may ONLY be alpha-numeric with dots ("+alphaNumericDotted+")"); } 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)) { throw new IllegalArgumentException(type+"."+property+" is an unknown property on type "+type); } String query = "select size(table."+property+") from "+type+" table where table.id = ?"; // FIXME: optimize by doing new list(id,size(table.property)) ... group by id for (Iterator iter = ids.iterator(); iter.hasNext();) { Integer id = (Integer) iter.next(); Integer count = (Integer) iQuery.queryUnique(query,new Object[]{id}); results.put(id,count); } return results; }

3,235,641

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 if (!type.matches(alphaNumericDotted)) { throw new IllegalArgumentException("Type argument to getCollectionCount may ONLY be alpha-numeric with dots ("+alphaNumericDotted+")"); } 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)) { throw new IllegalArgumentException(type+"."+property+" is an unknown property on type "+type); } String query = "select size(table."+property+") from "+type+" table where table.id = ?"; // FIXME: optimize by doing new list(id,size(table.property)) ... group by id for (Iterator iter = ids.iterator(); iter.hasNext();) { Integer id = (Integer) iter.next(); Integer count = (Integer) iQuery.queryUnique(query,new Object[]{id}); results.put(id,count); } return results; }

3,235,642

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 if (!type.matches(alphaNumericDotted)) { throw new IllegalArgumentException("Type argument to getCollectionCount may ONLY be alpha-numeric with dots ("+alphaNumericDotted+")"); } 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)) { throw new IllegalArgumentException(type+"."+property+" is an unknown property on type "+type); } String query = "select size(table."+property+") from "+type+" table where table.id = ?"; // FIXME: optimize by doing new list(id,size(table.property)) ... group by id for (Iterator iter = ids.iterator(); iter.hasNext();) { Integer id = (Integer) iter.next(); Integer count = (Integer) iQuery.queryUnique(query,new Object[]{id}); results.put(id,count); } return results; }

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 if (!type.matches(alphaNumericDotted)) { throw new IllegalArgumentException("Type argument to getCollectionCount may ONLY be alpha-numeric with dots ("+alphaNumericDotted+")"); } 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)) { throw new IllegalArgumentException(type+"."+property+" is an unknown property on type "+type); } String query = "select size(table."+property+") from "+type+" table where table.id = ?"; // FIXME: optimize by doing new list(id,size(table.property)) ... group by id for (Iterator iter = ids.iterator(); iter.hasNext();) { Long id = (Long) iter.next(); Integer count = (Integer) iQuery.queryUnique(query,new Object[]{id}); results.put(id,count); } return results; }

3,235,643

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.GetImagesQueryDefinition", PojosQP.klass(rootNodeType), PojosQP.ids(rootNodeIds), PojosQP.options(po.map())); List l = (List) iQuery.execute(q); collectCounts(l,po); return new HashSet(l); }

3,235,644

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.GetImagesQueryDefinition", PojosQP.klass(rootNodeType), PojosQP.ids(rootNodeIds), PojosQP.options(po.map())); List l = (List) iQuery.execute(q); collectCounts(l,po); return new HashSet(l); }

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( PojosGetImagesQueryDefinition.class.getName(), PojosQP.klass(rootNodeType), PojosQP.ids(rootNodeIds), PojosQP.options(po.map())); List l = (List) iQuery.execute(q); collectCounts(l,po); return new HashSet(l); }

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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, Set> params = new HashMap<String, Set>(); params.put("name_list",names); results = iQuery.queryListMap( "select e from Experimenter e " + "left outer join fetch e.group " + "left outer join fetch e.groups " + "where e.omeName in ( :name_list )", params ); for (Object object : results) { Experimenter e = (Experimenter) object; map.put(e.getOmeName(),e); } } /* ensures all ids appear in map */ for (Object object : names) { String name = (String) object; if (! map.containsKey(name)){ map.put(name,null); } } return map; }

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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( "ome.servics.query.GetImagesQueryDefinition", PojosQP.options(po.map())); List l = (List) iQuery.execute(q); collectCounts(l,po); return new HashSet(l); }

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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 loadContainerHierarchy() may not be null " + "if experimenter and group options are null."); if (! Project.class.equals(rootNodeType) && ! Dataset.class.equals(rootNodeType) && ! CategoryGroup.class.equals(rootNodeType) && ! Category.class.equals(rootNodeType)) throw new IllegalArgumentException( "Class parameter for loadContainerIHierarchy() must be in " + "{Project,Dataset,Category,CategoryGroup}, not " + rootNodeType); Query q = queryFactory.lookup( PojosLoadHierarchyQueryDefinition.class.getName(), PojosQP.klass(rootNodeType), PojosQP.ids(rootNodeIds), PojosQP.options(po.map())); // TODO Move PojosQP to PojosOptions List l = (List) iQuery.execute(q); collectCounts(l, po); return new HashSet(l); }

public Set loadContainerHierarchy(Class rootNodeType, @Validate(Long.class) Set rootNodeIds, Map options) { PojoOptions po = new PojoOptions(options); if (null==rootNodeIds && !po.isExperimenter()) throw new IllegalArgumentException( "Set of ids for loadContainerHierarchy() may not be null " + "if experimenter and group options are null."); if (! Project.class.equals(rootNodeType) && ! Dataset.class.equals(rootNodeType) && ! CategoryGroup.class.equals(rootNodeType) && ! Category.class.equals(rootNodeType)) throw new IllegalArgumentException( "Class parameter for loadContainerIHierarchy() must be in " + "{Project,Dataset,Category,CategoryGroup}, not " + rootNodeType); Query q = queryFactory.lookup( PojosLoadHierarchyQueryDefinition.class.getName(), PojosQP.klass(rootNodeType), PojosQP.ids(rootNodeIds), PojosQP.options(po.map())); // TODO Move PojosQP to PojosOptions List l = (List) iQuery.execute(q); collectCounts(l, po); return new HashSet(l); }

