bugged stringlengths 6 599k | fixed stringlengths 10 599k | __index_level_0__ int64 0 1.13M |
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public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) { ApplicationConfig config =... | public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) { ApplicationConfig config =... | 1,110,924 |
void readPedGenotypes(String[] f){ //input is a 3 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = max comparison distance (don't compute d' if markers are greater than this dist apart) inputOptions = f; File p... | void readPedGenotypes(String[] f){ //input is a 3 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = max comparison distance (don't compute d' if markers are greater than this dist apart) inputOptions = f; File p... | 1,110,925 |
void readPedGenotypes(String[] f){ //input is a 3 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = max comparison distance (don't compute d' if markers are greater than this dist apart) inputOptions = f; File p... | void readPedGenotypes(String[] f){ //input is a 3 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = max comparison distance (don't compute d' if markers are greater than this dist apart) inputOptions = f; File p... | 1,110,926 |
public void stateChanged(ChangeEvent e) { int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ exportMenuItems[0].setEnabled(true); exportMenuItems[1].setEnabled(true); }else if (tabNum == VIEW_TDT_NUM || tabNum... | public void stateChanged(ChangeEvent e) { int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ exportMenuItems[0].setEnabled(true); exportMenuItems[1].setEnabled(true); }else if (tabNum == VIEW_TDT_NUM || tabNum... | 1,110,927 |
public void stateChanged(ChangeEvent e) { int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ exportMenuItems[0].setEnabled(true); exportMenuItems[1].setEnabled(true); }else if (tabNum == VIEW_TDT_NUM || tabNum... | public void stateChanged(ChangeEvent e) { int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ exportMenuItems[0].setEnabled(true); exportMenuItems[1].setEnabled(true); }else if (tabNum == VIEW_TDT_NUM || tabNum... | 1,110,928 |
public void stateChanged(ChangeEvent e) { int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ exportMenuItems[0].setEnabled(true); exportMenuItems[1].setEnabled(true); }else if (tabNum == VIEW_TDT_NUM || tabNum... | public void stateChanged(ChangeEvent e) { int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ exportMenuItems[0].setEnabled(true); exportMenuItems[1].setEnabled(true); }else if (tabNum == VIEW_TDT_NUM || tabNum... | 1,110,929 |
public static void main(String[] args) { boolean nogui = false; //HaploView window; for(int i = 0;i<args.length;i++) { if(args[i].equals("-n") || args[i].equals("-h")) { nogui = true; } } if(nogui) { HaploText textOnly = new HaploTex... | public static void main(String[] args) { boolean nogui = false; //HaploView window; for(int i = 0;i<args.length;i++) { if(args[i].equals("-n") || args[i].equals("-h")) { nogui = true; } } if(nogui) { HaploText textOnly = new HaploTex... | 1,110,930 |
void processData() { maxCompDist = Long.parseLong(inputOptions[2])*1000; this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); final SwingWorker worker = new SwingWorker(){ public Object construct(){ dPrimeDisplay=null; theData.infoKnown = fals... | void processData() { maxCompDist = Long.parseLong(inputOptions[2])*1000; this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); final SwingWorker worker = new SwingWorker(){ public Object construct(){ dPrimeDisplay=null; theData.infoKnown = fals... | 1,110,931 |
public Object construct(){ dPrimeDisplay=null; theData.infoKnown = false; if (!(inputOptions[1].equals(""))){ readMarkers(new File(inputOptions[1])); } theData.generateDPrimeTable(maxCompDist); theDa... | public Object construct(){ dPrimeDisplay=null; theData.infoKnown = false; if (!(inputOptions[1].equals(""))){ readMarkers(new File(inputOptions[1])); } theData.generateDPrimeTable(maxCompDist); theDa... | 1,110,932 |
