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{ sizeBin = (widthStatDefault/histogramData.length); if (sizeBin < sizeBinDefault) { sizeBin = sizeBinDefault; widthStat = sizeBin*histogramData.length; } else widthStat = widthStatDefault; widthWin = BASIC_WIDTH+widthStat; lS = leftBorder+widthStat; } | { sizeBin = (widthStatDefault/histogramData.length); if (sizeBin < sizeBinDefault) { sizeBin = sizeBinDefault; widthStat = sizeBin*histogramData.length; } else widthStat = widthStatDefault; widthWin = BASIC_WIDTH+widthStat; lS = leftBorder+widthStat; } | void initSizeBin() { sizeBin = (widthStatDefault/histogramData.length); if (sizeBin < sizeBinDefault) { sizeBin = sizeBinDefault; widthStat = sizeBin*histogramData.length; } else widthStat = widthStatDefault; widthWin = BASIC_WIDTH+widthStat; lS = leftBorder+widthStat; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/1722ebf9ac60fc8e45cdc8d0049e85db5b86715c/HistogramPanel.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/pane/HistogramPanel.java |
{ super.paintComponent(g); Graphics2D g2D = (Graphics2D) g; g2D.setColor(bgColor); g2D.fillRect(0, 0, widthWin, HEIGHT); Font font = g2D.getFont(); FontMetrics fontMetrics = g2D.getFontMetrics(); int hFont = fontMetrics.getHeight(); Rectangle2D rStart = font.getStringBounds(min, g2D.getFontRenderContext()); int hStart = (int) rStart.getHeight(); Rectangle2D rEnd = font.getStringBounds(max, g2D.getFontRenderContext()); int hEnd = (int) rEnd.getHeight(); Rectangle2D rInput = font.getStringBounds("timepoint", g2D.getFontRenderContext()); int wInput = (int) rInput.getWidth(); g2D.setColor(axeColor); g2D.drawLine(leftBorder, topBorder-8, leftBorder, tS+5); g2D.drawLine(leftBorder, topBorder-8, leftBorder-3, topBorder-5); g2D.drawLine(leftBorder, topBorder-8, leftBorder+3, topBorder-5); g2D.drawLine(leftBorder-5, tS, lS+8, tS); g2D.drawLine(lS+5, tS-3, lS+8, tS); g2D.drawLine(lS+5, tS+3, lS+8, tS); g2D.drawString(min, 5, tS-window); g2D.drawLine(leftBorder-5, tS-window, leftBorder, tS-window); g2D.drawString(max, 5, topBorder+window); g2D.drawLine(leftBorder-5, topBorder+window, leftBorder, topBorder+window); g2D.drawString("timepoint", leftBorder+widthStat/2-wInput/2, tS+hFont+5); int xStartOutputPoints[] = {xStartOutput1, xStartOutput2, xStartOutput3}; int yStartOutputPoints[] = {yStartOutput1, yStartOutput2, yStartOutput3}; GeneralPath filledPolygonStartOutput = new GeneralPath(); filledPolygonStartOutput.moveTo(xStartOutputPoints[0], yStartOutputPoints[0]); for (int index = 1; index < xStartOutputPoints.length; index++) filledPolygonStartOutput.lineTo(xStartOutputPoints[index], yStartOutputPoints[index]); filledPolygonStartOutput.closePath(); g2D.setColor(startColor); g2D.drawString(curMin, 10, tS-hStart-hFont-window); g2D.fill(filledPolygonStartOutput); int xEndOutputPoints[] = {xEndOutput1, xEndOutput2, xEndOutput3}; int yEndOutputPoints[] = {yEndOutput1, yEndOutput2, yEndOutput3}; GeneralPath filledPolygonEndOutput = new GeneralPath(); filledPolygonEndOutput.moveTo(xEndOutputPoints[0], yEndOutputPoints[0]); for (int index = 1; index < xEndOutputPoints.length; index++) filledPolygonEndOutput.lineTo(xEndOutputPoints[index], yEndOutputPoints[index]); filledPolygonEndOutput.closePath(); g2D.setColor(endColor); g2D.drawString(curMax, 10, topBorder+hEnd+hFont+window); g2D.fill(filledPolygonEndOutput); g2D.setColor(binColor); g2D.drawString("Pixels", 5, topBorder+heightStat/2); g2D.drawString("intensity", 5, topBorder+heightStat/2+hEnd+5); PixelsStatsEntry entry; int min, max; int[] bin = new int[histogramData.length]; for (int i = 0; i < histogramData.length; i++) { entry = histogramData[i]; min = manager.convertRealIntoGraphics((int) entry.min); max = manager.convertRealIntoGraphics((int) entry.max); bin[i] = max; g2D.fillRect(leftBorder+i*sizeBin, max, sizeBin, min-max); } g2D.setColor(axeColor); int y, x; for (int i = 0; i < histogramData.length; i++) { y = bin[i]; x = leftBorder+(i+1)*sizeBin; g2D.drawLine(x, y, x, topBorder+heightStat+5); } g2D.setColor(layerColor); Rectangle2D endOutput = new Rectangle2D.Double(leftBorder, topBorder, widthStat, heightEnd); g2D.fill(endOutput); Rectangle2D startOutput = new Rectangle2D.Double(leftBorder, controlOutputStart, widthStat, heightStart); g2D.fill(startOutput); g2D.setColor(endColor); g2D.draw(endOutput); g2D.setColor(startColor); g2D.draw(startOutput); } | { super.paintComponent(g); Graphics2D g2D = (Graphics2D) g; g2D.setColor(bgColor); g2D.fillRect(0, 0, widthWin, HEIGHT); Font font = g2D.getFont(); FontMetrics fontMetrics = g2D.getFontMetrics(); int hFont = fontMetrics.getHeight(); Rectangle2D rStart = font.getStringBounds(min, g2D.getFontRenderContext()); int hStart = (int) rStart.getHeight(); Rectangle2D rEnd = font.getStringBounds(max, g2D.getFontRenderContext()); int hEnd = (int) rEnd.getHeight(); Rectangle2D rInput = font.getStringBounds("timepoint", g2D.getFontRenderContext()); int wInput = (int) rInput.getWidth(); g2D.setColor(axeColor); g2D.drawLine(leftBorder, topBorder-8, leftBorder, tS+5); g2D.drawLine(leftBorder, topBorder-8, leftBorder-3, topBorder-5); g2D.drawLine(leftBorder, topBorder-8, leftBorder+3, topBorder-5); g2D.drawLine(leftBorder-5, tS, lS+8, tS); g2D.drawLine(lS+5, tS-3, lS+8, tS); g2D.drawLine(lS+5, tS+3, lS+8, tS); g2D.drawString(min, 5, tS-window); g2D.drawLine(leftBorder-5, tS-window, leftBorder, tS-window); g2D.drawString(max, 5, topBorder+window); g2D.drawLine(leftBorder-5, topBorder+window, leftBorder, topBorder+window); g2D.drawString("timepoint", leftBorder+widthStat/2-wInput/2, tS+hFont+5); int xStartOutputPoints[] = {xStartOutput1, xStartOutput2, xStartOutput3}; int yStartOutputPoints[] = {yStartOutput1, yStartOutput2, yStartOutput3}; GeneralPath filledPolygonStartOutput = new GeneralPath(); filledPolygonStartOutput.moveTo(xStartOutputPoints[0], yStartOutputPoints[0]); for (int index = 1; index < xStartOutputPoints.length; index++) filledPolygonStartOutput.lineTo(xStartOutputPoints[index], yStartOutputPoints[index]); filledPolygonStartOutput.closePath(); g2D.setColor(startColor); g2D.drawString(curMin, 10, tS-hStart-hFont-window); g2D.fill(filledPolygonStartOutput); int xEndOutputPoints[] = {xEndOutput1, xEndOutput2, xEndOutput3}; int yEndOutputPoints[] = {yEndOutput1, yEndOutput2, yEndOutput3}; GeneralPath filledPolygonEndOutput = new GeneralPath(); filledPolygonEndOutput.moveTo(xEndOutputPoints[0], yEndOutputPoints[0]); for (int index = 1; index < xEndOutputPoints.length; index++) filledPolygonEndOutput.lineTo(xEndOutputPoints[index], yEndOutputPoints[index]); filledPolygonEndOutput.closePath(); g2D.setColor(endColor); g2D.drawString(curMax, 10, topBorder+hEnd+hFont+window); g2D.fill(filledPolygonEndOutput); paintBins(g2D, hEnd); g2D.setColor(layerColor); Rectangle2D endOutput = new Rectangle2D.Double(leftBorder, topBorder, widthStat, heightEnd); g2D.fill(endOutput); Rectangle2D startOutput = new Rectangle2D.Double(leftBorder, controlOutputStart, widthStat, heightStart); g2D.fill(startOutput); g2D.setColor(endColor); g2D.draw(endOutput); g2D.setColor(startColor); g2D.draw(startOutput); } | public void paintComponent(Graphics g) { super.paintComponent(g); Graphics2D g2D = (Graphics2D) g; g2D.setColor(bgColor); g2D.fillRect(0, 0, widthWin, HEIGHT); Font font = g2D.getFont(); FontMetrics fontMetrics = g2D.getFontMetrics(); int hFont = fontMetrics.getHeight(); Rectangle2D rStart = font.getStringBounds(min, g2D.getFontRenderContext()); int hStart = (int) rStart.getHeight(); Rectangle2D rEnd = font.getStringBounds(max, g2D.getFontRenderContext()); int hEnd = (int) rEnd.getHeight(); Rectangle2D rInput = font.getStringBounds("timepoint", g2D.getFontRenderContext()); int wInput = (int) rInput.getWidth(); g2D.setColor(axeColor); //y-axis g2D.drawLine(leftBorder, topBorder-8, leftBorder, tS+5); g2D.drawLine(leftBorder, topBorder-8, leftBorder-3, topBorder-5); g2D.drawLine(leftBorder, topBorder-8, leftBorder+3, topBorder-5); // x-axis g2D.drawLine(leftBorder-5, tS, lS+8, tS); g2D.drawLine(lS+5, tS-3, lS+8, tS); g2D.drawLine(lS+5, tS+3, lS+8, tS); // draw output interval g2D.drawString(min, 5, tS-window); g2D.drawLine(leftBorder-5, tS-window, leftBorder, tS-window); g2D.drawString(max, 5, topBorder+window); g2D.drawLine(leftBorder-5, topBorder+window, leftBorder, topBorder+window); g2D.drawString("timepoint", leftBorder+widthStat/2-wInput/2, tS+hFont+5); //knob start output int xStartOutputPoints[] = {xStartOutput1, xStartOutput2, xStartOutput3}; int yStartOutputPoints[] = {yStartOutput1, yStartOutput2, yStartOutput3}; GeneralPath filledPolygonStartOutput = new GeneralPath(); filledPolygonStartOutput.moveTo(xStartOutputPoints[0], yStartOutputPoints[0]); for (int index = 1; index < xStartOutputPoints.length; index++) filledPolygonStartOutput.lineTo(xStartOutputPoints[index], yStartOutputPoints[index]); filledPolygonStartOutput.closePath(); // paint with selected color g2D.setColor(startColor); g2D.drawString(curMin, 10, tS-hStart-hFont-window); g2D.fill(filledPolygonStartOutput); //knob end output int xEndOutputPoints[] = {xEndOutput1, xEndOutput2, xEndOutput3}; int yEndOutputPoints[] = {yEndOutput1, yEndOutput2, yEndOutput3}; GeneralPath filledPolygonEndOutput = new GeneralPath(); filledPolygonEndOutput.moveTo(xEndOutputPoints[0], yEndOutputPoints[0]); for (int index = 1; index < xEndOutputPoints.length; index++) filledPolygonEndOutput.lineTo(xEndOutputPoints[index], yEndOutputPoints[index]); filledPolygonEndOutput.closePath(); g2D.setColor(endColor); g2D.drawString(curMax, 10, topBorder+hEnd+hFont+window); g2D.fill(filledPolygonEndOutput); //paint histogram g2D.setColor(binColor); g2D.drawString("Pixels", 5, topBorder+heightStat/2); g2D.drawString("intensity", 5, topBorder+heightStat/2+hEnd+5); PixelsStatsEntry entry; int min, max; int[] bin = new int[histogramData.length]; for (int i = 0; i < histogramData.length; i++) { entry = histogramData[i]; min = manager.convertRealIntoGraphics((int) entry.min); max = manager.convertRealIntoGraphics((int) entry.max); bin[i] = max; g2D.fillRect(leftBorder+i*sizeBin, max, sizeBin, min-max); } g2D.setColor(axeColor); int y, x; for (int i = 0; i < histogramData.length; i++) { y = bin[i]; x = leftBorder+(i+1)*sizeBin; g2D.drawLine(x, y, x, topBorder+heightStat+5); } // paint layered rectangles g2D.setColor(layerColor); //end rectangle Rectangle2D endOutput = new Rectangle2D.Double(leftBorder, topBorder, widthStat, heightEnd); g2D.fill(endOutput); //start rectangle Rectangle2D startOutput = new Rectangle2D.Double(leftBorder, controlOutputStart, widthStat, heightStart); g2D.fill(startOutput); g2D.setColor(endColor); g2D.draw(endOutput); g2D.setColor(startColor); g2D.draw(startOutput); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/1722ebf9ac60fc8e45cdc8d0049e85db5b86715c/HistogramPanel.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/pane/HistogramPanel.java |
{ curMax = "end: "+v; repaint(0, 0, leftBorder, HEIGHT); } | { curMax = "end: "+v; repaint(0, 0, leftBorder, HEIGHT); } | void setCurMax(int v) { curMax = "end: "+v; repaint(0, 0, leftBorder, HEIGHT); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/1722ebf9ac60fc8e45cdc8d0049e85db5b86715c/HistogramPanel.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/pane/HistogramPanel.java |
{ curMin = "start: "+v; repaint(0, 0, leftBorder, HEIGHT); } | { curMin = "start: "+v; repaint(0, 0, leftBorder, HEIGHT); } | void setCurMin(int v) { curMin = "start: "+v; repaint(0, 0, leftBorder, HEIGHT); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/1722ebf9ac60fc8e45cdc8d0049e85db5b86715c/HistogramPanel.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/pane/HistogramPanel.java |
{ curMin = "start: "+s; curMax = "end: "+e; } | { curMin = "start: "+s; curMax = "end: "+e; } | private void setInputWindow(int s, int e) { curMin = "start: "+s; curMax = "end: "+e; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/1722ebf9ac60fc8e45cdc8d0049e85db5b86715c/HistogramPanel.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/pane/HistogramPanel.java |