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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 }

public Collection retrieveCollection(IObject arg0, String arg1, Map arg2) { IObject context = (IObject) iQuery.getById(arg0.getClass(),arg0.getId()); Collection c = (Collection) context.retrieve(arg1); iQuery.initialize(c); return c; // FIXME not type.o.null safe }

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private void datasetNodeNavigation(DatasetData d, DefaultMutableTreeNode node, boolean isExpanding) { DefaultTreeModel treeModel = (DefaultTreeModel) view.tree.getModel(); Integer datasetID = new Integer(d.getId()); node.removeAllChildren(); if (isExpanding) { Set images = agentCtrl.getImages(d.getId()); //TODO: loading will never be displayed b/c we are in the // same thread. if (images.size() != 0) { addNodesToDatasetMaps(datasetID, node, images); addImagesToDataset(images, node); } else treeModel.insertNodeInto(new DefaultMutableTreeNode(EMPTY), node, node.getChildCount()); } else treeModel.insertNodeInto(new DefaultMutableTreeNode(LOADING), node, node.getChildCount()); treeModel.reload(node); }

private void datasetNodeNavigation(DatasetData d, DefaultMutableTreeNode node, boolean isExpanding) { DefaultTreeModel treeModel = (DefaultTreeModel) view.tree.getModel(); Integer datasetID = new Integer(d.getId()); node.removeAllChildren(); if (isExpanding) { Set images = agentCtrl.getImages(d.getId()); //TODO: loading will never be displayed b/c we are in the // same thread. if (images.size() != 0) { addNodesToDatasetMaps(datasetID, node, images); addImagesToDataset(images, node); } else { treeModel.insertNodeInto(new DefaultMutableTreeNode(EMPTY), node, node.getChildCount()); } else { treeModel.insertNodeInto(new DefaultMutableTreeNode(LOADING), node, node.getChildCount()); treeModel.reload(node); }

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private void datasetNodeNavigation(DatasetData d, DefaultMutableTreeNode node, boolean isExpanding) { DefaultTreeModel treeModel = (DefaultTreeModel) view.tree.getModel(); Integer datasetID = new Integer(d.getId()); node.removeAllChildren(); if (isExpanding) { Set images = agentCtrl.getImages(d.getId()); //TODO: loading will never be displayed b/c we are in the // same thread. if (images.size() != 0) { addNodesToDatasetMaps(datasetID, node, images); addImagesToDataset(images, node); } else treeModel.insertNodeInto(new DefaultMutableTreeNode(EMPTY), node, node.getChildCount()); } else treeModel.insertNodeInto(new DefaultMutableTreeNode(LOADING), node, node.getChildCount()); treeModel.reload(node); }

private void datasetNodeNavigation(DatasetData d, DefaultMutableTreeNode node, boolean isExpanding) { DefaultTreeModel treeModel = (DefaultTreeModel) view.tree.getModel(); Integer datasetID = new Integer(d.getId()); node.removeAllChildren(); if (isExpanding) { Set images = agentCtrl.getImages(d.getId()); //TODO: loading will never be displayed b/c we are in the // same thread. if (images.size() != 0) { addNodesToDatasetMaps(datasetID, node, images); addImagesToDataset(images, node); } else treeModel.insertNodeInto(new DefaultMutableTreeNode(EMPTY), node, node.getChildCount()); } } else treeModel.insertNodeInto(new DefaultMutableTreeNode(LOADING), node, node.getChildCount()); } treeModel.reload(node); }

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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 Proc."); } recv.getRuntime().getRuntime().setTraceFunction((RubyProc) trace_func); return 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 Proc."); } return trace_func; }

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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.isBlockGiven()) { // We pass depth zero since we know this only applies to newly created local scope blockArg = runtime.newProc(); blockArg.getBlock().isLambda = context.getCurrentBlock().isLambda; context.getCurrentScope().setValue(argsNode.getBlockArgNode().getCount(), blockArg, 0); } try { prepareArguments(context, runtime, receiver, args); getArity().checkArity(runtime, args); traceCall(context, runtime, receiver, name); return EvaluationState.eval(context, body, receiver); } catch (JumpException je) { if (je.getJumpType() == JumpException.JumpType.ReturnJump) { if (je.getPrimaryData() == this) { return (IRubyObject)je.getSecondaryData(); } } throw je; } finally { traceReturn(context, runtime, receiver, name); } }

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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 RubyList(args); argsList.remove(args.length - 1); RubyObject val = recv.funcall(ruby.intern("[]"), argsList.toRubyArray()); switch (getMId().intValue()) { case 0: /* OR */ if (val.isTrue()) { return val; } else { val = rval.eval(ruby, self); } break; case 1: /* AND */ if (val.isFalse()) { return val; } else { val = rval.eval(ruby, self); } break; default: val = val.funcall(getMId(), rval.eval(ruby, self)); } args[args.length - 1] = val; return recv.funcall(ruby.intern("[]="), args); }