void readPedGenotypes(String[] f){ //input is a 3 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = max comparison distance (don't compute d' if markers are greater than this dist apart) inputOptions = f; File p... | void readPedGenotypes(String[] f){ //input is a 3 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = max comparison distance (don't compute d' if markers are greater than this dist apart) inputOptions = f; File p... | 1,110,933 |
void readPhasedGenotypes(String[] f){ //input is a 3 element array with //inputOptions[0] = haps file //inputOptions[1] = info file (null if none) //inputOptions[2] = max comparison distance (don't compute d' if markers are greater than this dist apart) //these are not available f... | void readPhasedGenotypes(String[] f){ //input is a 3 element array with //inputOptions[0] = haps file //inputOptions[1] = info file (null if none) //inputOptions[2] = max comparison distance (don't compute d' if markers are greater than this dist apart) //these are not available f... | 1,110,934 |
public static Volume getVolume( String volName ) { Volume vol = null; // Initialize the volumes array and create default volume if it has not been done yet if ( volumes == null ) { getDefaultVolume(); } vol = (Volume) volumes.get( volName ); return vol; } | public static Volume getVolume( String volName ) { Volume vol = null; // Initialize the volumes array and create default volume if it has not been done yet if ( volumes == null ) { getDefaultVolume(); } vol = (Volume) volumes.get( volName ); return vol; } | 1,110,935 |
public TablePane(SQLTable m, PlayPen parentPP) { super(parentPP.getPlayPenContentPane()); setModel(m); setOpaque(true); setInsertionPoint(COLUMN_INDEX_NONE); //dt = new DropTarget(parentPP, new TablePaneDropListener(this)); dtl = new TablePaneDropListener(this); updateUI(); } | public TablePane(SQLTable m, PlayPen parentPP) { super(parentPP.getPlayPenContentPane()); setModel(m); setOpaque(true); setInsertionPoint(COLUMN_INDEX_NONE); //dt = new DropTarget(parentPP, new TablePaneDropListener(this)); dtl = new TablePaneDropListener(this); updateUI(); } | 1,110,936 |
public void dbStructureChanged(SQLObjectEvent e) { if (e.getSource() == model.getColumnsFolder()) { int numCols = e.getChildren().length; columnSelection = new ArrayList(numCols); for (int i = 0; i < numCols; i++) { columnSelection.add(Boolean.FALSE); } columnHighlight = new ArrayList(numCols); for (in... | public void dbStructureChanged(SQLObjectEvent e) { if (e.getSource() == model.getColumnsFolder()) { int numCols = e.getChildren().length; columnSelection = new ArrayList<Boolean>(numCols); for (int i = 0; i < numCols; i++) { columnSelection.add(Boolean.FALSE); } columnHighlight = new ArrayList(numCols); ... | 1,110,937 |
public void dbStructureChanged(SQLObjectEvent e) { if (e.getSource() == model.getColumnsFolder()) { int numCols = e.getChildren().length; columnSelection = new ArrayList(numCols); for (int i = 0; i < numCols; i++) { columnSelection.add(Boolean.FALSE); } columnHighlight = new ArrayList(numCols); for (in... | public void dbStructureChanged(SQLObjectEvent e) { if (e.getSource() == model.getColumnsFolder()) { int numCols = e.getChildren().length; columnSelection = new ArrayList(numCols); for (int i = 0; i < numCols; i++) { columnSelection.add(Boolean.FALSE); } columnHighlight = new ArrayList<Color>(numCols); ... | 1,110,938 |
protected void fireSelectionEvent(SelectionEvent e) { if (logger.isDebugEnabled()) { logger.debug("Notifying "+selectionListeners.size() +" listeners of selection change"); } Iterator it = selectionListeners.iterator(); if (e.getType() == SelectionEvent.SELECTION_EVENT) { while (it.hasNext()) { ((Sele... | protected void fireSelectionEvent(SelectionEvent e) { if (logger.isDebugEnabled()) { logger.debug("Notifying "+selectionListeners.size() +" listeners of selection change"); } Iterator<SelectionListener> it = selectionListeners.iterator(); if (e.getType() == SelectionEvent.SELECTION_EVENT) { while (it.has... | 1,110,939 |