{ xEndOutput1 = x; xEndOutput2 = x-triangleH; xEndOutput3 = x-triangleH; yEndOutput1 = y; yEndOutput2 = y-triangleW; yEndOutput3 = y+triangleW; } | { xEndOutput1 = x; xEndOutput2 = x-triangleH; xEndOutput3 = x-triangleH; yEndOutput1 = y; yEndOutput2 = y-triangleW; yEndOutput3 = y+triangleW; } | void setKnobOutputEnd(int x, int y) { xEndOutput1 = x; xEndOutput2 = x-triangleH; xEndOutput3 = x-triangleH; yEndOutput1 = y; yEndOutput2 = y-triangleW; yEndOutput3 = y+triangleW; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/1722ebf9ac60fc8e45cdc8d0049e85db5b86715c/HistogramPanel.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/pane/HistogramPanel.java |
{ xStartOutput1 = x; xStartOutput2 = x+triangleH; xStartOutput3 = x+triangleH; yStartOutput1 = y; yStartOutput2 = y-triangleW; yStartOutput3 = y+triangleW; } | { xStartOutput1 = x; xStartOutput2 = x+triangleH; xStartOutput3 = x+triangleH; yStartOutput1 = y; yStartOutput2 = y-triangleW; yStartOutput3 = y+triangleW; } | void setKnobOutputStart(int x, int y) { xStartOutput1 = x; xStartOutput2 = x+triangleH; xStartOutput3 = x+triangleH; yStartOutput1 = y; yStartOutput2 = y-triangleW; yStartOutput3 = y+triangleW; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/1722ebf9ac60fc8e45cdc8d0049e85db5b86715c/HistogramPanel.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/pane/HistogramPanel.java |
{ min = "Min: "+m; max = "Max: "+M; } | { min = "Min: "+m; max = "Max: "+M; } | private void setWindowLimits(int m, int M) { min = "Min: "+m; max = "Max: "+M; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/1722ebf9ac60fc8e45cdc8d0049e85db5b86715c/HistogramPanel.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/pane/HistogramPanel.java |
{ yEndOutput1 = y; yEndOutput2 = y-triangleW; yEndOutput3 = y+triangleW; } | { yEndOutput1 = y; yEndOutput2 = y-triangleW; yEndOutput3 = y+triangleW; } | void updateEndOutputKnob(int y) { yEndOutput1 = y; yEndOutput2 = y-triangleW; yEndOutput3 = y+triangleW; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/1722ebf9ac60fc8e45cdc8d0049e85db5b86715c/HistogramPanel.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/pane/HistogramPanel.java |
{ heightEnd = y-topBorder; curMax = "end: "+yReal; updateEndOutputKnob(y); repaint(); } | { heightEnd = y-topBorder; curMax = "end: "+yReal; updateEndOutputKnob(y); repaint(); } | void updateInputEnd(int y, int yReal) { heightEnd = y-topBorder; curMax = "end: "+yReal; updateEndOutputKnob(y); repaint(); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/1722ebf9ac60fc8e45cdc8d0049e85db5b86715c/HistogramPanel.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/pane/HistogramPanel.java |
{ controlOutputStart = y; heightStart = tS-y; curMin = "start: "+yReal; updateStartOutputKnob(y); repaint(); } | { controlOutputStart = y; heightStart = tS-y; curMin = "start: "+yReal; updateStartOutputKnob(y); repaint(); } | void updateInputStart(int y, int yReal) { controlOutputStart = y; heightStart = tS-y; curMin = "start: "+yReal; updateStartOutputKnob(y); repaint(); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/1722ebf9ac60fc8e45cdc8d0049e85db5b86715c/HistogramPanel.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/pane/HistogramPanel.java |
{ yStartOutput1 = y; yStartOutput2 = y-triangleW; yStartOutput3 = y+triangleW; } | { yStartOutput1 = y; yStartOutput2 = y-triangleW; yStartOutput3 = y+triangleW; } | void updateStartOutputKnob(int y) { yStartOutput1 = y; yStartOutput2 = y-triangleW; yStartOutput3 = y+triangleW; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/1722ebf9ac60fc8e45cdc8d0049e85db5b86715c/HistogramPanel.java/clean/SRC/org/openmicroscopy/shoola/agents/rnd/pane/HistogramPanel.java |
public boolean isDisplayed() { return model.isDisplayed(); } | public boolean isDisplayed() { return model.isDisplayed(); } | public boolean isDisplayed() { return model.isDisplayed(); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/146920a8791fff71320ced0f240b9d8f3d319a13/BrowserComponent.java/clean/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserComponent.java |
/* d = TreeViewerTranslator.transformDataObject(img, userID, groupID); if (editorType == CATEGORY_EXPLORER) { if (m == Classifier.CLASSIFY_MODE) { last = getLastSelectedDisplay(); if (last == null) createNodes(nodes, d, null); else createNodes(nodes, d, last.getParentDisplay()); } else removeNodes(nodes); } else if (editorType == PROJECT_EXPLORER || editorType == IMAGES_EXPLORER) */ | public void refreshClassification(ImageData[] images, Set categories, int m) { switch (model.getState()) { case NEW: case READY: break; default: new IllegalStateException("This method can only be invoked " + "in the NEW or READY state."); } if (categories == null) throw new IllegalArgumentException("Categories shouln't be null."); if (images == null) throw new IllegalArgumentException("No image."); if (images.length == 0) throw new IllegalArgumentException("No image."); if (m != Classifier.CLASSIFY_MODE && m != Classifier.DECLASSIFY_MODE) throw new IllegalArgumentException("Classification mode not " + "supported."); ImageData img; ClassificationVisitor visitor; List nodes; //long userID = model.getUserID(); //long groupID = model.getRootGroupID(); int editorType = model.getBrowserType(); if (editorType == CATEGORY_EXPLORER) { refreshTree(); return; } for (int i = 0; i < images.length; i++) { img = images[i]; visitor = new ClassificationVisitor(this, img, categories); accept(visitor, TreeImageDisplayVisitor.TREEIMAGE_NODE_ONLY); nodes = visitor.getFoundNodes(); /* d = TreeViewerTranslator.transformDataObject(img, userID, groupID); if (editorType == CATEGORY_EXPLORER) { if (m == Classifier.CLASSIFY_MODE) { last = getLastSelectedDisplay(); if (last == null) createNodes(nodes, d, null); else createNodes(nodes, d, last.getParentDisplay()); } else removeNodes(nodes); } else if (editorType == PROJECT_EXPLORER || editorType == IMAGES_EXPLORER) */ view.updateNodes(nodes, img); } } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/146920a8791fff71320ced0f240b9d8f3d319a13/BrowserComponent.java/clean/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserComponent.java |
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PartialNameVisitor v = new PartialNameVisitor(view.isPartialName()); accept(v, TreeImageDisplayVisitor.TREEIMAGE_NODE_ONLY); | public void setRefreshedHierarchy(Map nodes, List expandedTopNodes) { if (model.getState() != LOADING_DATA) throw new IllegalStateException("This method cannot be invoked "+ "in the LOADING_DATA state."); long userID = model.getUserID(); long groupID = model.getRootGroupID(); view.setViews(TreeViewerTranslator.refreshHierarchy(nodes, expandedTopNodes, userID, groupID)); model.fireContainerCountLoading(); model.getParentModel().setStatus(false, "", true); fireStateChange(); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/146920a8791fff71320ced0f240b9d8f3d319a13/BrowserComponent.java/clean/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserComponent.java |
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/* SortCmd cmd; TreeImageDisplay node; if (model.getBrowserType() == Browser.IMAGES_EXPLORER) node = view.getTreeRoot(); else node = getLastSelectedDisplay(); cmd = new SortCmd(this, sortType, node); cmd.execute(); */ | public void sortTreeNodes(int sortType) { switch (model.getState()) { case COUNTING_ITEMS: case LOADING_DATA: case LOADING_LEAVES: case DISCARDED: throw new IllegalStateException( "This method cannot be invoked in the LOADING_DATA, "+ " LOADING_LEAVES or DISCARDED state."); } switch (sortType) { case SORT_NODES_BY_DATE: case SORT_NODES_BY_NAME: break; default: throw new IllegalArgumentException("SortType not supported."); } view.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); /* SortCmd cmd; TreeImageDisplay node; if (model.getBrowserType() == Browser.IMAGES_EXPLORER) node = view.getTreeRoot(); else node = getLastSelectedDisplay(); cmd = new SortCmd(this, sortType, node); cmd.execute(); //view.setSortedNodes(cmd.getSortedNodes(), node); */ view.sortNodes(sortType); view.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/146920a8791fff71320ced0f240b9d8f3d319a13/BrowserComponent.java/clean/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserComponent.java |
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public void sortTreeNodes(int sortType) { switch (model.getState()) { case COUNTING_ITEMS: case LOADING_DATA: case LOADING_LEAVES: case DISCARDED: throw new IllegalStateException( "This method cannot be invoked in the LOADING_DATA, "+ " LOADING_LEAVES or DISCARDED state."); } switch (sortType) { case SORT_NODES_BY_DATE: case SORT_NODES_BY_NAME: break; default: throw new IllegalArgumentException("SortType not supported."); } view.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); /* SortCmd cmd; TreeImageDisplay node; if (model.getBrowserType() == Browser.IMAGES_EXPLORER) node = view.getTreeRoot(); else node = getLastSelectedDisplay(); cmd = new SortCmd(this, sortType, node); cmd.execute(); //view.setSortedNodes(cmd.getSortedNodes(), node); */ view.sortNodes(sortType); view.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/146920a8791fff71320ced0f240b9d8f3d319a13/BrowserComponent.java/clean/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserComponent.java |
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Criteria criteria = new Criteria(); | Criteria c = new Criteria(); | private static Criteria buildBasicImagesCriteria() { Criteria criteria = new Criteria(); //Specify which fields we want for the image. criteria.addWantedField("name"); criteria.addWantedField("created"); //Specify which fields we want for the pixels. criteria.addWantedField("default_pixels"); return criteria; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/73d218b1f03225366903abf43d50c4be713e767b/ImageMapper.java/clean/SRC/org/openmicroscopy/shoola/env/data/map/ImageMapper.java |
criteria.addWantedField("name"); criteria.addWantedField("created"); | c.addWantedField("name"); c.addWantedField("created"); | private static Criteria buildBasicImagesCriteria() { Criteria criteria = new Criteria(); //Specify which fields we want for the image. criteria.addWantedField("name"); criteria.addWantedField("created"); //Specify which fields we want for the pixels. criteria.addWantedField("default_pixels"); return criteria; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/73d218b1f03225366903abf43d50c4be713e767b/ImageMapper.java/clean/SRC/org/openmicroscopy/shoola/env/data/map/ImageMapper.java |
criteria.addWantedField("default_pixels"); return criteria; | c.addWantedField("default_pixels"); PixelsMapper.fieldsForPixels(c, "default_pixels"); return c; | private static Criteria buildBasicImagesCriteria() { Criteria criteria = new Criteria(); //Specify which fields we want for the image. criteria.addWantedField("name"); criteria.addWantedField("created"); //Specify which fields we want for the pixels. criteria.addWantedField("default_pixels"); return criteria; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/73d218b1f03225366903abf43d50c4be713e767b/ImageMapper.java/clean/SRC/org/openmicroscopy/shoola/env/data/map/ImageMapper.java |
Criteria criteria = PixelsMapper.buildPixelsCriteria(id); | Criteria c = PixelsMapper.buildPixelsCriteria(id); | public static Criteria buildImageCriteria(int id) { Criteria criteria = PixelsMapper.buildPixelsCriteria(id); //Specify which fields we want for the image. criteria.addWantedField("name"); criteria.addWantedField("description"); criteria.addWantedField("inserted"); criteria.addWantedField("created"); criteria.addWantedField("owner"); criteria.addWantedField("datasets"); //Specify which fields we want for the datasets. criteria.addWantedField("datasets", "name"); //Fields for the owner. UserMapper.objectOwnerCriteria(criteria); return criteria; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/73d218b1f03225366903abf43d50c4be713e767b/ImageMapper.java/clean/SRC/org/openmicroscopy/shoola/env/data/map/ImageMapper.java |
criteria.addWantedField("name"); criteria.addWantedField("description"); criteria.addWantedField("inserted"); criteria.addWantedField("created"); criteria.addWantedField("owner"); criteria.addWantedField("datasets"); | c.addWantedField("name"); c.addWantedField("description"); c.addWantedField("inserted"); c.addWantedField("created"); c.addWantedField("owner"); c.addWantedField("datasets"); | public static Criteria buildImageCriteria(int id) { Criteria criteria = PixelsMapper.buildPixelsCriteria(id); //Specify which fields we want for the image. criteria.addWantedField("name"); criteria.addWantedField("description"); criteria.addWantedField("inserted"); criteria.addWantedField("created"); criteria.addWantedField("owner"); criteria.addWantedField("datasets"); //Specify which fields we want for the datasets. criteria.addWantedField("datasets", "name"); //Fields for the owner. UserMapper.objectOwnerCriteria(criteria); return criteria; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/73d218b1f03225366903abf43d50c4be713e767b/ImageMapper.java/clean/SRC/org/openmicroscopy/shoola/env/data/map/ImageMapper.java |