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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 RubyList(args); argsList.remove(args.length - 1); RubyObject val = recv.funcall(ruby.intern("[]"), argsList.toRubyArray()); switch (getMId().intValue()) { case 0: /* OR */ if (val.isTrue()) { return val; } else { val = rval.eval(ruby, self); } break; case 1: /* AND */ if (val.isFalse()) { return val; } else { val = rval.eval(ruby, self); } break; default: val = val.funcall(getMId(), rval.eval(ruby, self)); } args[args.length - 1] = val; return 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 RubyList(args); argsList.remove(args.length - 1); RubyObject val = recv.funcall(ruby.intern("[]"), argsList.toRubyArray()); switch (getMId().intValue()) { case 0: /* OR */ if (val.isTrue()) { return val; } else { val = rval.eval(ruby, self); } break; case 1: /* AND */ if (val.isFalse()) { return val; } else { val = rval.eval(ruby, self); } break; default: val = val.funcall(getMId(), rval.eval(ruby, self)); } args.set(args.size() - 1, val); return recv.funcall(ruby.intern("[]="), args); }

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private void performSearch() { int index = view.getSearchType(); String regEx = view.getSearchValue(); FindRegExCmd cmd = new FindRegExCmd(view.model.getParentModel(), regEx, index); cmd.execute(); }

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public void handleCancellation() { String info = "The data saving has been cancelled."; registry.getLogger().info(this, info); registry.getUserNotifier().notifyInfo("Data Saving Cancellation", info); }

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public List childNodes() { return Collections.EMPTY_LIST; }

public List childNodes() { return EMPTY_LIST; }

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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); return args; }

public static RubyPointer 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); return args; }

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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); return args; }

public static RubyObject[] setupArgs(Ruby ruby, RubyObject self, ArrayNode node) { String file = ruby.getSourceFile(); int line = ruby.getSourceLine(); RubyPointer args = new RubyPointer(node.getArrayList(ruby, self)); ruby.setSourceFile(file); ruby.setSourceLine(line); return args; }

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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); }

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 result; }

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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); ruby.defineReadonlyVariable("$VERBOSE", warning ? ruby.getTrue() : ruby.getNil()); ruby.defineGlobalConstant("ARGV", lArgv); ruby.defineReadonlyVariable("$-p", (sDoPrint ? ruby.getTrue() : ruby.getNil())); ruby.defineReadonlyVariable("$-n", (sDoLoop ? ruby.getTrue() : ruby.getNil())); ruby.defineReadonlyVariable("$-a", (sDoSplit ? ruby.getTrue() : ruby.getNil())); ruby.defineReadonlyVariable("$-l", (sDoLine ? ruby.getTrue() : ruby.getNil())); ruby.defineReadonlyVariable("$*", lArgv); ruby.defineVariable(new RubyGlobal.StringGlobalVariable(ruby, "$0", RubyString.newString(ruby, iFileName))); ruby.initLoad(sLoadDirectories); //require additional libraries int lNbRequire = sRequireFirst.size(); try { for (int i = 0; i < lNbRequire; i++) RubyKernel.require(ruby.getRubyTopSelf(), new RubyString(ruby, (String) sRequireFirst.get(i))); // +++ INode lScript = ruby.parse(iReader2Eval, iFileName); // DumpVisitor laVisitor = new DumpVisitor(); // lScript.accept(laVisitor); // ruby.getRuntime().getOutputStream().println(laVisitor.dump()); if (sDoPrint) { // FIXME lScript = new ParserSupport().appendPrintToBlock(lScript); // ruby.getParserHelper().rb_parser_append_print(); } if (sDoLoop) { // FIXME lScript = new ParserSupport().appendWhileLoopToBlock(lScript, sDoLine, sDoSplit); // ruby.getParserHelper().rb_parser_while_loop(sDoLine, sDoSplit); } if (sCheckOnly) { DumpVisitor lVisitor = new DumpVisitor(); lScript.accept(lVisitor); ruby.getRuntime().getOutputStream().println(lVisitor.dump()); } else { ruby.eval(lScript); } } catch (RaiseException rExcptn) { ruby.getRuntime().printError(rExcptn.getException()); } catch (ThrowJump throwJump) { ruby.getRuntime().printError(throwJump.getNameError()); } catch (RubyBugException lBug) { ruby.getRuntime().getErrorStream().print(lBug.getMessage()); } }

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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 textFound = tokenizer.nextToken(); if (textFound.startsWith("http://") || textFound.startsWith("ftp://") || textFound.startsWith("https://") || textFound.startsWith("www.") || textFound.startsWith("\\") || textFound.indexOf("://") != -1) { builder.append("<a href=\"").append(textFound).append("\" target=_blank>").append(textFound).append("</a>"); } else if (emoticonManager.getEmoticon(textFound) != null) { Emoticon emot = emoticonManager.getEmoticon(textFound); URL url = emoticonManager.getEmoticonURL(emot); File file = URLFileSystem.url2File(url); builder.append("<img src=\"").append(url.toExternalForm()).append("\" />"); } else { builder.append(textFound); } } return builder.toString(); }