protected void fireSelectionEvent(SelectionEvent e) { if (logger.isDebugEnabled()) { logger.debug("Notifying "+selectionListeners.size() +" listeners of selection change"); } Iterator it = selectionListeners.iterator(); if (e.getType() == SelectionEvent.SELECTION_EVENT) { while (it.hasNext()) { ((Sele... | protected void fireSelectionEvent(SelectionEvent e) { if (logger.isDebugEnabled()) { logger.debug("Notifying "+selectionListeners.size() +" listeners of selection change"); } Iterator it = selectionListeners.iterator(); if (e.getType() == SelectionEvent.SELECTION_EVENT) { while (it.hasNext()) { it.nex... | 1,110,940 |
protected void fireSelectionEvent(SelectionEvent e) { if (logger.isDebugEnabled()) { logger.debug("Notifying "+selectionListeners.size() +" listeners of selection change"); } Iterator it = selectionListeners.iterator(); if (e.getType() == SelectionEvent.SELECTION_EVENT) { while (it.hasNext()) { ((Sele... | protected void fireSelectionEvent(SelectionEvent e) { if (logger.isDebugEnabled()) { logger.debug("Notifying "+selectionListeners.size() +" listeners of selection change"); } Iterator it = selectionListeners.iterator(); if (e.getType() == SelectionEvent.SELECTION_EVENT) { while (it.hasNext()) { ((Sele... | 1,110,941 |
public void setModel(SQLTable m) { SQLTable old = model; if (m == null) { throw new IllegalArgumentException("model may not be null"); } else { model = m; } if (old != null) { try { ArchitectUtils.unlistenToHierarchy(this, old); } catch (ArchitectException e) { logger.error("Caught exception while... | public void setModel(SQLTable m) { SQLTable old = model; if (m == null) { throw new IllegalArgumentException("model may not be null"); } else { model = m; } if (old != null) { try { ArchitectUtils.unlistenToHierarchy(this, old); } catch (ArchitectException e) { logger.error("Caught exception while... | 1,110,942 |
public void setModel(SQLTable m) { SQLTable old = model; if (m == null) { throw new IllegalArgumentException("model may not be null"); } else { model = m; } if (old != null) { try { ArchitectUtils.unlistenToHierarchy(this, old); } catch (ArchitectException e) { logger.error("Caught exception while... | public void setModel(SQLTable m) { SQLTable old = model; if (m == null) { throw new IllegalArgumentException("model may not be null"); } else { model = m; } if (old != null) { try { ArchitectUtils.unlistenToHierarchy(this, old); } catch (ArchitectException e) { logger.error("Caught exception while... | 1,110,943 |
public Dimension getPreferredSize(JComponent jc) { TablePane c = (TablePane) jc; SQLTable table = c.getModel(); if (table == null) return null; int height = 0; int width = 0; try { Insets insets = c.getInsets(); java.util.List columnList = table.getColumns(); int cols = columnList.size(); Font font = c.g... | public Dimension getPreferredSize(JComponent jc) { TablePane c = (TablePane) jc; SQLTable table = c.getModel(); if (table == null) return null; int height = 0; int width = 0; try { Insets insets = c.getInsets(); java.util.List columnList = table.getColumns(); int cols = columnList.size(); Font font = c.g... | 1,110,945 |
public Dimension getPreferredSize(JComponent jc) { TablePane c = (TablePane) jc; SQLTable table = c.getModel(); if (table == null) return null; int height = 0; int width = 0; try { Insets insets = c.getInsets(); java.util.List columnList = table.getColumns(); int cols = columnList.size(); Font font = c.g... | public Dimension getPreferredSize(JComponent jc) { TablePane c = (TablePane) jc; SQLTable table = c.getModel(); if (table == null) return null; int height = 0; int width = 0; try { Insets insets = c.getInsets(); java.util.List columnList = table.getColumns(); int cols = columnList.size(); Font font = c.g... | 1,110,946 |
public PairwiseLinkage computeDPrime(int pos1, int pos2){ compsDone++; int doublehet = 0; int[][] twoMarkerHaplos = new int[3][3]; for (int i = 0; i < twoMarkerHaplos.length; i++){ for (int j = 0; j < twoMarkerHaplos[i].length; j++){ twoMarkerHaplos[i][j] = 0; ... | public PairwiseLinkage computeDPrime(int pos1, int pos2){ compsDone++; int doublehet = 0; int[][] twoMarkerHaplos = new int[3][3]; for (int i = 0; i < twoMarkerHaplos.length; i++){ for (int j = 0; j < twoMarkerHaplos[i].length; j++){ twoMarkerHaplos[i][j] = 0; ... | 1,110,947 |