criteria.addWantedField("datasets", "name"); | c.addWantedField("datasets", "name"); | public static Criteria buildImageCriteria(int id) { Criteria criteria = PixelsMapper.buildPixelsCriteria(id); //Specify which fields we want for the image. criteria.addWantedField("name"); criteria.addWantedField("description"); criteria.addWantedField("inserted"); criteria.addWantedField("created"); criteria.addWantedField("owner"); criteria.addWantedField("datasets"); //Specify which fields we want for the datasets. criteria.addWantedField("datasets", "name"); //Fields for the owner. UserMapper.objectOwnerCriteria(criteria); return criteria; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/73d218b1f03225366903abf43d50c4be713e767b/ImageMapper.java/clean/SRC/org/openmicroscopy/shoola/env/data/map/ImageMapper.java |
UserMapper.objectOwnerCriteria(criteria); | UserMapper.objectOwnerCriteria(c); | public static Criteria buildImageCriteria(int id) { Criteria criteria = PixelsMapper.buildPixelsCriteria(id); //Specify which fields we want for the image. criteria.addWantedField("name"); criteria.addWantedField("description"); criteria.addWantedField("inserted"); criteria.addWantedField("created"); criteria.addWantedField("owner"); criteria.addWantedField("datasets"); //Specify which fields we want for the datasets. criteria.addWantedField("datasets", "name"); //Fields for the owner. UserMapper.objectOwnerCriteria(criteria); return criteria; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/73d218b1f03225366903abf43d50c4be713e767b/ImageMapper.java/clean/SRC/org/openmicroscopy/shoola/env/data/map/ImageMapper.java |
return criteria; | return c; | public static Criteria buildImageCriteria(int id) { Criteria criteria = PixelsMapper.buildPixelsCriteria(id); //Specify which fields we want for the image. criteria.addWantedField("name"); criteria.addWantedField("description"); criteria.addWantedField("inserted"); criteria.addWantedField("created"); criteria.addWantedField("owner"); criteria.addWantedField("datasets"); //Specify which fields we want for the datasets. criteria.addWantedField("datasets", "name"); //Fields for the owner. UserMapper.objectOwnerCriteria(criteria); return criteria; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/73d218b1f03225366903abf43d50c4be713e767b/ImageMapper.java/clean/SRC/org/openmicroscopy/shoola/env/data/map/ImageMapper.java |
static void buildImageSummary(Image img, ImageSummary is) | static ImageSummary buildImageSummary(Image img, ImageSummary is) | static void buildImageSummary(Image img, ImageSummary is) { is.setID(img.getID()); is.setName(img.getName()); is.setPixelsIDs(fillListPixelsID(img.getDefaultPixels())); is.setDate(PrimitiveTypesMapper.getTimestamp(img.getCreated())); //is.setImageServerPixelsID(fillListPixelsID(px)); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/73d218b1f03225366903abf43d50c4be713e767b/ImageMapper.java/clean/SRC/org/openmicroscopy/shoola/env/data/map/ImageMapper.java |
is.setDate(PrimitiveTypesMapper.getTimestamp(img.getCreated())); | List pixels = fillPixels(img.getDefaultPixels()); if (pixels.size() > 0) is.setDefaultPixels((PixelsDescription) pixels.get(0)); return is; | static void buildImageSummary(Image img, ImageSummary is) { is.setID(img.getID()); is.setName(img.getName()); is.setPixelsIDs(fillListPixelsID(img.getDefaultPixels())); is.setDate(PrimitiveTypesMapper.getTimestamp(img.getCreated())); //is.setImageServerPixelsID(fillListPixelsID(px)); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/73d218b1f03225366903abf43d50c4be713e767b/ImageMapper.java/clean/SRC/org/openmicroscopy/shoola/env/data/map/ImageMapper.java |
if (defaultPix != null) { empty.setPixelsIDs(fillListPixelsID(defaultPix)); empty.setPixels(fillPixels(defaultPix)); } | empty.setPixelsIDs(fillListPixelsID(defaultPix)); empty.setPixels(fillPixels(defaultPix)); | public static void fillImage(Image image, ImageData empty) { //Fill in the data coming from OMEDS object. empty.setID(image.getID()); empty.setName(image.getName()); empty.setDescription(image.getDescription()); empty.setCreated(PrimitiveTypesMapper.getTimestamp(image.getCreated())); empty.setInserted( PrimitiveTypesMapper.getTimestamp(image.getInserted())); //Fill in the data coming from Experimenter. Experimenter owner = image.getOwner(); empty.setOwnerID(owner.getID()); empty.setOwnerFirstName(owner.getFirstName()); empty.setOwnerLastName(owner.getLastName()); empty.setOwnerEmail(owner.getEmail()); empty.setOwnerInstitution(owner.getInstitution()); //Fill in the data coming from Group. Group group = owner.getGroup(); empty.setOwnerGroupID(group.getID()); empty.setOwnerGroupName(group.getName()); //dataset summary list. List datasets = new ArrayList(); Iterator i = image.getDatasets().iterator(); Dataset d; while (i.hasNext()) { d = (Dataset) i.next(); datasets.add(new DatasetSummary(d.getID(), d.getName())); } empty.setDatasets(datasets); // pixelsDescription list. Pixels defaultPix = image.getDefaultPixels(); if (defaultPix != null) { empty.setPixelsIDs(fillListPixelsID(defaultPix)); empty.setPixels(fillPixels(defaultPix)); } } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/73d218b1f03225366903abf43d50c4be713e767b/ImageMapper.java/clean/SRC/org/openmicroscopy/shoola/env/data/map/ImageMapper.java |
{ int[] ids = new int[1]; ids[0] = px.getID(); return ids; } | { int[] ids = new int[1]; if (px == null) return ids; ids[0] = px.getID(); return ids; } | private static int[] fillListPixelsID(Pixels px) { int[] ids = new int[1]; ids[0] = px.getID(); return ids; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/73d218b1f03225366903abf43d50c4be713e767b/ImageMapper.java/clean/SRC/org/openmicroscopy/shoola/env/data/map/ImageMapper.java |
{ List pixels = new ArrayList(); PixelsDescription pxd = new PixelsDescription(); pxd.setID(px.getID()); if (px.getSizeX() != null) pxd.setSizeX((px.getSizeX()).intValue()); if (px.getSizeY() != null) pxd.setSizeY((px.getSizeY()).intValue()); if (px.getSizeZ() != null) pxd.setSizeZ((px.getSizeZ()).intValue()); if (px.getSizeC() != null) pxd.setSizeC((px.getSizeC()).intValue()); if (px.getSizeT() != null) pxd.setSizeT((px.getSizeT()).intValue()); pxd.setPixelType(px.getPixelType()); pxd.setImageServerUrl(px.getRepository().getImageServerURL()); if (px.getImageServerID() != null) pxd.setImageServerID((px.getImageServerID()).longValue()); | { List pixels = new ArrayList(); if (px == null) return pixels; PixelsDescription pxd = new PixelsDescription(); pxd.setID(px.getID()); if (px.getSizeX() != null) pxd.setSizeX((px.getSizeX()).intValue()); if (px.getSizeY() != null) pxd.setSizeY((px.getSizeY()).intValue()); if (px.getSizeZ() != null) pxd.setSizeZ((px.getSizeZ()).intValue()); if (px.getSizeC() != null) pxd.setSizeC((px.getSizeC()).intValue()); if (px.getSizeT() != null) pxd.setSizeT((px.getSizeT()).intValue()); pxd.setPixelType(px.getPixelType()); pxd.setImageServerUrl(px.getRepository().getImageServerURL()); if (px.getImageServerID() != null) pxd.setImageServerID((px.getImageServerID()).longValue()); | private static List fillPixels(Pixels px) { List pixels = new ArrayList(); PixelsDescription pxd = new PixelsDescription(); pxd.setID(px.getID()); if (px.getSizeX() != null) pxd.setSizeX((px.getSizeX()).intValue()); if (px.getSizeY() != null) pxd.setSizeY((px.getSizeY()).intValue()); if (px.getSizeZ() != null) pxd.setSizeZ((px.getSizeZ()).intValue()); if (px.getSizeC() != null) pxd.setSizeC((px.getSizeC()).intValue()); if (px.getSizeT() != null) pxd.setSizeT((px.getSizeT()).intValue()); pxd.setPixelType(px.getPixelType()); pxd.setImageServerUrl(px.getRepository().getImageServerURL()); if (px.getImageServerID() != null) pxd.setImageServerID((px.getImageServerID()).longValue()); pxd.setPixels(px); pixels.add(pxd); return pixels; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/73d218b1f03225366903abf43d50c4be713e767b/ImageMapper.java/clean/SRC/org/openmicroscopy/shoola/env/data/map/ImageMapper.java |
pixels.add(pxd); return pixels; } | pixels.add(pxd); return pixels; } | private static List fillPixels(Pixels px) { List pixels = new ArrayList(); PixelsDescription pxd = new PixelsDescription(); pxd.setID(px.getID()); if (px.getSizeX() != null) pxd.setSizeX((px.getSizeX()).intValue()); if (px.getSizeY() != null) pxd.setSizeY((px.getSizeY()).intValue()); if (px.getSizeZ() != null) pxd.setSizeZ((px.getSizeZ()).intValue()); if (px.getSizeC() != null) pxd.setSizeC((px.getSizeC()).intValue()); if (px.getSizeT() != null) pxd.setSizeT((px.getSizeT()).intValue()); pxd.setPixelType(px.getPixelType()); pxd.setImageServerUrl(px.getRepository().getImageServerURL()); if (px.getImageServerID() != null) pxd.setImageServerID((px.getImageServerID()).longValue()); pxd.setPixels(px); pixels.add(pxd); return pixels; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/73d218b1f03225366903abf43d50c4be713e767b/ImageMapper.java/clean/SRC/org/openmicroscopy/shoola/env/data/map/ImageMapper.java |
lensMenu = LensMenu.getMenu(lensComponent); menu = lensMenu.getPopupMenu(); | LensUI(LensComponent lensComponent, int w, int h) { this.lensComponent = lensComponent; setSize(new Dimension(w,h)); setOpaque(false); setShowCrossHair(true); mouseListener = new LensMouseListener(this); addMouseListener(mouseListener); addMouseMotionListener(mouseListener); addMouseWheelListener(mouseListener); lensMenu = LensMenu.getMenu(lensComponent); menu = lensMenu.getPopupMenu(); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/29b0b8d77292efe37e6130bac1e4416901230654/LensUI.java/buggy/SRC/org/openmicroscopy/shoola/util/ui/lens/LensUI.java |
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zoomWindow.setLensWidthHeight(lensModel.getWidth(), lensModel.getHeight()); | zoomWindow.setLensWidthHeight(lensModel.getWidth(), lensModel.getHeight()); | void setLensLocation(int x, int y) { lensModel.setLensLocation(x,y); lens.setLocation(lensModel.getScaledX(),lensModel.getScaledY()); zoomWindow.setZoomImage(lensModel.getZoomedImage()); zoomWindow.setLensXY(lensModel.getX(), lensModel.getY()); zoomWindow.setLensWidthHeight(lensModel.getWidth(), lensModel.getHeight()); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/54a6dc1cc81e06c2190546075a6c5a04f18d9bb5/LensController.java/buggy/SRC/org/openmicroscopy/shoola/util/ui/lens/LensController.java |
scaledW = (int)(w*lensModel.getImageZoomFactor()); scaledH = (int)(h*lensModel.getImageZoomFactor()); | scaledW = (int) (w*lensModel.getImageZoomFactor()); scaledH = (int) (h*lensModel.getImageZoomFactor()); | void setLensSize(int w, int h) { int scaledW, scaledH; scaledW = (int)(w*lensModel.getImageZoomFactor()); scaledH = (int)(h*lensModel.getImageZoomFactor()); if (lens.getX()+scaledW > lensModel.getImageScaledWidth()) { scaledW = lensModel.getImageScaledWidth()-lens.getX(); w = (int)(scaledW/lensModel.getImageZoomFactor()); } if (lens.getY()+scaledH > lensModel.getImageScaledHeight()) { scaledH = lensModel.getImageScaledHeight()-lens.getY(); h = (int)(scaledH/lensModel.getImageZoomFactor()); } lensModel.setWidth(w); lensModel.setHeight(h); lens.setSize(scaledW, scaledH); zoomWindow.setZoomImage(lensModel.getZoomedImage()); zoomWindow.setLensWidthHeight(lensModel.getWidth(), lensModel.getHeight()); setZoomUISize(); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/54a6dc1cc81e06c2190546075a6c5a04f18d9bb5/LensController.java/buggy/SRC/org/openmicroscopy/shoola/util/ui/lens/LensController.java |