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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()); return model; } else if (child instanceof CategoryGroupData) { CategoryGroupData data = (CategoryGroupData) child; CategoryGroup model = new CategoryGroup(); model.setName(data.getName()); model.setDescription(data.getDescription()); return model; } else if (child instanceof DatasetData) { if (!(parent instanceof ProjectData)) throw new IllegalArgumentException("Parent not valid."); DatasetData data = (DatasetData) child; Dataset model = new Dataset(); model.setName(data.getName()); model.setDescription(data.getDescription()); model.linkProject(new Project(new Long(parent.getId()), false)); return model; } else if (child instanceof CategoryData) { if (!(parent instanceof CategoryGroupData)) throw new IllegalArgumentException("Parent not valid."); CategoryData data = (CategoryData) child; Category model = new Category(); model.setName(data.getName()); model.setDescription(data.getDescription()); model.linkCategoryGroup(new CategoryGroup(new Long(parent.getId()), false)); return model; } else if (child instanceof ImageData) { if (!(parent instanceof CategoryData) && !(parent instanceof DatasetData)) throw new IllegalArgumentException("Parent not valid."); ImageData data = (ImageData) child; Image model = new Image(); model.setName(data.getName()); model.setDescription(data.getDescription()); if (parent instanceof CategoryData) model.linkCategory(new Category(new Long(parent.getId()), false)); else if (parent instanceof DatasetData) model.linkDataset(new Dataset(new Long(parent.getId()), false)); return model; } throw new IllegalArgumentException("DataObject not supported."); }

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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)) throw new IllegalArgumentException("Child not valid."); Project p = (Project) parent; Dataset d = (Dataset) child; ProjectDatasetLink link; Iterator it = d.iterateProjectLinks(); while (it.hasNext()) { link = (ProjectDatasetLink) it.next(); if (p.getId().equals(link.parent().getId())) p.addProjectDatasetLink(link, false); } } else if (parent instanceof CategoryGroup) { if (!(child instanceof Category)) throw new IllegalArgumentException("Child not valid."); CategoryGroup p = (CategoryGroup) parent; Category d = (Category) child; CategoryGroupCategoryLink link; Iterator it = d.iterateCategoryGroupLinks(); while (it.hasNext()) { link = (CategoryGroupCategoryLink) it.next(); if (p.getId().equals(link.parent().getId())) p.addCategoryGroupCategoryLink(link, false); } } else if (parent instanceof Dataset) { if (!(child instanceof Image)) throw new IllegalArgumentException("Child not valid."); Dataset p = (Dataset) parent; Image d = (Image) child; DatasetImageLink link; Iterator it = d.iterateDatasetLinks(); while (it.hasNext()) { link = (DatasetImageLink) it.next(); if (p.getId().equals(link.parent().getId())) p.addDatasetImageLink(link, false); } } else if (parent instanceof Category) { if (!(child instanceof Image)) throw new IllegalArgumentException("Child not valid."); Category p = (Category) parent; Image d = (Image) child; CategoryImageLink link; Iterator it = d.iterateCategoryLinks(); while (it.hasNext()) { link = (CategoryImageLink) it.next(); if (p.getId().equals(link.parent().getId())) p.addCategoryImageLink(link, false); } } throw new IllegalArgumentException("DataObject not supported."); }

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public MockServiceFactory() throws NullPointerException { super(SERVICE); }

private MockServiceFactory() throws NullPointerException { super(SERVICE); }

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public ISourcePosition getPosition(ISourcePosition startPosition) { return src.getPosition(startPosition); }

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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 = (ImageData) (((TreeImageDisplay) o1).getUserObject()); ImageData i2 = (ImageData) (((TreeImageDisplay) o2).getUserObject()); int r = i1.getInserted().compareTo(i2.getInserted()); int v = 0; if (r < 0) v = -1; else if (r > 0) v = 1; if (ascending) return v; return -v; } }; break; case Browser.SORT_NODES_BY_NAME: default: c = new Comparator() { public int compare(Object o1, Object o2) { String s1 = o1.toString().toLowerCase(); String s2 = o2.toString().toLowerCase(); int result = s1.compareTo(s2); int v = 0; if (result < 0) v = -1; else if (result > 0) v = 1; if (ascending) return v; return -v; } }; } Collections.sort(nodes, c); return nodes; }

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 = (ImageData) (((TreeImageDisplay) o1).getUserObject()); ImageData i2 = (ImageData) (((TreeImageDisplay) o2).getUserObject()); 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); int v = 0; if (r < 0) v = -1; else if (r > 0) v = 1; if (ascending) return v; return -v; } }; break; case Browser.SORT_NODES_BY_NAME: default: c = new Comparator() { public int compare(Object o1, Object o2) { String s1 = o1.toString().toLowerCase(); String s2 = o2.toString().toLowerCase(); int result = s1.compareTo(s2); int v = 0; if (result < 0) v = -1; else if (result > 0) v = 1; if (ascending) return v; return -v; } }; } Collections.sort(nodes, c); return nodes; }

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public int compare(Object o1, Object o2) { ImageData i1 = (ImageData) (((TreeImageDisplay) o1).getUserObject()); ImageData i2 = (ImageData) (((TreeImageDisplay) o2).getUserObject()); int r = i1.getInserted().compareTo(i2.getInserted()); int v = 0; if (r < 0) v = -1; else if (r > 0) v = 1; if (ascending) return v; return -v; }

public int compare(Object o1, Object o2) { ImageData i1 = (ImageData) (((TreeImageDisplay) o1).getUserObject()); ImageData i2 = (ImageData) (((TreeImageDisplay) o2).getUserObject()); 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); int v = 0; if (r < 0) v = -1; else if (r > 0) v = 1; if (ascending) return v; return -v; }

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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: checkFieldValue(R_AREA); break; case G_AREA: checkFieldValue(G_AREA); break; case B_AREA: checkFieldValue(B_AREA); }// end switch } catch(NumberFormatException nfe) { throw nfe; //just to be on the safe side... } }

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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(); if (valRed == null || !valRed.equals(red)) view.getRArea().setText(red); if (valGreen == null || !valGreen.equals(green)) view.getGArea().setText(green); if (valBlue == null || !valBlue.equals(blue)) view.getBArea().setText(blue); }