void generateDPrimeTable(long maxdist){ //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset dPrimeTable = new PairwiseLinkage[Chromosome.getSize()][Chromosome.getSize()]; long negMaxdist = -1*maxdist; totalComps = (Chromosome.getSize()*(C... | void generateDPrimeTable(){ //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset dPrimeTable = new PairwiseLinkage[Chromosome.getSize()][Chromosome.getSize()]; long negMaxdist = -1*maxdist; totalComps = (Chromosome.getSize()*(Chromosome.ge... | 1,110,948 |
void generateDPrimeTable(long maxdist){ //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset dPrimeTable = new PairwiseLinkage[Chromosome.getSize()][Chromosome.getSize()]; long negMaxdist = -1*maxdist; totalComps = (Chromosome.getSize()*(C... | void generateDPrimeTable(long maxdist){ //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset dPrimeTable = new PairwiseLinkage[Chromosome.getSize()][Chromosome.getSize()]; totalComps = (Chromosome.getSize()*(Chromosome.getSize()-1))/2; ... | 1,110,949 |
void generateDPrimeTable(long maxdist){ //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset dPrimeTable = new PairwiseLinkage[Chromosome.getSize()][Chromosome.getSize()]; long negMaxdist = -1*maxdist; totalComps = (Chromosome.getSize()*(C... | void generateDPrimeTable(long maxdist){ //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset dPrimeTable = new PairwiseLinkage[Chromosome.getSize()][Chromosome.getSize()]; long negMaxdist = -1*maxdist; totalComps = (Chromosome.getSize()*(C... | 1,110,950 |
void prepareMarkerInput(File infile, long maxdist, String[][] hapmapGoodies) throws IOException, HaploViewException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position... | void prepareMarkerInput(File infile, long md, String[][] hapmapGoodies) throws IOException, HaploViewException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position. the... | 1,110,951 |
void prepareMarkerInput(File infile, long maxdist, String[][] hapmapGoodies) throws IOException, HaploViewException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position... | void prepareMarkerInput(File infile, long maxdist, String[][] hapmapGoodies) throws IOException, HaploViewException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position... | 1,110,952 |
public void mouseClicked(MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON1_MASK) == InputEvent.BUTTON1_MASK) { int clickX = e.getX(); int clickY = e.getY(); if (showWM && worldmapRect.contains(clickX,clickY)){ //convert a click on the wo... | public void mouseClicked(MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON1_MASK) == InputEvent.BUTTON1_MASK) { int clickX = e.getX(); int clickY = e.getY(); if (showWM && wmInteriorRect.contains(clickX,clickY)){ //convert a click on the ... | 1,110,953 |
public void mouseClicked(MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON1_MASK) == InputEvent.BUTTON1_MASK) { int clickX = e.getX(); int clickY = e.getY(); if (showWM && worldmapRect.contains(clickX,clickY)){ //convert a click on the wo... | public void mouseClicked(MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON1_MASK) == InputEvent.BUTTON1_MASK) { int clickX = e.getX(); int clickY = e.getY(); if (showWM && worldmapRect.contains(clickX,clickY)){ //convert a click on the wo... | 1,110,954 |
public void mouseClicked(MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON1_MASK) == InputEvent.BUTTON1_MASK) { int clickX = e.getX(); int clickY = e.getY(); if (showWM && worldmapRect.contains(clickX,clickY)){ //convert a click on the wo... | public void mouseClicked(MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON1_MASK) == InputEvent.BUTTON1_MASK) { int clickX = e.getX(); int clickY = e.getY(); if (showWM && worldmapRect.contains(clickX,clickY)){ //convert a click on the wo... | 1,110,955 |
public void mouseDragged(MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON1_MASK) == InputEvent.BUTTON1_MASK) { //conveniently, we can tell what do do with the drag event //based on what the cursor is if (getCursor() == Cursor.getPredefinedCursor(Cursor... | public void mouseDragged(MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON1_MASK) == InputEvent.BUTTON1_MASK) { //conveniently, we can tell what do do with the drag event //based on what the cursor is if (getCursor() == Cursor.getPredefinedCursor(Cursor... | 1,110,956 |