w = (int)(scaledW/lensModel.getImageZoomFactor()); | w = (int) (scaledW/lensModel.getImageZoomFactor()); | void setLensSize(int w, int h) { int scaledW, scaledH; scaledW = (int)(w*lensModel.getImageZoomFactor()); scaledH = (int)(h*lensModel.getImageZoomFactor()); if (lens.getX()+scaledW > lensModel.getImageScaledWidth()) { scaledW = lensModel.getImageScaledWidth()-lens.getX(); w = (int)(scaledW/lensModel.getImageZoomFactor()); } if (lens.getY()+scaledH > lensModel.getImageScaledHeight()) { scaledH = lensModel.getImageScaledHeight()-lens.getY(); h = (int)(scaledH/lensModel.getImageZoomFactor()); } lensModel.setWidth(w); lensModel.setHeight(h); lens.setSize(scaledW, scaledH); zoomWindow.setZoomImage(lensModel.getZoomedImage()); zoomWindow.setLensWidthHeight(lensModel.getWidth(), lensModel.getHeight()); setZoomUISize(); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/54a6dc1cc81e06c2190546075a6c5a04f18d9bb5/LensController.java/buggy/SRC/org/openmicroscopy/shoola/util/ui/lens/LensController.java |
h = (int)(scaledH/lensModel.getImageZoomFactor()); | h = (int) (scaledH/lensModel.getImageZoomFactor()); | void setLensSize(int w, int h) { int scaledW, scaledH; scaledW = (int)(w*lensModel.getImageZoomFactor()); scaledH = (int)(h*lensModel.getImageZoomFactor()); if (lens.getX()+scaledW > lensModel.getImageScaledWidth()) { scaledW = lensModel.getImageScaledWidth()-lens.getX(); w = (int)(scaledW/lensModel.getImageZoomFactor()); } if (lens.getY()+scaledH > lensModel.getImageScaledHeight()) { scaledH = lensModel.getImageScaledHeight()-lens.getY(); h = (int)(scaledH/lensModel.getImageZoomFactor()); } lensModel.setWidth(w); lensModel.setHeight(h); lens.setSize(scaledW, scaledH); zoomWindow.setZoomImage(lensModel.getZoomedImage()); zoomWindow.setLensWidthHeight(lensModel.getWidth(), lensModel.getHeight()); setZoomUISize(); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/54a6dc1cc81e06c2190546075a6c5a04f18d9bb5/LensController.java/buggy/SRC/org/openmicroscopy/shoola/util/ui/lens/LensController.java |
lensModel.getHeight()); | lensModel.getHeight()); | void setLensSize(int w, int h) { int scaledW, scaledH; scaledW = (int)(w*lensModel.getImageZoomFactor()); scaledH = (int)(h*lensModel.getImageZoomFactor()); if (lens.getX()+scaledW > lensModel.getImageScaledWidth()) { scaledW = lensModel.getImageScaledWidth()-lens.getX(); w = (int)(scaledW/lensModel.getImageZoomFactor()); } if (lens.getY()+scaledH > lensModel.getImageScaledHeight()) { scaledH = lensModel.getImageScaledHeight()-lens.getY(); h = (int)(scaledH/lensModel.getImageZoomFactor()); } lensModel.setWidth(w); lensModel.setHeight(h); lens.setSize(scaledW, scaledH); zoomWindow.setZoomImage(lensModel.getZoomedImage()); zoomWindow.setLensWidthHeight(lensModel.getWidth(), lensModel.getHeight()); setZoomUISize(); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/54a6dc1cc81e06c2190546075a6c5a04f18d9bb5/LensController.java/buggy/SRC/org/openmicroscopy/shoola/util/ui/lens/LensController.java |
return path.replace('/', '\\'); | return path.replace('\\', '/'); | private String getCorrectedPath(String path) { return path.replace('/', '\\'); } | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/c26f5a170c752d9d1d5b884dd7eb60b982637269/FileFinder.java/buggy/cobertura/src/net/sourceforge/cobertura/util/FileFinder.java |
Set images = model.getBrowser().getSelectedDisplays(); Iterator i = images.iterator(); while (i.hasNext()) { is = (ImageData) ((ImageDisplay) i.next()).getHierarchyObject(); | if (model != null) { Set images = model.getBrowser().getSelectedDisplays(); Iterator i = images.iterator(); ImageDisplay d; while (i.hasNext()) { d = (ImageDisplay) i.next(); is = (ImageData) d.getHierarchyObject(); eventBus.post(new ViewImage(is.getId(), is.getDefaultPixels().getId(), is.getName())); } } else { | public void execute() { if (model != null && hierarchyObject == null) { ImageDisplay selectedDisplay = model.getBrowser(). getLastSelectedDisplay(); hierarchyObject = (DataObject) selectedDisplay.getHierarchyObject(); } if (hierarchyObject == null) return; if (hierarchyObject instanceof DatasetData) HiViewerAgent.browse(Browse.DATASET, ((DatasetData) hierarchyObject).getId(), model.getRootLevel(), model.getRootID()); else if (hierarchyObject instanceof ProjectData) HiViewerAgent.browse(Browse.PROJECT, ((ProjectData) hierarchyObject).getId(), model.getRootLevel(), model.getRootID()); else if (hierarchyObject instanceof CategoryGroupData) HiViewerAgent.browse(Browse.CATEGORY_GROUP, ((CategoryGroupData) hierarchyObject).getId(), model.getRootLevel(), model.getRootID()); else if (hierarchyObject instanceof CategoryData) HiViewerAgent.browse(Browse.CATEGORY, ((CategoryData) hierarchyObject).getId(), model.getRootLevel(), model.getRootID()); else if (hierarchyObject instanceof ImageData) { EventBus eventBus = HiViewerAgent.getRegistry().getEventBus(); ImageData is = (ImageData) hierarchyObject; Set images = model.getBrowser().getSelectedDisplays(); Iterator i = images.iterator(); while (i.hasNext()) { is = (ImageData) ((ImageDisplay) i.next()).getHierarchyObject(); eventBus.post(new ViewImage(is.getId(), is.getDefaultPixels().getId(), is.getName())); } } } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/c513fc33e821b9c890f8a2c7a4a60440417fbe92/ViewCmd.java/clean/SRC/org/openmicroscopy/shoola/agents/hiviewer/cmd/ViewCmd.java |
if (!isRegistered) { | boolean reg = TransportManager.isRegistered(SparkManager.getConnection(), transport); if (!reg) { | private void addTransport(final Transport transport) { final StatusBar statusBar = SparkManager.getWorkspace().getStatusBar(); final JPanel commandPanel = statusBar.getCommandPanel(); final boolean isRegistered = TransportManager.isRegistered(SparkManager.getConnection(), transport); final RolloverButton button = new RolloverButton(); if (!isRegistered) { button.setIcon(transport.getInactiveIcon()); } else { button.setIcon(transport.getIcon()); } button.setToolTipText(transport.getInstructions()); commandPanel.add(button); button.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { if (!isRegistered) { TransportManager.registerWithService(SparkManager.getConnection(), transport.getServiceName()); // Send Presence Presence presence = statusBar.getPresence(); statusBar.changeAvailability(presence); } else { int confirm = JOptionPane.showConfirmDialog(SparkManager.getMainWindow(), "Would you like to disable this active transport?", "Disable Transport", JOptionPane.YES_NO_OPTION); if (confirm == JOptionPane.YES_OPTION) { try { TransportManager.unregister(SparkManager.getConnection(), transport.getServiceName()); } catch (XMPPException e1) { e1.printStackTrace(); } } } } }); uiMap.put(transport, button); statusBar.invalidate(); statusBar.validate(); statusBar.repaint(); } | 52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/741ee521da25f1d1608a575dbda0a84d216ed278/GatewayPlugin.java/buggy/src/java/org/jivesoftware/sparkimpl/plugin/gateways/GatewayPlugin.java |
try { populateTransports(SparkManager.getConnection()); } catch (Exception e) { return; } for (final Transport transport : TransportManager.getTransports()) { addTransport(transport); } SparkManager.getConnection().addPacketListener(new PacketListener() { public void processPacket(Packet packet) { Presence presence = (Presence)packet; Transport transport = TransportManager.getTransport(packet.getFrom()); if (transport != null) { boolean registered = presence != null && presence.getMode() != null; RolloverButton button = uiMap.get(transport); if (!registered) { button.setIcon(transport.getInactiveIcon()); } else { button.setIcon(transport.getIcon()); | SwingWorker thread = new SwingWorker() { public Object construct() { try { populateTransports(SparkManager.getConnection()); for (final Transport transport : TransportManager.getTransports()) { addTransport(transport); | public void initialize() { try { populateTransports(SparkManager.getConnection()); } catch (Exception e) { return; } for (final Transport transport : TransportManager.getTransports()) { addTransport(transport); } SparkManager.getConnection().addPacketListener(new PacketListener() { public void processPacket(Packet packet) { Presence presence = (Presence)packet; Transport transport = TransportManager.getTransport(packet.getFrom()); if (transport != null) { boolean registered = presence != null && presence.getMode() != null; RolloverButton button = uiMap.get(transport); if (!registered) { button.setIcon(transport.getInactiveIcon()); } else { button.setIcon(transport.getIcon()); } } } }, new PacketTypeFilter(Presence.class)); } | 52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/741ee521da25f1d1608a575dbda0a84d216ed278/GatewayPlugin.java/buggy/src/java/org/jivesoftware/sparkimpl/plugin/gateways/GatewayPlugin.java |
}, new PacketTypeFilter(Presence.class)); | public void initialize() { try { populateTransports(SparkManager.getConnection()); } catch (Exception e) { return; } for (final Transport transport : TransportManager.getTransports()) { addTransport(transport); } SparkManager.getConnection().addPacketListener(new PacketListener() { public void processPacket(Packet packet) { Presence presence = (Presence)packet; Transport transport = TransportManager.getTransport(packet.getFrom()); if (transport != null) { boolean registered = presence != null && presence.getMode() != null; RolloverButton button = uiMap.get(transport); if (!registered) { button.setIcon(transport.getInactiveIcon()); } else { button.setIcon(transport.getIcon()); } } } }, new PacketTypeFilter(Presence.class)); } | 52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/741ee521da25f1d1608a575dbda0a84d216ed278/GatewayPlugin.java/buggy/src/java/org/jivesoftware/sparkimpl/plugin/gateways/GatewayPlugin.java |
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public void finished() { Boolean b = (Boolean)get(); if (!b) { return; } SparkManager.getConnection().addPacketListener(new PacketListener() { public void processPacket(Packet packet) { Presence presence = (Presence)packet; Transport transport = TransportManager.getTransport(packet.getFrom()); if (transport != null) { boolean registered = presence != null && presence.getMode() != null; if (presence.getType() == Presence.Type.UNAVAILABLE) { registered = false; } RolloverButton button = uiMap.get(transport); if (!registered) { button.setIcon(transport.getInactiveIcon()); } else { button.setIcon(transport.getIcon()); } } } }, new PacketTypeFilter(Presence.class)); } }; thread.start(); | public void initialize() { try { populateTransports(SparkManager.getConnection()); } catch (Exception e) { return; } for (final Transport transport : TransportManager.getTransports()) { addTransport(transport); } SparkManager.getConnection().addPacketListener(new PacketListener() { public void processPacket(Packet packet) { Presence presence = (Presence)packet; Transport transport = TransportManager.getTransport(packet.getFrom()); if (transport != null) { boolean registered = presence != null && presence.getMode() != null; RolloverButton button = uiMap.get(transport); if (!registered) { button.setIcon(transport.getInactiveIcon()); } else { button.setIcon(transport.getIcon()); } } } }, new PacketTypeFilter(Presence.class)); } | 52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/741ee521da25f1d1608a575dbda0a84d216ed278/GatewayPlugin.java/buggy/src/java/org/jivesoftware/sparkimpl/plugin/gateways/GatewayPlugin.java |
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if (presence == null || presence.getType() == Presence.Type.UNAVAILABLE) { registered = false; } | public static boolean isRegistered(XMPPConnection con, Transport transport) { Presence presence = con.getRoster().getPresence(transport.getServiceName()); boolean registered = presence != null && presence.getMode() != null; return registered; } | 52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/741ee521da25f1d1608a575dbda0a84d216ed278/TransportManager.java/buggy/src/java/org/jivesoftware/sparkimpl/plugin/gateways/transports/TransportManager.java |