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public Object getData() { LocalPreferences pref = SettingsManager.getLocalPreferences(); String nickname = pref.getDefaultNickname(); if (nickname == null) { nickname = SparkManager.getSessionManager().getUsername(); } boolean showTime = pref.isTimeDisplayedInChat(); preferences.showDatesInChat(showTime); return preferences; }

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public IDataSet getData() throws Exception { return new XmlDataSet(new FileInputStream("sql/db-export.xml")); }

public IDataSet getData() throws Exception { URL file = this.getClass().getClassLoader().getResource("db-export.xml"); return new XmlDataSet(new FileInputStream(file.getFile())); }

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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.getBean("dataSource"); } if (null==c) { c = new DatabaseConnection(ds.getConnection()); DatabaseOperation.CLEAN_INSERT.execute(c,getData()); } }

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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.getBean("dataSource"); } if (null==c) { c = new DatabaseConnection(ds.getConnection()); DatabaseOperation.CLEAN_INSERT.execute(c,getData()); } }

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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 img = (Image) i.next(); assertTrue("Fully initialized",Hibernate.isInitialized(img.getDatasets())); } }

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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 img = (Image) i.next(); assertTrue("Fully initialized",Hibernate.isInitialized(img.getDatasets())); } }

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 img = (Image) i.next(); 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())); } } }

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public void respondMouseClick(PInputEvent event) { getParent().removeChild(this); t.respondMouseClick(pushParentNode(event,t)); }

public void respondMouseClick(PInputEvent event) { if(getParent() != null) getParent().removeChild(this); t.respondMouseClick(pushParentNode(event,t)); }

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public void respondMouseDoubleClick(PInputEvent event) { getParent().removeChild(this); t.respondMouseDoubleClick(pushParentNode(event,t)); }

public void respondMouseDoubleClick(PInputEvent event) { if(getParent() != null) getParent().removeChild(this); t.respondMouseDoubleClick(pushParentNode(event,t)); }

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public void respondMousePress(PInputEvent event) { getParent().removeChild(this); t.respondMousePress(pushParentNode(event,t)); }

public void respondMousePress(PInputEvent event) { if(getParent() != null) getParent().removeChild(this); t.respondMousePress(pushParentNode(event,t)); }

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public void respondMouseRelease(PInputEvent event) { getParent().removeChild(this); t.respondMouseRelease(pushParentNode(event,t)); }

public void respondMouseRelease(PInputEvent event) { if(getParent() != null) getParent().removeChild(this); t.respondMouseRelease(pushParentNode(event,t)); }

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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; }

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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 HashSet(Arrays.asList(new Dataset[]{d1,d2,d2})));// d1.setImages(new HashSet(Arrays.asList(new Image[]{i1})));// d2.setImages(new HashSet(Arrays.asList(new Image[]{i2})));// d3.setImages(new HashSet(Arrays.asList(new Image[]{i3})));// i1.setCreated(new Date());// i2.setInserted(new Date());// i1.setDatasets(new HashSet(Arrays.asList(new Dataset[]{d1})));// i2.setDatasets(new HashSet(Arrays.asList(new Dataset[]{d2})));// i3.setDatasets(new HashSet(Arrays.asList(new Dataset[]{d3}))); }

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public void removeNotes(Event e) { for (DisplayedNote removeMe : dd.getTree().getSelectedNotes()) { removeMe.deleteSelfAndChildren(); } }

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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.class)) table = "DatasetImageLink"; else if (klass.equals(Project.class)) table = "ProjectDatasetLink"; else if (klass.equals(CategoryGroup.class)) table = "CategoryGroupCategoryLink"; if (table == null) return null; String sql = "select link from "+table+" as link where " + "link.parent.id = :parentID and link.child.id = :childID"; IQuery service = getIQueryService(); Parameters param = new Parameters(); param.addLong("parentID", parent.getId()); param.addLong("childID", child.getId()); return service.findByQuery(sql, param); } catch (Exception e) { handleException(e, "Cannot retrieve the requested link for "+ "parent ID: "+parent.getId()+" and child ID: "+child.getId()); } return null; }

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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.class)) table = "DatasetImageLink"; else if (klass.equals(Project.class)) table = "ProjectDatasetLink"; else if (klass.equals(CategoryGroup.class)) table = "CategoryGroupCategoryLink"; if (table == null) return null; String sql = "select link from "+table+" as link where " + "link.parent.id = :parentID and link.child.id in " + "(:childIDs)"; IQuery service = getIQueryService(); Parameters param = new Parameters(); param.addLong("parentID", parent.getId()); param.addList("childIDs", children); return service.findAllByQuery(sql, param); } catch (Exception e) { handleException(e, "Cannot retrieve the requested link for "+ "parent ID: "+parent.getId()); } return null; }

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public RubyRegexpException(String msg) { super(msg); }