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dialog.setLocationRelativeTo(SparkManager.getMainWindow()); | public static void registerWithService(final XMPPConnection con, final String serviceName) { final JPanel mainPanel = new JPanel(); mainPanel.setLayout(new BorderLayout()); final TransportRegistrationPanel regPanel = new TransportRegistrationPanel(serviceName); mainPanel.add(regPanel, BorderLayout.CENTER); final JPanel buttonPanel = new JPanel(new FlowLayout(FlowLayout.RIGHT)); final RolloverButton registerButton = new RolloverButton("Register", null); final RolloverButton cancelButton = new RolloverButton("Cancel", null); buttonPanel.add(registerButton); buttonPanel.add(cancelButton); mainPanel.add(buttonPanel, BorderLayout.SOUTH); // Create Dialog Transport transport = TransportManager.getTransport(serviceName); final JDialog dialog = new JDialog(SparkManager.getMainWindow(), transport.getTitle(), true); dialog.add(mainPanel); dialog.pack(); dialog.setLocationRelativeTo(SparkManager.getMainWindow()); dialog.setSize(400, 200); registerButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { String username = regPanel.getScreenName(); String password = regPanel.getPassword(); if (!ModelUtil.hasLength(username) || !ModelUtil.hasLength(password)) { JOptionPane.showMessageDialog(mainPanel, "Username and/or Password need to be supplied.", "Registration Error", JOptionPane.ERROR_MESSAGE); return; } try { registerUser(con, serviceName, username, password); // Send updated presence. } catch (XMPPException e1) { JOptionPane.showMessageDialog(mainPanel, "Unable to register with Transport.", "Registration Error", JOptionPane.ERROR_MESSAGE); } dialog.dispose(); } }); cancelButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { dialog.dispose(); } }); dialog.setVisible(true); } | 52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/741ee521da25f1d1608a575dbda0a84d216ed278/TransportManager.java/buggy/src/java/org/jivesoftware/sparkimpl/plugin/gateways/transports/TransportManager.java |
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public static void registerWithService(final XMPPConnection con, final String serviceName) { final JPanel mainPanel = new JPanel(); mainPanel.setLayout(new BorderLayout()); final TransportRegistrationPanel regPanel = new TransportRegistrationPanel(serviceName); mainPanel.add(regPanel, BorderLayout.CENTER); final JPanel buttonPanel = new JPanel(new FlowLayout(FlowLayout.RIGHT)); final RolloverButton registerButton = new RolloverButton("Register", null); final RolloverButton cancelButton = new RolloverButton("Cancel", null); buttonPanel.add(registerButton); buttonPanel.add(cancelButton); mainPanel.add(buttonPanel, BorderLayout.SOUTH); // Create Dialog Transport transport = TransportManager.getTransport(serviceName); final JDialog dialog = new JDialog(SparkManager.getMainWindow(), transport.getTitle(), true); dialog.add(mainPanel); dialog.pack(); dialog.setLocationRelativeTo(SparkManager.getMainWindow()); dialog.setSize(400, 200); registerButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { String username = regPanel.getScreenName(); String password = regPanel.getPassword(); if (!ModelUtil.hasLength(username) || !ModelUtil.hasLength(password)) { JOptionPane.showMessageDialog(mainPanel, "Username and/or Password need to be supplied.", "Registration Error", JOptionPane.ERROR_MESSAGE); return; } try { registerUser(con, serviceName, username, password); // Send updated presence. } catch (XMPPException e1) { JOptionPane.showMessageDialog(mainPanel, "Unable to register with Transport.", "Registration Error", JOptionPane.ERROR_MESSAGE); } dialog.dispose(); } }); cancelButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { dialog.dispose(); } }); dialog.setVisible(true); } | 52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/741ee521da25f1d1608a575dbda0a84d216ed278/TransportManager.java/buggy/src/java/org/jivesoftware/sparkimpl/plugin/gateways/transports/TransportManager.java |
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getFileSet(dir); | FileSet fileSet = getFileSet(dir); fileSet.createInclude().setName("**/*.class"); | private void createFilesetForDirectory(File dir) { getFileSet(dir); } | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/a670a0ef78cf3202902926dd2a32a79b05d6f75d/InstrumentTask.java/clean/cobertura/src/net/sourceforge/cobertura/ant/InstrumentTask.java |
throw new BuildException("'includeClasses' is required when 'fromClasspath' is used"); | throw new BuildException("'includeClasses' is required when 'instrumentationClasspath' is used"); | private void processInstrumentationClasspath() { if (includeClassesRegexs.size() == 0) { throw new BuildException("'includeClasses' is required when 'fromClasspath' is used"); } String[] sources = instrumentationClasspath.list(); for (int i = 0; i < sources.length; i++) { File fileOrDir = new File(sources[i]); if (fileOrDir.exists()) { if (fileOrDir.isDirectory()) { createFilesetForDirectory(fileOrDir); } else { addFileToFilesets(fileOrDir); } } } } | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/a670a0ef78cf3202902926dd2a32a79b05d6f75d/InstrumentTask.java/clean/cobertura/src/net/sourceforge/cobertura/ant/InstrumentTask.java |
active = false; | imageDisplay = false; | ViewerUIF(ViewerCtrl control, Registry registry, PixelsDimensions pxsDims, int defaultT, int defaultZ) { super(""); this.control = control; im = IconManager.getInstance(registry); windowWidth = DEFAULT_WINDOW_SIZE; windowHeight = DEFAULT_WINDOW_SIZE; active = false; int maxT = pxsDims.sizeT-1, maxZ = pxsDims.sizeZ-1; setJMenuBar(createMenuBar(maxZ, maxT)); initBars(registry, maxT, defaultT, maxZ, defaultZ); initSliders(maxT, defaultT, maxZ, defaultZ); initContainers(); buildGUI(); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/02bc3351cbc1f2e45d28539c79317f881c2ec11b/ViewerUIF.java/clean/SRC/org/openmicroscopy/shoola/agents/viewer/ViewerUIF.java |
private void buildGUI() { Container container = getContentPane(); container.add(toolBar, BorderLayout.NORTH); container.add(buildMain(), BorderLayout.WEST); container.add(scrollPane, BorderLayout.CENTER); container.add(bottomBar, BorderLayout.SOUTH); //Configure the display buttons in the TaskBar. //configureDisplayButtons(); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/02bc3351cbc1f2e45d28539c79317f881c2ec11b/ViewerUIF.java/clean/SRC/org/openmicroscopy/shoola/agents/viewer/ViewerUIF.java |
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if (!active) { | if (!imageDisplay) { | void setImage(BufferedImage img) { if (!active) { int w = img.getWidth()+2*START, h = img.getHeight()+2*START; setSizePaintedComponents(new Dimension(w, h)); w += 2*START; h += 2*START; setWindowSize(w, h); } canvas.paintImage(img); active = true; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/02bc3351cbc1f2e45d28539c79317f881c2ec11b/ViewerUIF.java/clean/SRC/org/openmicroscopy/shoola/agents/viewer/ViewerUIF.java |
active = true; | setImageDisplay(true); | void setImage(BufferedImage img) { if (!active) { int w = img.getWidth()+2*START, h = img.getHeight()+2*START; setSizePaintedComponents(new Dimension(w, h)); w += 2*START; h += 2*START; setWindowSize(w, h); } canvas.paintImage(img); active = true; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/02bc3351cbc1f2e45d28539c79317f881c2ec11b/ViewerUIF.java/clean/SRC/org/openmicroscopy/shoola/agents/viewer/ViewerUIF.java |
xImageCanvas = 0; yImageCanvas = 0; | public LensCanvas() { setDoubleBuffered(true); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/6cdba81978070c672e8a5dc97117fa5d977eb25f/LensCanvas.java/buggy/SRC/org/openmicroscopy/shoola/agents/viewer/canvas/LensCanvas.java |
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isInit = true; | public ZoomPanel(ImageInspectorManager manager) { this.manager = manager; setDoubleBuffered(true); setBackground(Viewer.BACKGROUND_COLOR); magFactor = ImageInspectorManager.ZOOM_DEFAULT; isInit = true; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/020251919a9bc041ddec075006ba48f2bcfddd48/ZoomPanel.java/clean/SRC/org/openmicroscopy/shoola/agents/viewer/transform/zooming/ZoomPanel.java |
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BufferedImage image = manager.getBufferedImage(); | public void paint(Graphics g) { super.paintComponent(g); BufferedImage image = manager.getBufferedImage(); Graphics2D g2D = (Graphics2D) g; if (isInit) setLocation(); g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); g2D.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY); g2D.setColor(Color.black); AffineTransform at = new AffineTransform(); at.scale(magFactor, magFactor); BufferedImage bimg = new BufferedImage(image.getWidth(), image.getHeight(), BufferedImage.TYPE_INT_RGB); RescaleOp rop = new RescaleOp((float) magFactor, 0.0f, null); rop.filter(image, bimg); BufferedImageOp biop = new AffineTransformOp(at, AffineTransformOp.TYPE_BILINEAR); g2D.drawImage(bimg, biop, x, y); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/020251919a9bc041ddec075006ba48f2bcfddd48/ZoomPanel.java/clean/SRC/org/openmicroscopy/shoola/agents/viewer/transform/zooming/ZoomPanel.java |
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if (isInit) setLocation(); | setLocation(); | public void paint(Graphics g) { super.paintComponent(g); BufferedImage image = manager.getBufferedImage(); Graphics2D g2D = (Graphics2D) g; if (isInit) setLocation(); g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); g2D.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY); g2D.setColor(Color.black); AffineTransform at = new AffineTransform(); at.scale(magFactor, magFactor); BufferedImage bimg = new BufferedImage(image.getWidth(), image.getHeight(), BufferedImage.TYPE_INT_RGB); RescaleOp rop = new RescaleOp((float) magFactor, 0.0f, null); rop.filter(image, bimg); BufferedImageOp biop = new AffineTransformOp(at, AffineTransformOp.TYPE_BILINEAR); g2D.drawImage(bimg, biop, x, y); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/020251919a9bc041ddec075006ba48f2bcfddd48/ZoomPanel.java/clean/SRC/org/openmicroscopy/shoola/agents/viewer/transform/zooming/ZoomPanel.java |
g2D.setColor(Color.black); AffineTransform at = new AffineTransform(); at.scale(magFactor, magFactor); BufferedImage bimg = new BufferedImage(image.getWidth(), image.getHeight(), BufferedImage.TYPE_INT_RGB); RescaleOp rop = new RescaleOp((float) magFactor, 0.0f, null); rop.filter(image, bimg); BufferedImageOp biop = new AffineTransformOp(at, AffineTransformOp.TYPE_BILINEAR); | g2D.setColor(Color.black); | public void paint(Graphics g) { super.paintComponent(g); BufferedImage image = manager.getBufferedImage(); Graphics2D g2D = (Graphics2D) g; if (isInit) setLocation(); g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); g2D.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY); g2D.setColor(Color.black); AffineTransform at = new AffineTransform(); at.scale(magFactor, magFactor); BufferedImage bimg = new BufferedImage(image.getWidth(), image.getHeight(), BufferedImage.TYPE_INT_RGB); RescaleOp rop = new RescaleOp((float) magFactor, 0.0f, null); rop.filter(image, bimg); BufferedImageOp biop = new AffineTransformOp(at, AffineTransformOp.TYPE_BILINEAR); g2D.drawImage(bimg, biop, x, y); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/020251919a9bc041ddec075006ba48f2bcfddd48/ZoomPanel.java/clean/SRC/org/openmicroscopy/shoola/agents/viewer/transform/zooming/ZoomPanel.java |
public void paintImage(double level, int x, int y) | public void paintImage(double level, int w, int h) | public void paintImage(double level, int x, int y) { magFactor = level; isInit = false; this.x = x; this.y = y; repaint(); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/020251919a9bc041ddec075006ba48f2bcfddd48/ZoomPanel.java/clean/SRC/org/openmicroscopy/shoola/agents/viewer/transform/zooming/ZoomPanel.java |
isInit = false; this.x = x; this.y = y; | this.w = w; this.h = h; BufferedImage image = manager.getBufferedImage(); AffineTransform at = new AffineTransform(); at.scale(magFactor, magFactor); bimg = new BufferedImage(image.getWidth(), image.getHeight(), BufferedImage.TYPE_INT_RGB); RescaleOp rop = new RescaleOp((float) magFactor, 0.0f, null); rop.filter(image, bimg); biop = new AffineTransformOp(at, AffineTransformOp.TYPE_BILINEAR); | public void paintImage(double level, int x, int y) { magFactor = level; isInit = false; this.x = x; this.y = y; repaint(); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/020251919a9bc041ddec075006ba48f2bcfddd48/ZoomPanel.java/clean/SRC/org/openmicroscopy/shoola/agents/viewer/transform/zooming/ZoomPanel.java |
Rectangle d = getBounds(); x = (int) (d.width-manager.getImageWidth())/2; y = (int) (d.height-manager.getImageHeight())/2; | Rectangle r = manager.getScrollPane().getViewportBorderBounds(); x = (int) (r.width-w)/2; y = (int) (r.height-h)/2; | private void setLocation() { Rectangle d = getBounds(); x = (int) (d.width-manager.getImageWidth())/2; y = (int) (d.height-manager.getImageHeight())/2; if (x < 0) x = 0; if (y < 0) y = 0; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/020251919a9bc041ddec075006ba48f2bcfddd48/ZoomPanel.java/clean/SRC/org/openmicroscopy/shoola/agents/viewer/transform/zooming/ZoomPanel.java |