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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(fname); } // fname = findFile(fname); if (fname == null) { throw new RubyException("No such file to load -- " + fname.getValue()); } // volatile ID last_func; // volatile VALUE wrapper = 0; // ruby_errinfo = Qnil; /* ensure */ RubyVarmap.push(ruby); pushClass(); RubyModule wrapper = ruby_wrapper; ruby.setRubyCRef(ruby.getTopCRef()); if (!wrap) { ruby.secure(4); /* should alter global state */ ruby.setRubyClass(ruby.getClasses().getObjectClass()); ruby_wrapper = null; } else { /* load in anonymous module as toplevel */ ruby_wrapper = RubyModule.m_newModule(ruby); ruby.setRubyClass(ruby_wrapper); self = ruby.getRubyTopSelf().m_clone(); self.extendObject(ruby.getRubyClass()); PUSH_CREF(ruby_wrapper); } ruby.getRubyFrame().push(); ruby.getRubyFrame().setLastFunc(null); ruby.getRubyFrame().setLastClass(null); ruby.getRubyFrame().setSelf(self); ruby.getRubyFrame().setCbase(new NodeFactory(ruby).newDefaultNode(NODE.NODE_CREF, ruby.getRubyClass(), null, null)); ruby.getRubyScope().push(); /* default visibility is private at loading toplevel */ setActMethodScope(SCOPE_PRIVATE); RubyId last_func = ruby.getRubyFrame().getLastFunc(); try { // RubyId last_func = ruby.getRubyFrame().getLastFunc(); // DEFER_INTS; ruby.setInEval(ruby.getInEval() + 1); // +++ try { File rubyFile = new File(fname.getValue()); StringBuffer sb = new StringBuffer((int)rubyFile.length()); BufferedReader br = new BufferedReader(new FileReader(rubyFile)); String line; while ((line = br.readLine()) != null) { sb.append(line).append('\n'); } br.close(); ruby.getRubyParser().compileString(sb.toString(), fname, 0); } catch (IOException ioExcptn) { System.out.println("Cannot read Rubyfile: \"" + fname.getValue() + "\""); System.out.println("IOEception: " + ioExcptn.getMessage()); } // --- ruby.setInEval(ruby.getInEval() - 1); eval(self, ruby.getParserHelper().getEvalTree()); // evalNode } catch (RubyException excptn) { } ruby.getRubyFrame().setLastFunc(last_func); /*if (ruby.getRubyScope().getFlags() == SCOPE_ALLOCA && ruby.getRubyClass() == ruby.getClasses().getObjectClass()) { if (ruby_scope->local_tbl) free(ruby_scope->local_tbl); }*/ ruby.setRubyCRef(savedCRef); ruby.getRubyScope().pop(); ruby.getRubyFrame().pop(); popClass(); RubyVarmap.pop(ruby); ruby_wrapper = wrapper; /*if (ruby_nerrs > 0) { ruby_nerrs = 0; rb_exc_raise(ruby_errinfo); }*/ }

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(fname); } // fname = findFile(fname); if (fname == null) { throw new RubyException("No such file to load -- " + fname.getValue()); } // volatile ID last_func; // volatile VALUE wrapper = 0; // ruby_errinfo = Qnil; /* ensure */ RubyVarmap.push(ruby); pushClass(); RubyModule wrapper = ruby_wrapper; ruby.setRubyCRef(ruby.getTopCRef()); if (!wrap) { ruby.secure(4); /* should alter global state */ ruby.setRubyClass(ruby.getClasses().getObjectClass()); ruby_wrapper = null; } else { /* load in anonymous module as toplevel */ ruby_wrapper = RubyModule.m_newModule(ruby); ruby.setRubyClass(ruby_wrapper); self = ruby.getRubyTopSelf().m_clone(); self.extendObject(ruby.getRubyClass()); PUSH_CREF(ruby_wrapper); } ruby.getRubyFrame().push(); ruby.getRubyFrame().setLastFunc(null); ruby.getRubyFrame().setLastClass(null); ruby.getRubyFrame().setSelf(self); ruby.getRubyFrame().setCbase(new NodeFactory(ruby).newDefaultNode(NODE.NODE_CREF, ruby.getRubyClass(), null, null)); ruby.getRubyScope().push(); /* default visibility is private at loading toplevel */ setActMethodScope(SCOPE_PRIVATE); RubyId last_func = ruby.getRubyFrame().getLastFunc(); try { // RubyId last_func = ruby.getRubyFrame().getLastFunc(); // DEFER_INTS; ruby.setInEval(ruby.getInEval() + 1); // +++ try { File rubyFile = new File(fname.getValue()); StringBuffer sb = new StringBuffer((int)rubyFile.length()); BufferedReader br = new BufferedReader(new FileReader(rubyFile)); String line; while ((line = br.readLine()) != null) { sb.append(line).append('\n'); } br.close(); ruby.getRubyParser().compileString(fname.getValue(), RubyString.m_newString(ruby, sb.toString()), 0); } catch (IOException ioExcptn) { System.out.println("Cannot read Rubyfile: \"" + fname.getValue() + "\""); System.out.println("IOEception: " + ioExcptn.getMessage()); } // --- ruby.setInEval(ruby.getInEval() - 1); eval(self, ruby.getParserHelper().getEvalTree()); // evalNode } catch (RubyException excptn) { } ruby.getRubyFrame().setLastFunc(last_func); /*if (ruby.getRubyScope().getFlags() == SCOPE_ALLOCA && ruby.getRubyClass() == ruby.getClasses().getObjectClass()) { if (ruby_scope->local_tbl) free(ruby_scope->local_tbl); }*/ ruby.setRubyCRef(savedCRef); ruby.getRubyScope().pop(); ruby.getRubyFrame().pop(); popClass(); RubyVarmap.pop(ruby); ruby_wrapper = wrapper; /*if (ruby_nerrs > 0) { ruby_nerrs = 0; rb_exc_raise(ruby_errinfo); }*/ }