RubyString string = new RubyString(runtime, line); | RubyString string = runtime.newString(line); | public IRubyObject backtrace() { IRubyObject rubyTrace = super.backtrace(); if (rubyTrace.isNil()) return rubyTrace; RubyArray array = (RubyArray) rubyTrace; StackTraceElement[] stackTrace = cause.getStackTrace(); for (int i=stackTrace.length-1; i>=0; i--) { StackTraceElement element = stackTrace[i]; String line = element.toString(); RubyString string = new RubyString(runtime, line); array.unshift(string); } return rubyTrace; } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/9f2efc63a858fa0507245b207025eab027840a04/NativeException.java/buggy/src/org/jruby/NativeException.java |
hook = (Runnable) shutdownHooks.removeFirst(); | hook = (Runnable) shutdownHooks.removeLast(); | private void notifyShutdownHooks() { while (!shutdownHooks.isEmpty()) { Runnable hook; synchronized (shutdownHooks) { hook = (Runnable) shutdownHooks.removeFirst(); } try { hook.run(); } catch (Throwable e) { log.warn("Error from kernel shutdown hook", e); } } } | 52533 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52533/4e058fb9713f5562d177ef9ad0111005cd8cf4b9/SimpleKernel.java/buggy/kernel/src/java/org/gbean/kernel/simple/SimpleKernel.java |
if (directive == null) | Directive d; try { d = (Directive) desc.dirClass.newInstance(); } catch (Exception e) { | public Object build(BuildContext bc) throws BuildException { if (directive == null) throw new BuildException("Error instantiating Directive object for #" + desc.name); return directive.build(this, bc); } | 52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/67f3bf2b9347218e8efc5ecece60bb5f03730152/DirectiveBuilder.java/buggy/webmacro/src/org/webmacro/directive/DirectiveBuilder.java |
return directive.build(this, bc); | }; return d.build(this, bc); | public Object build(BuildContext bc) throws BuildException { if (directive == null) throw new BuildException("Error instantiating Directive object for #" + desc.name); return directive.build(this, bc); } | 52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/67f3bf2b9347218e8efc5ecece60bb5f03730152/DirectiveBuilder.java/buggy/webmacro/src/org/webmacro/directive/DirectiveBuilder.java |
System.err.println ("render: >"); | protected String renderGT() { System.err.println ("render: >"); return ">"; } | 52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/58f597f486d55f02379b21ea0b08e5858ea34948/HTMLPageRenderer.java/clean/wiki/src/org/tcdi/opensource/wiki/renderer/HTMLPageRenderer.java |
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System.err.println ("render: <"); | protected String renderLT() { System.err.println ("render: <"); return "<"; } | 52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/58f597f486d55f02379b21ea0b08e5858ea34948/HTMLPageRenderer.java/clean/wiki/src/org/tcdi/opensource/wiki/renderer/HTMLPageRenderer.java |
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throws org.hibernate.HibernateException, java.sql.SQLException | throws org.hibernate.HibernateException, java.sql.SQLException | public Object doInHibernate(org.hibernate.Session session) throws org.hibernate.HibernateException, java.sql.SQLException { Experimenter o = (Experimenter) session.get(Experimenter.class, new Integer(1)); if (o == null) { o = new Experimenter(); o.setOmeName("test"); session.save(o); } Event e = (Event) session.get(Event.class, new Integer(1)); if (e == null) { e = new Event(); e.setName("test"); session.save(e); } ome.model.core.Pixels p = new ome.model.core.Pixels(); p.setSizeX(new Integer(1)); p.setSizeY(new Integer(1)); p.setSizeZ(new Integer(1)); p.setSizeC(new Integer(1)); p.setSizeT(new Integer(1)); p.setSha1("09bc7b2dcc9a510f4ab3a40c47f7a4cb77954356"); // "pixels" p.setBigEndian(Boolean.TRUE); p.setCreationEvent(e); p.setOwner(o); session.save(p); return null; }; | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/68fcf3cc1b9292144736bb3f929fd5962e8aa2b0/PlaneIOUnitTest.java/clean/components/omeio-nio/test/ome/io/nio/itests/PlaneIOUnitTest.java |
Experimenter o = (Experimenter) session.get(Experimenter.class, new Integer(1)); if (o == null) { o = new Experimenter(); o.setOmeName("test"); session.save(o); } | Experimenter e = new Experimenter(); e.setOmeName("test"); session.save(e); | public Object doInHibernate(org.hibernate.Session session) throws org.hibernate.HibernateException, java.sql.SQLException { Experimenter o = (Experimenter) session.get(Experimenter.class, new Integer(1)); if (o == null) { o = new Experimenter(); o.setOmeName("test"); session.save(o); } Event e = (Event) session.get(Event.class, new Integer(1)); if (e == null) { e = new Event(); e.setName("test"); session.save(e); } ome.model.core.Pixels p = new ome.model.core.Pixels(); p.setSizeX(new Integer(1)); p.setSizeY(new Integer(1)); p.setSizeZ(new Integer(1)); p.setSizeC(new Integer(1)); p.setSizeT(new Integer(1)); p.setSha1("09bc7b2dcc9a510f4ab3a40c47f7a4cb77954356"); // "pixels" p.setBigEndian(Boolean.TRUE); p.setCreationEvent(e); p.setOwner(o); session.save(p); return null; }; | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/68fcf3cc1b9292144736bb3f929fd5962e8aa2b0/PlaneIOUnitTest.java/clean/components/omeio-nio/test/ome/io/nio/itests/PlaneIOUnitTest.java |
Event e = (Event) session.get(Event.class, new Integer(1)); if (e == null) { e = new Event(); e.setName("test"); session.save(e); } ome.model.core.Pixels p = new ome.model.core.Pixels(); p.setSizeX(new Integer(1)); p.setSizeY(new Integer(1)); p.setSizeZ(new Integer(1)); p.setSizeC(new Integer(1)); p.setSizeT(new Integer(1)); p.setSha1("09bc7b2dcc9a510f4ab3a40c47f7a4cb77954356"); p.setBigEndian(Boolean.TRUE); p.setCreationEvent(e); p.setOwner(o); session.save(p); return null; }; | return e; } | public Object doInHibernate(org.hibernate.Session session) throws org.hibernate.HibernateException, java.sql.SQLException { Experimenter o = (Experimenter) session.get(Experimenter.class, new Integer(1)); if (o == null) { o = new Experimenter(); o.setOmeName("test"); session.save(o); } Event e = (Event) session.get(Event.class, new Integer(1)); if (e == null) { e = new Event(); e.setName("test"); session.save(e); } ome.model.core.Pixels p = new ome.model.core.Pixels(); p.setSizeX(new Integer(1)); p.setSizeY(new Integer(1)); p.setSizeZ(new Integer(1)); p.setSizeC(new Integer(1)); p.setSizeT(new Integer(1)); p.setSha1("09bc7b2dcc9a510f4ab3a40c47f7a4cb77954356"); // "pixels" p.setBigEndian(Boolean.TRUE); p.setCreationEvent(e); p.setOwner(o); session.save(p); return null; }; | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/68fcf3cc1b9292144736bb3f929fd5962e8aa2b0/PlaneIOUnitTest.java/clean/components/omeio-nio/test/ome/io/nio/itests/PlaneIOUnitTest.java |
protected void setUp() | protected void setUp() throws IOException | protected void setUp() { String[] paths = new String[] { "config.xml", "data.xml", "hibernate.xml" }; ctx = new ClassPathXmlApplicationContext(paths); ht = (HibernateTemplate) ctx.getBean("hibernateTemplate"); ht.execute(new HibernateCallback() { public Object doInHibernate(org.hibernate.Session session) throws org.hibernate.HibernateException, java.sql.SQLException { Experimenter o = (Experimenter) session.get(Experimenter.class, new Integer(1)); if (o == null) { o = new Experimenter(); o.setOmeName("test"); session.save(o); } Event e = (Event) session.get(Event.class, new Integer(1)); if (e == null) { e = new Event(); e.setName("test"); session.save(e); } ome.model.core.Pixels p = new ome.model.core.Pixels(); p.setSizeX(new Integer(1)); p.setSizeY(new Integer(1)); p.setSizeZ(new Integer(1)); p.setSizeC(new Integer(1)); p.setSizeT(new Integer(1)); p.setSha1("09bc7b2dcc9a510f4ab3a40c47f7a4cb77954356"); // "pixels" p.setBigEndian(Boolean.TRUE); p.setCreationEvent(e); p.setOwner(o); session.save(p); return null; }; }); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/68fcf3cc1b9292144736bb3f929fd5962e8aa2b0/PlaneIOUnitTest.java/clean/components/omeio-nio/test/ome/io/nio/itests/PlaneIOUnitTest.java |
String[] paths = new String[] { "config.xml", "data.xml", "hibernate.xml" }; ctx = new ClassPathXmlApplicationContext(paths); ht = (HibernateTemplate) ctx.getBean("hibernateTemplate"); ht.execute(new HibernateCallback() { public Object doInHibernate(org.hibernate.Session session) throws org.hibernate.HibernateException, java.sql.SQLException { Experimenter o = (Experimenter) session.get(Experimenter.class, new Integer(1)); if (o == null) { o = new Experimenter(); o.setOmeName("test"); session.save(o); } Event e = (Event) session.get(Event.class, new Integer(1)); if (e == null) { e = new Event(); e.setName("test"); session.save(e); } ome.model.core.Pixels p = new ome.model.core.Pixels(); p.setSizeX(new Integer(1)); p.setSizeY(new Integer(1)); p.setSizeZ(new Integer(1)); p.setSizeC(new Integer(1)); p.setSizeT(new Integer(1)); p.setSha1("09bc7b2dcc9a510f4ab3a40c47f7a4cb77954356"); p.setBigEndian(Boolean.TRUE); p.setCreationEvent(e); p.setOwner(o); session.save(p); return null; }; }); | initHibernate(); createExperimenter(); createEvent(); createPixels(); createPlanes(); | protected void setUp() { String[] paths = new String[] { "config.xml", "data.xml", "hibernate.xml" }; ctx = new ClassPathXmlApplicationContext(paths); ht = (HibernateTemplate) ctx.getBean("hibernateTemplate"); ht.execute(new HibernateCallback() { public Object doInHibernate(org.hibernate.Session session) throws org.hibernate.HibernateException, java.sql.SQLException { Experimenter o = (Experimenter) session.get(Experimenter.class, new Integer(1)); if (o == null) { o = new Experimenter(); o.setOmeName("test"); session.save(o); } Event e = (Event) session.get(Event.class, new Integer(1)); if (e == null) { e = new Event(); e.setName("test"); session.save(e); } ome.model.core.Pixels p = new ome.model.core.Pixels(); p.setSizeX(new Integer(1)); p.setSizeY(new Integer(1)); p.setSizeZ(new Integer(1)); p.setSizeC(new Integer(1)); p.setSizeT(new Integer(1)); p.setSha1("09bc7b2dcc9a510f4ab3a40c47f7a4cb77954356"); // "pixels" p.setBigEndian(Boolean.TRUE); p.setCreationEvent(e); p.setOwner(o); session.save(p); return null; }; }); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/68fcf3cc1b9292144736bb3f929fd5962e8aa2b0/PlaneIOUnitTest.java/clean/components/omeio-nio/test/ome/io/nio/itests/PlaneIOUnitTest.java |
PixelsService service = PixelsService.getInstance(); PixelBuffer pixbuf = service.getPixelBuffer(pixels); MappedByteBuffer plane = pixbuf.getPlane(0, 0, 0); byte[] messageDigest = calculateMessageDigest(plane); System.out.println("Size: " + plane); FileOutputStream stream = new FileOutputStream("/tmp/file"); stream.getChannel().write(plane); assertEquals(bytesToHex(originalDigests[0]), bytesToHex(messageDigest)); | public void testInitialPlane() { } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/68fcf3cc1b9292144736bb3f929fd5962e8aa2b0/PlaneIOUnitTest.java/clean/components/omeio-nio/test/ome/io/nio/itests/PlaneIOUnitTest.java |
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String stringPattern = RubyString.stringValue(args[0]).getValue(); | String stringPattern = RubyString.stringValue(args[0]).toString(); | private RubyRegexp getPattern(IRubyObject[] args) { if (args.length == 0) { isWhitespace = true; return RubyRegexp.newRegexp(runtime, "\\s+", 0, null); } if (args[0] instanceof RubyRegexp) { // Even if we have whitespace-only explicit regexp we do not // mark it as whitespace. Apparently, this is so ruby can // still get the do not ignore the front match behavior. return RubyRegexp.regexpValue(args[0]); } String stringPattern = RubyString.stringValue(args[0]).getValue(); if (stringPattern.equals(" ")) { isWhitespace = true; return RubyRegexp.newRegexp(runtime, "\\s+", 0, null); } return RubyRegexp.newRegexp(runtime, unescapeString(stringPattern), 0, null); } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/9f2efc63a858fa0507245b207025eab027840a04/Split.java/clean/src/org/jruby/util/Split.java |
addResult(((RubyString) matchValue).getValue()); | addResult(((RubyString) matchValue).toString()); | private void process() { if (limit == 1) { result.add(splitee); return; } int last = 0; int beg = 0; int hits = 0; int len = splitee.length(); while ((beg = pattern.searchAgain(splitee)) > -1) { hits++; RubyMatchData matchData = (RubyMatchData) runtime.getCurrentContext().getBackref(); int end = matchData.matchEndPosition(); // Skip first positive lookahead match if (beg == 0 && beg == end) { continue; } // Whitespace splits are supposed to ignore leading whitespace if (beg != 0 || !isWhitespace) { addResult(substring(splitee, last, (beg == last && end == beg) ? 1 : beg - last)); // Add to list any /(.)/ matched. long extraPatterns = matchData.getSize(); for (int i = 1; i < extraPatterns; i++) { IRubyObject matchValue = matchData.group(i); if (!matchValue.isNil()) { addResult(((RubyString) matchValue).getValue()); } } } last = end; if (hits + 1 == limit) { break; } } if (hits == 0) { addResult(splitee); } else if (last <= len) { addResult(substring(splitee, last, len - last)); } if (limit == 0 && result.size() > 0) { for (int size = result.size() - 1; size >= 0 && ((String) result.get(size)).length() == 0; size--) { result.remove(size); } } } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/9f2efc63a858fa0507245b207025eab027840a04/Split.java/clean/src/org/jruby/util/Split.java |
public PixelBuffer (Integer id, Pixels pixels) | PixelBuffer (Pixels pixels) | public PixelBuffer (Integer id, Pixels pixels) { if (id == null) throw new NullPointerException("Expecting a not-null id."); this.pixels = pixels; this.id = id; path = Helper.getPixelsPath(id); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/c6065155c8d58fa2e2cf56d5d32b743b599a8a5f/PixelBuffer.java/buggy/components/omeio-nio/src/ome/io/nio/PixelBuffer.java |
if (id == null) throw new NullPointerException("Expecting a not-null id."); | if (pixels == null) throw new NullPointerException( "Expecting a not-null pixels element."); | public PixelBuffer (Integer id, Pixels pixels) { if (id == null) throw new NullPointerException("Expecting a not-null id."); this.pixels = pixels; this.id = id; path = Helper.getPixelsPath(id); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/c6065155c8d58fa2e2cf56d5d32b743b599a8a5f/PixelBuffer.java/buggy/components/omeio-nio/src/ome/io/nio/PixelBuffer.java |
this.id = id; path = Helper.getPixelsPath(id); | path = Helper.getPixelsPath(pixels.getId()); | public PixelBuffer (Integer id, Pixels pixels) { if (id == null) throw new NullPointerException("Expecting a not-null id."); this.pixels = pixels; this.id = id; path = Helper.getPixelsPath(id); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/c6065155c8d58fa2e2cf56d5d32b743b599a8a5f/PixelBuffer.java/buggy/components/omeio-nio/src/ome/io/nio/PixelBuffer.java |
return 2; | return 16; | int getBitDepth() { return 2; // FIXME pixels.getPixelsType(); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/c6065155c8d58fa2e2cf56d5d32b743b599a8a5f/PixelBuffer.java/buggy/components/omeio-nio/src/ome/io/nio/PixelBuffer.java |
public MappedByteBuffer getPlane(Integer z, Integer c, Integer t) throws IOException { Long offset = getPlaneOffset(z, c, t); Integer size = getPlaneSize(); return getRegion(size, offset); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/c6065155c8d58fa2e2cf56d5d32b743b599a8a5f/PixelBuffer.java/buggy/components/omeio-nio/src/ome/io/nio/PixelBuffer.java |
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planeSize = getSizeX() * getSizeY() * getBitDepth(); | planeSize = getSizeX() * getSizeY() * getByteWidth(); | public Integer getPlaneSize() { if (planeSize == null) planeSize = getSizeX() * getSizeY() * getBitDepth(); return planeSize; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/c6065155c8d58fa2e2cf56d5d32b743b599a8a5f/PixelBuffer.java/buggy/components/omeio-nio/src/ome/io/nio/PixelBuffer.java |
reverse = new ReverseModelMapper(); | protected void setUp() throws Exception { DataSource dataSource = (DataSource) factory.ctx.getBean("dataSource"); data = new OMEData(); data.setDataSource(dataSource); psrv = factory.getPojosService(); q = factory.getQueryService(); u = factory.getUpdateService(); mapper = new Model2PojosMapper(); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0aa4af63b981e511b5fb82621bc6293945ca0d64/PojosServiceTest.java/clean/components/shoola-adapter/test/ome/adapters/pojos/itests/PojosServiceTest.java |
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Image img = (Image) reverse.map(imgData); img = (Image) psrv.createDataObject(img,null); assertNotNull("We should get something back",img); assertNotNull("Should have an id",img.getId()); Image img2 = (Image) q.getById(Image.class,img.getId()); assertNotNull("And we should be able to find it again.",img2); | public void testNowLetsTryToSaveSomething() throws Exception { // prepare data ImageData imgData = new ImageData(); imgData.setName("My test image"); imgData.setDescription("My test description"); // convert it // FIXME mapper.reverse } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0aa4af63b981e511b5fb82621bc6293945ca0d64/PojosServiceTest.java/clean/components/shoola-adapter/test/ome/adapters/pojos/itests/PojosServiceTest.java |
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public void visitBeanDefinition(BeanDefinition beanDefinition) throws BeansException { super.visitBeanDefinition(beanDefinition); | public void visitBeanDefinition(BeanDefinition beanDefinition, Object data) throws BeansException { super.visitBeanDefinition(beanDefinition, data); | public void visitBeanDefinition(BeanDefinition beanDefinition) throws BeansException { super.visitBeanDefinition(beanDefinition); if (!(beanDefinition instanceof RootBeanDefinition)) { return; } RootBeanDefinition rootBeanDefinition = ((RootBeanDefinition) beanDefinition); Class beanType = rootBeanDefinition.getBeanClass(); for (Iterator iterator = lifecycleMap.entrySet().iterator(); iterator.hasNext();) { Map.Entry entry = (Map.Entry) iterator.next(); Class lifecycleInterface = (Class) entry.getKey(); LifecycleMethods value = (LifecycleMethods) entry.getValue(); if (lifecycleInterface.isAssignableFrom(beanType)) { if (rootBeanDefinition.getInitMethodName() == null) { rootBeanDefinition.setInitMethodName(value.initMethodName); } if (rootBeanDefinition.getDestroyMethodName() == null) { rootBeanDefinition.setDestroyMethodName(value.destroyMethodName); } if (rootBeanDefinition.getInitMethodName() != null && rootBeanDefinition.getDestroyMethodName() != null) { return; } } } } | 52533 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52533/6a661ce4fbc3261ed4b3a744b1e1919df53cbbf7/LifecycleDetector.java/buggy/kernel/src/java/org/gbean/spring/LifecycleDetector.java |
void visitBeanFactory(ConfigurableListableBeanFactory beanRegistry) throws BeansException; | void visitBeanFactory(ConfigurableListableBeanFactory beanRegistry, Object data) throws BeansException; | void visitBeanFactory(ConfigurableListableBeanFactory beanRegistry) throws BeansException; | 52533 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52533/6a661ce4fbc3261ed4b3a744b1e1919df53cbbf7/SpringVisitor.java/buggy/kernel/src/java/org/gbean/spring/SpringVisitor.java |
synchronized(_clock) { if ((TIME - dateTime) > 1000) { date = new Date(TIME); } return date; } | synchronized(_lock) { if (_clock != null) { if ((TIME - dateTime) > 1000) { date = new Date(TIME); } } else { date = new Date(); } return date; } | public static Date getDate() { synchronized(_clock) { if ((TIME - dateTime) > 1000) { date = new Date(TIME); } return date; } } | 52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/65c210c2e5230f99b78b769799e9e54e3fcce30a/Clock.java/buggy/webmacro/src/org/webmacro/util/Clock.java |
args = (args != null) ? args : new RubyObject[0]; | public RubyObject execute(RubyObject recv, RubyObject[] args, Ruby ruby) { testArgsCount(args); // testArgsClass(args); return invokeMethod(recv, args, ruby); } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/12847c6fd28fea4e223d132ced46eb1b4cb9de9a/ReflectionCallbackMethod.java/buggy/org/jruby/core/ReflectionCallbackMethod.java |
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if (methodArgs == null || methodArgs.length == 0) { | if (methodArgs.length == 0) { | protected String getExceptedArgsString(RubyObject[] methodArgs) { StringBuffer sb = new StringBuffer(); sb.append("Wrong arguments:"); if (methodArgs == null || methodArgs.length == 0) { sb.append(" No args"); } else { sb.append(" ("); for (int i = 0; i < methodArgs.length; i++) { if (i > 0) { sb.append(", "); } String className = methodArgs[i].getClass().getName(); className = className.substring(className.lastIndexOf(".Ruby") + 5); sb.append("a"); if (className.charAt(0) == 'A' || className.charAt(0) == 'E' || className.charAt(0) == 'I' || className.charAt(0) == 'O' || className.charAt(0) == 'U') { sb.append("n"); } sb.append(className); } sb.append(")"); } sb.append(" given, "); if (args == null || args.length == 0) { sb.append("no arguments excepted."); } else { sb.append("("); for (int i = 0; i < args.length; i++) { if (i > 0) { sb.append(","); } String className = args[i].getName(); sb.append("a").append(className.substring(className.lastIndexOf(".Ruby") + 5)); } if (restArgs) { sb.append(", ..."); } sb.append(") excepted."); } return sb.toString(); } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/12847c6fd28fea4e223d132ced46eb1b4cb9de9a/ReflectionCallbackMethod.java/buggy/org/jruby/core/ReflectionCallbackMethod.java |
if (args == null || args.length == 0) { | if (args.length == 0) { | protected String getExceptedArgsString(RubyObject[] methodArgs) { StringBuffer sb = new StringBuffer(); sb.append("Wrong arguments:"); if (methodArgs == null || methodArgs.length == 0) { sb.append(" No args"); } else { sb.append(" ("); for (int i = 0; i < methodArgs.length; i++) { if (i > 0) { sb.append(", "); } String className = methodArgs[i].getClass().getName(); className = className.substring(className.lastIndexOf(".Ruby") + 5); sb.append("a"); if (className.charAt(0) == 'A' || className.charAt(0) == 'E' || className.charAt(0) == 'I' || className.charAt(0) == 'O' || className.charAt(0) == 'U') { sb.append("n"); } sb.append(className); } sb.append(")"); } sb.append(" given, "); if (args == null || args.length == 0) { sb.append("no arguments excepted."); } else { sb.append("("); for (int i = 0; i < args.length; i++) { if (i > 0) { sb.append(","); } String className = args[i].getName(); sb.append("a").append(className.substring(className.lastIndexOf(".Ruby") + 5)); } if (restArgs) { sb.append(", ..."); } sb.append(") excepted."); } return sb.toString(); } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/12847c6fd28fea4e223d132ced46eb1b4cb9de9a/ReflectionCallbackMethod.java/buggy/org/jruby/core/ReflectionCallbackMethod.java |
if (methodArgs == null) { methodArgs = new Object[0]; } | protected RubyObject invokeMethod(RubyObject recv, Object[] methodArgs, Ruby ruby) { if (methodArgs == null) { methodArgs = new Object[0]; } if (restArgs) { RubyObject[] restArray = new RubyObject[methodArgs.length - (args.length - 1)]; Object[] newMethodArgs = new Object[args.length]; System.arraycopy(methodArgs, args.length - 1, restArray, 0, methodArgs.length - (args.length - 1)); System.arraycopy(methodArgs, 0, newMethodArgs, 0, args.length - 1); newMethodArgs[args.length - 1] = restArray; methodArgs = newMethodArgs; } if (staticMethod) { Object[] newMethodArgs = new Object[methodArgs.length + 1]; System.arraycopy(methodArgs, 0, newMethodArgs, 1, methodArgs.length); newMethodArgs[0] = ruby; methodArgs = newMethodArgs; } try { return (RubyObject)getMethod().invoke(staticMethod ? null : recv, methodArgs); } catch (IllegalAccessException iaExcptn) { throw new RuntimeException("IllegalAccessException: Cannot invoke method \"" + methodName + "\" in class \"" + klass.getName() + "\" by Reflection."); } catch (IllegalArgumentException iaExcptn) { throw new RuntimeException("IllegalArgumentException: Cannot invoke method \"" + methodName + "\" in class \"" + klass.getName() + "\" by Reflection."); } catch (InvocationTargetException itExcptn) { throw new RuntimeException("InvocationTargetException: Cannot invoke method \"" + methodName + "\" in class \"" + klass.getName() + "\" by Reflection."); } } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/12847c6fd28fea4e223d132ced46eb1b4cb9de9a/ReflectionCallbackMethod.java/buggy/org/jruby/core/ReflectionCallbackMethod.java |