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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(fname); } // fname = findFile(fname); if (fname == null) { throw new RubyException("No such file to load -- " + fname.getValue()); } // volatile ID last_func; // volatile VALUE wrapper = 0; // ruby_errinfo = Qnil; /* ensure */ RubyVarmap.push(ruby); pushClass(); RubyModule wrapper = ruby_wrapper; ruby.setRubyCRef(ruby.getTopCRef()); if (!wrap) { ruby.secure(4); /* should alter global state */ ruby.setRubyClass(ruby.getClasses().getObjectClass()); ruby_wrapper = null; } else { /* load in anonymous module as toplevel */ ruby_wrapper = RubyModule.m_newModule(ruby); ruby.setRubyClass(ruby_wrapper); self = ruby.getRubyTopSelf().m_clone(); self.extendObject(ruby.getRubyClass()); PUSH_CREF(ruby_wrapper); } ruby.getRubyFrame().push(); ruby.getRubyFrame().setLastFunc(null); ruby.getRubyFrame().setLastClass(null); ruby.getRubyFrame().setSelf(self); ruby.getRubyFrame().setCbase(new NodeFactory(ruby).newDefaultNode(NODE.NODE_CREF, ruby.getRubyClass(), null, null)); ruby.getRubyScope().push(); /* default visibility is private at loading toplevel */ setActMethodScope(SCOPE_PRIVATE); RubyId last_func = ruby.getRubyFrame().getLastFunc(); try { // RubyId last_func = ruby.getRubyFrame().getLastFunc(); // DEFER_INTS; ruby.setInEval(ruby.getInEval() + 1); // +++ try { File rubyFile = new File(fname.getValue()); StringBuffer sb = new StringBuffer((int)rubyFile.length()); BufferedReader br = new BufferedReader(new FileReader(rubyFile)); String line; while ((line = br.readLine()) != null) { sb.append(line).append('\n'); } br.close(); ruby.getRubyParser().compileString(sb.toString(), fname, 0); } catch (IOException ioExcptn) { System.out.println("Cannot read Rubyfile: \"" + fname.getValue() + "\""); System.out.println("IOEception: " + ioExcptn.getMessage()); } // --- ruby.setInEval(ruby.getInEval() - 1); eval(self, ruby.getParserHelper().getEvalTree()); // evalNode } catch (RubyException excptn) { } ruby.getRubyFrame().setLastFunc(last_func); /*if (ruby.getRubyScope().getFlags() == SCOPE_ALLOCA && ruby.getRubyClass() == ruby.getClasses().getObjectClass()) { if (ruby_scope->local_tbl) free(ruby_scope->local_tbl); }*/ ruby.setRubyCRef(savedCRef); ruby.getRubyScope().pop(); ruby.getRubyFrame().pop(); popClass(); RubyVarmap.pop(ruby); ruby_wrapper = wrapper; /*if (ruby_nerrs > 0) { ruby_nerrs = 0; rb_exc_raise(ruby_errinfo); }*/ }

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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 && u.getProtocol().equals("file")) { File f = new File(u.getFile()); if (!f.exists()) u = null; } if (u == null) u = _servletClassLoader.getResource(name); if (u == null) u = super.getResource(name); return u; } catch (MalformedURLException e) { _log.warning("MalformedURLException caught in " + "ServletBroker.getResource for " + name); return null; } }

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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 && u.getProtocol().equals("file")) { File f = new File(u.getFile()); if (!f.exists()) u = null; } if (u == null) u = _servletClassLoader.getResource(name); if (u == null) u = super.getResource(name); return u; } catch (MalformedURLException e) { _log.warning("MalformedURLException caught in " + "ServletBroker.getResource for " + name); return null; } }

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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 && u.getProtocol().equals("file")) { File f = new File(u.getFile()); if (!f.exists()) u = null; } if (u == null) u = _servletClassLoader.getResource(name); if (u == null) u = super.getResource(name); return u; } catch (MalformedURLException e) { _log.warning("MalformedURLException caught in " + "ServletBroker.getResource for " + name); return 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 && u.getProtocol().equals("file")) { File f = new File(u.getFile()); if (!f.exists()) u = null; } if (u == null) { u = _servletClassLoader.getResource(name); if (u == null) { u = super.getResource(name); return u; } catch (MalformedURLException e) { _log.warning("MalformedURLException caught in " + "ServletBroker.getResource for " + name); return null; } }

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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 && u.getProtocol().equals("file")) { File f = new File(u.getFile()); if (!f.exists()) u = null; } if (u == null) u = _servletClassLoader.getResource(name); if (u == null) u = super.getResource(name); return u; } catch (MalformedURLException e) { _log.warning("MalformedURLException caught in " + "ServletBroker.getResource for " + name); return 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 && u.getProtocol().equals("file")) { File f = new File(u.getFile()); if (!f.exists()) u = null; } } if (u == null) u = _servletClassLoader.getResource(name); } if (u == null) u = super.getResource(name); return u; } catch (MalformedURLException e) { _log.warning("MalformedURLException caught in " + "ServletBroker.getResource for " + name); return null; } }

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public void actionPerformed(ActionEvent e) { long now = System.currentTimeMillis(); if (now - lastTypedCharTime > 2000) { if (!sendNotification) { // send cancel SparkManager.getMessageEventManager().sendCancelledNotification(getParticipantJID(), threadID); sendNotification = true; } } }

public void actionPerformed(ActionEvent e) {long now = System.currentTimeMillis();if (now - lastTypedCharTime > 2000) {if (!sendNotification) {// send cancelSparkManager.getMessageEventManager().sendCancelledNotification(getParticipantJID(), threadID);sendNotification = true;}}}