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System.arraycopy(methodArgs, args.length - 1, restArray, 0, methodArgs.length - (args.length - 1)); | try { System.arraycopy(methodArgs, args.length - 1, restArray, 0, methodArgs.length - (args.length - 1)); } catch (ArrayIndexOutOfBoundsException aioobExcptn) { throw new RuntimeException("Cannot call \"" + methodName + "\" in class \"" + klass.getName() + "\". " + getExceptedArgsString((RubyObject[])methodArgs)); } | protected RubyObject invokeMethod(RubyObject recv, Object[] methodArgs, Ruby ruby) { if (methodArgs == null) { methodArgs = new Object[0]; } if (restArgs) { RubyObject[] restArray = new RubyObject[methodArgs.length - (args.length - 1)]; Object[] newMethodArgs = new Object[args.length]; System.arraycopy(methodArgs, args.length - 1, restArray, 0, methodArgs.length - (args.length - 1)); System.arraycopy(methodArgs, 0, newMethodArgs, 0, args.length - 1); newMethodArgs[args.length - 1] = restArray; methodArgs = newMethodArgs; } if (staticMethod) { Object[] newMethodArgs = new Object[methodArgs.length + 1]; System.arraycopy(methodArgs, 0, newMethodArgs, 1, methodArgs.length); newMethodArgs[0] = ruby; methodArgs = newMethodArgs; } try { return (RubyObject)getMethod().invoke(staticMethod ? null : recv, methodArgs); } catch (IllegalAccessException iaExcptn) { throw new RuntimeException("IllegalAccessException: Cannot invoke method \"" + methodName + "\" in class \"" + klass.getName() + "\" by Reflection."); } catch (IllegalArgumentException iaExcptn) { throw new RuntimeException("IllegalArgumentException: Cannot invoke method \"" + methodName + "\" in class \"" + klass.getName() + "\" by Reflection."); } catch (InvocationTargetException itExcptn) { throw new RuntimeException("InvocationTargetException: Cannot invoke method \"" + methodName + "\" in class \"" + klass.getName() + "\" by Reflection."); } } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/12847c6fd28fea4e223d132ced46eb1b4cb9de9a/ReflectionCallbackMethod.java/buggy/org/jruby/core/ReflectionCallbackMethod.java |
} catch (IllegalAccessException iaExcptn) { | } catch (Exception excptn) { excptn.printStackTrace(); return null; } /* } catch (IllegalAccessException iaExcptn) { | protected RubyObject invokeMethod(RubyObject recv, Object[] methodArgs, Ruby ruby) { if (methodArgs == null) { methodArgs = new Object[0]; } if (restArgs) { RubyObject[] restArray = new RubyObject[methodArgs.length - (args.length - 1)]; Object[] newMethodArgs = new Object[args.length]; System.arraycopy(methodArgs, args.length - 1, restArray, 0, methodArgs.length - (args.length - 1)); System.arraycopy(methodArgs, 0, newMethodArgs, 0, args.length - 1); newMethodArgs[args.length - 1] = restArray; methodArgs = newMethodArgs; } if (staticMethod) { Object[] newMethodArgs = new Object[methodArgs.length + 1]; System.arraycopy(methodArgs, 0, newMethodArgs, 1, methodArgs.length); newMethodArgs[0] = ruby; methodArgs = newMethodArgs; } try { return (RubyObject)getMethod().invoke(staticMethod ? null : recv, methodArgs); } catch (IllegalAccessException iaExcptn) { throw new RuntimeException("IllegalAccessException: Cannot invoke method \"" + methodName + "\" in class \"" + klass.getName() + "\" by Reflection."); } catch (IllegalArgumentException iaExcptn) { throw new RuntimeException("IllegalArgumentException: Cannot invoke method \"" + methodName + "\" in class \"" + klass.getName() + "\" by Reflection."); } catch (InvocationTargetException itExcptn) { throw new RuntimeException("InvocationTargetException: Cannot invoke method \"" + methodName + "\" in class \"" + klass.getName() + "\" by Reflection."); } } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/12847c6fd28fea4e223d132ced46eb1b4cb9de9a/ReflectionCallbackMethod.java/buggy/org/jruby/core/ReflectionCallbackMethod.java |
} | }*/ | protected RubyObject invokeMethod(RubyObject recv, Object[] methodArgs, Ruby ruby) { if (methodArgs == null) { methodArgs = new Object[0]; } if (restArgs) { RubyObject[] restArray = new RubyObject[methodArgs.length - (args.length - 1)]; Object[] newMethodArgs = new Object[args.length]; System.arraycopy(methodArgs, args.length - 1, restArray, 0, methodArgs.length - (args.length - 1)); System.arraycopy(methodArgs, 0, newMethodArgs, 0, args.length - 1); newMethodArgs[args.length - 1] = restArray; methodArgs = newMethodArgs; } if (staticMethod) { Object[] newMethodArgs = new Object[methodArgs.length + 1]; System.arraycopy(methodArgs, 0, newMethodArgs, 1, methodArgs.length); newMethodArgs[0] = ruby; methodArgs = newMethodArgs; } try { return (RubyObject)getMethod().invoke(staticMethod ? null : recv, methodArgs); } catch (IllegalAccessException iaExcptn) { throw new RuntimeException("IllegalAccessException: Cannot invoke method \"" + methodName + "\" in class \"" + klass.getName() + "\" by Reflection."); } catch (IllegalArgumentException iaExcptn) { throw new RuntimeException("IllegalArgumentException: Cannot invoke method \"" + methodName + "\" in class \"" + klass.getName() + "\" by Reflection."); } catch (InvocationTargetException itExcptn) { throw new RuntimeException("InvocationTargetException: Cannot invoke method \"" + methodName + "\" in class \"" + klass.getName() + "\" by Reflection."); } } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/12847c6fd28fea4e223d132ced46eb1b4cb9de9a/ReflectionCallbackMethod.java/buggy/org/jruby/core/ReflectionCallbackMethod.java |
if (args == null && methodArgs != null && methodArgs.length > 0) { throw new RubyArgumentException(getExceptedArgsString(methodArgs)); } else if (args == null && (methodArgs == null || methodArgs.length == 0)) { return; | if (args.length == 0) { if (methodArgs.length > 0) { throw new RubyArgumentException(getExceptedArgsString(methodArgs)); } | protected void testArgsCount(RubyObject[] methodArgs) { if (args == null && methodArgs != null && methodArgs.length > 0) { throw new RubyArgumentException(getExceptedArgsString(methodArgs)); } else if (args == null && (methodArgs == null || methodArgs.length == 0)) { return; } else if (restArgs) { if (methodArgs == null && (args.length == 1)) { return; } else if (methodArgs.length < (args.length - 1)) { throw new RubyArgumentException(getExceptedArgsString(methodArgs)); } } else { if ((methodArgs == null) || (methodArgs.length != args.length)) { throw new RubyArgumentException(getExceptedArgsString(methodArgs)); } } } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/12847c6fd28fea4e223d132ced46eb1b4cb9de9a/ReflectionCallbackMethod.java/buggy/org/jruby/core/ReflectionCallbackMethod.java |
if (methodArgs == null && (args.length == 1)) { return; } else if (methodArgs.length < (args.length - 1)) { | if (methodArgs.length < (args.length - 1)) { | protected void testArgsCount(RubyObject[] methodArgs) { if (args == null && methodArgs != null && methodArgs.length > 0) { throw new RubyArgumentException(getExceptedArgsString(methodArgs)); } else if (args == null && (methodArgs == null || methodArgs.length == 0)) { return; } else if (restArgs) { if (methodArgs == null && (args.length == 1)) { return; } else if (methodArgs.length < (args.length - 1)) { throw new RubyArgumentException(getExceptedArgsString(methodArgs)); } } else { if ((methodArgs == null) || (methodArgs.length != args.length)) { throw new RubyArgumentException(getExceptedArgsString(methodArgs)); } } } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/12847c6fd28fea4e223d132ced46eb1b4cb9de9a/ReflectionCallbackMethod.java/buggy/org/jruby/core/ReflectionCallbackMethod.java |
if ((methodArgs == null) || (methodArgs.length != args.length)) { | if (methodArgs.length != args.length) { | protected void testArgsCount(RubyObject[] methodArgs) { if (args == null && methodArgs != null && methodArgs.length > 0) { throw new RubyArgumentException(getExceptedArgsString(methodArgs)); } else if (args == null && (methodArgs == null || methodArgs.length == 0)) { return; } else if (restArgs) { if (methodArgs == null && (args.length == 1)) { return; } else if (methodArgs.length < (args.length - 1)) { throw new RubyArgumentException(getExceptedArgsString(methodArgs)); } } else { if ((methodArgs == null) || (methodArgs.length != args.length)) { throw new RubyArgumentException(getExceptedArgsString(methodArgs)); } } } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/12847c6fd28fea4e223d132ced46eb1b4cb9de9a/ReflectionCallbackMethod.java/buggy/org/jruby/core/ReflectionCallbackMethod.java |
return value.getClass(); | return value != null ? value.getClass() : Object.class; | public Class getJavaClass() { return value.getClass(); } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/6fda4255fb336c02e8aa77d67d7707262531e781/JavaObject.java/buggy/src/org/jruby/javasupport/JavaObject.java |
public void setIvar(RubyId id, RubyObject value) { | public RubyObject setIvar(RubyId id, RubyObject value) { return null; | public void setIvar(RubyId id, RubyObject value) { //return null; } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/f1e2c45b99e6f9a2be3f15f5fd7ad91c7e086a2c/RubyObject.java/clean/org/jruby/RubyObject.java |
System.out.println("BAD PATTERN: " + e.getPattern()); | public String[] getNames() { try { getFiles(); } catch (PatternSyntaxException e) { System.out.println("BAD PATTERN: " + e.getPattern()); // This can happen if someone does Dir.glob("{") or similiar. return new String[] {}; } Collection allMatchedNames = new TreeSet(); for (Iterator iter = patterns.iterator(); iter.hasNext();) { GlobPattern pattern = (GlobPattern) iter.next(); allMatchedNames.addAll(pattern.getMatchedFiles()); } return (String[]) allMatchedNames.toArray(new String[allMatchedNames.size()]); } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/b4a189a27604d62c317938f16a124fb9dab1e94a/Glob.java/buggy/src/org/jruby/util/Glob.java |
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try { target = (Collection) source.getClass().newInstance(); model2target.put(source,target); } catch (InstantiationException ie){ throw new RuntimeException(ie); } catch (IllegalAccessException iae){ throw new RuntimeException(iae); } | if (Set.class.isAssignableFrom(source.getClass())) { target = new HashSet(); } else if (List.class.isAssignableFrom(source.getClass())) { target = new ArrayList(); } else { throw new RuntimeException("Unknown collection type: " +source.getClass()); } model2target.put(source,target); | public Collection findCollection(Collection source){ if (source==null) return null; Collection target = (Collection) model2target.get(source); if (null==target) { try { target = (Collection) source.getClass().newInstance(); // TODO do we want to use the map here? model2target.put(source,target); } catch (InstantiationException ie){ throw new RuntimeException(ie); } catch (IllegalAccessException iae){ throw new RuntimeException(iae); } } return target; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/ModelMapper.java/buggy/components/common/src/ome/util/ModelMapper.java |
if (null == current | current instanceof Integer | current instanceof String) { | if (null == current || current instanceof Number || current instanceof String) | public Object findTarget(Object current){ // IMMUTABLES if (null == current | current instanceof Integer | current instanceof String) // TODO can use findTarget then for these as well. { return current; } else // Special cases TODO put into doFindTarget if (current instanceof Date){ return new Timestamp(((Date)current).getTime()); // FIXME should cache these in model2pojo } Object target = model2target.get(current); if (null == target) { Class targetType = findClass(current.getClass()); if (null != targetType){ try { target = targetType.newInstance(); } catch (Exception e) { throw new RuntimeException("Internal error: could not instantiate object of type "+targetType+" while trying to map "+current,e); } model2target.put(current,target); } else { throw new RuntimeException("Internal error: could not find target class type for "+current.getClass()); } } return target; } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0b36a8e77f5bacb7e122d76ffce01866205b09d7/ModelMapper.java/buggy/components/common/src/ome/util/ModelMapper.java |
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