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public void closeChatRoom() { super.closeChatRoom(); SparkManager.getMessageEventManager().removeMessageEventRequestListener(messageEventRequestListener); SparkManager.getChatManager().removeChat(this); SparkManager.getConnection().removePacketListener(this); }

public void closeChatRoom() { super.closeChatRoom(); SparkManager.getChatManager().removeChat(this); SparkManager.getConnection().removePacketListener(this); }

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public void insertUpdate(DocumentEvent e) { checkForText(e); lastTypedCharTime = System.currentTimeMillis(); // If the user pauses for more than two seconds, send out a new notice. if (sendNotification) { try { if (sendTypingNotification) { SparkManager.getMessageEventManager().sendComposingNotification(getParticipantJID(), threadID); } sendNotification = false; } catch (Exception exception) { Log.error("Error updating", exception); } } }

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public IRubyObject execute(IRubyObject recv, IRubyObject[] args) { Method method = findMatchingMethod(args); if (method == null) { if (callSuper) { return recv.getRuntime().callSuper(args); } else { throw new ArgumentError(recv.getRuntime(), "wrong argument count or types."); } } int argsLength = args != null ? args.length : 0; Object[] newArgs = new Object[argsLength]; for (int i = 0; i < argsLength; i++) { newArgs[i] = JavaUtil.convertRubyToJava(recv.getRuntime(), args[i], method.getParameterTypes()[i]); } try { Object receiver = !singleton ? ((RubyJavaObject)recv).getValue() : null; return JavaUtil.convertJavaToRuby(recv.getRuntime(), method.invoke(receiver, newArgs)); } catch (InvocationTargetException itExcptn) { convertException(recv.getRuntime(), (Exception)itExcptn.getTargetException()); return recv.getRuntime().getNil(); } catch (Exception excptn) { Asserts.notReached(); return null; } }

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protected void setUp() throws Exception { sr = new SaxReader("type.xml"); }

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protected void tearDown() throws Exception { sr = null; }

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public void testONE() { Set set = sr.parse(); log.info("Results of parse:"+set); for (Iterator it = set.iterator(); it.hasNext();) { SemanticType st = (SemanticType) it.next(); VelocityHelper vh = new VelocityHelper(); vh.put("type",st); Map h = new HashMap(); h.put("test", "this was a dynamic key test"); vh.put("test", h); String s = vh.invoke("ome/dsl/mapping.vm"); log.info("Results of invoke:"+s); } }

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public void testONE() { Set set = sr.parse(); log.info("Results of parse:"+set); for (Iterator it = set.iterator(); it.hasNext();) { SemanticType st = (SemanticType) it.next(); VelocityHelper vh = new VelocityHelper(); vh.put("type",st); Map h = new HashMap(); h.put("test", "this was a dynamic key test"); vh.put("test", h); String s = vh.invoke("ome/dsl/mapping.vm"); log.info("Results of invoke:"+s); } }

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public void testReal() throws Exception { SaxReader nsr = new SaxReader("Mappings.xml"); for (Iterator it = nsr.parse().iterator(); it.hasNext();) { SemanticType st = (SemanticType) it.next(); VelocityHelper vh = new VelocityHelper(); vh.put("type",st); FileWriter fw = new FileWriter("/tmp/"+st.getId().replaceAll("[.]","_")+".hbm.xml"); vh.invoke("ome/dsl/mapping.vm",fw); fw.flush(); fw.close(); } }

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public void testWithWriting() throws Exception{ Set set = sr.parse(); for (Iterator it = set.iterator(); it.hasNext();) { SemanticType st = (SemanticType) it.next(); VelocityHelper vh = new VelocityHelper(); vh.put("type",st); FileWriter fw = new FileWriter("/tmp/"+st.getId().replaceAll("[.]","_")+".hbm.xml"); vh.invoke("ome/dsl/mapping.vm",fw); fw.flush(); fw.close(); } }

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public ToolBar(Registry registry, ImageInspectorManager manager, double magFactor) { setBorder(null); setLayout(new FlowLayout(FlowLayout.LEFT)); putClientProperty("JToolBar.isRollover", new Boolean(true)); zoomBar = new ZoomBar(this, registry, manager, magFactor); add(zoomBar); add(separator); }

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public void actionPerformed(ActionEvent e) { int index = Integer.parseInt(e.getActionCommand()); try { switch (index) { case SAVE: saveDisplayOptions(); break; case RESET_DEFAULTS: resetDefaults(); break; case GREY: case RGB: case HSB: activateRenderingModel(index); break; } } catch(NumberFormatException nfe) { throw new Error("Invalid Action ID "+index, nfe); } }

public void actionPerformed(ActionEvent e) { int index = -1; try { switch (index) { case SAVE: saveDisplayOptions(); break; case RESET_DEFAULTS: resetDefaults(); break; case GREY: case RGB: case HSB: activateRenderingModel(index); break; } } catch(NumberFormatException nfe) { throw new Error("Invalid Action ID "+index, nfe); } }

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public void activateRenderingModel(int i) { Class c = getRendererClass(i); presentation.setModelPane(activate(c), true); QuantumPane qp = presentation.getQuantumPane(); if (i == GREY) { qp.setSelectionWavelengthsEnable(false); ChannelData[] channelData = getChannelData(); for (int j = 0; j < channelData.length; j++) { if (isActive(j)) { qp.setSelectedWavelength(j); presentation.getTabs().setSelectedIndex( RenderingAgtUIF.POS_MODEL); break; } } } else qp.setSelectionWavelengthsEnable(true); abstraction.setModel(i); }

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public RenderingAgtUIF getReferenceFrame() { return presentation; }

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