public void mouseDragged(MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON1_MASK) == InputEvent.BUTTON1_MASK) { //conveniently, we can tell what do do with the drag event //based on what the cursor is if (getCursor() == Cursor.getPredefinedCursor(Cursor... | public void mouseDragged(MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON1_MASK) == InputEvent.BUTTON1_MASK) { //conveniently, we can tell what do do with the drag event //based on what the cursor is if (getCursor() == Cursor.getPredefinedCursor(Cursor... | 1,110,957 |
public void mousePressed (MouseEvent e) { Rectangle blockselector = new Rectangle(clickXShift-boxRadius,clickYShift - boxRadius, (Chromosome.getFilteredSize()*boxSize), boxSize); //if users right clicks & holds, pop up the info if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == ... | public void mousePressed (MouseEvent e) { Rectangle blockselector = new Rectangle(clickXShift-boxRadius,clickYShift - boxRadius, (Chromosome.getFilteredSize()*boxSize), boxSize); //if users right clicks & holds, pop up the info if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == ... | 1,110,958 |
public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | 1,110,959 |
public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | 1,110,960 |
public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | 1,110,961 |
public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | 1,110,962 |
public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | 1,110,963 |
public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | 1,110,964 |
public TagScript createTagScript(String name, Attributes attributes) throws Exception { Class type = (Class) tags.get(name); if ( type != null ) { Tag tag = (Tag) type.newInstance(); return TagScript.newInstance(tag); } return null; } | public TagScript createTagScript(String name, Attributes attributes) throws Exception { Class type = (Class) tags.get(name); if ( type != null ) { Tag tag = (Tag) type.newInstance(); return TagScript.newInstance(tag); } return null; } | 1,110,966 |
public void actionPerformed(ActionEvent e) { // This can not easily be replaced with ArchitectPanelBuilder // because the current CompareDMPanel is not an ArchitectPanel // (and has no intention of becoming one, without some work). final JDialog d = new JDialog(ArchitectFrame.getMainInstance(), "Comp... | public void actionPerformed(ActionEvent e) { // This can not easily be replaced with ArchitectPanelBuilder // because the current CompareDMPanel is not an ArchitectPanel // (and has no intention of becoming one, without some work). final JDialog d = new JDialog(ArchitectFrame.getMainInstance(), "Comp... | 1,110,967 |
public void parseMoreResults(String wga) throws PlinkException { File moreResultsFile = new File(wga); results = hv.getPlinkData(); columns = hv.getPlinkColumns(); Vector newColumns = new Vector(); Vector ignoredMarkers = new Vector(); boolean addColumns = false; try... | public void parseMoreResults(String wga) throws PlinkException { File moreResultsFile = new File(wga); results = hv.getPlinkData(); columns = hv.getPlinkColumns(); Vector newColumns = new Vector(); Vector ignoredMarkers = new Vector(); boolean addColumns = false; try... | 1,110,968 |
public void parseMoreResults(String wga) throws PlinkException { File moreResultsFile = new File(wga); results = hv.getPlinkData(); columns = hv.getPlinkColumns(); Vector newColumns = new Vector(); Vector ignoredMarkers = new Vector(); boolean addColumns = false; try... | public void parseMoreResults(String wga) throws PlinkException { File moreResultsFile = new File(wga); results = hv.getPlinkData(); columns = hv.getPlinkColumns(); Vector newColumns = new Vector(); Vector ignoredMarkers = new Vector(); boolean addColumns = false; try... | 1,110,969 |
public double getChiSq(int type) { if(!this.chiSet){ if (type == 1){ this.chiSqVal = Math.pow( (this.counts[0][0] - this.counts[0][1]),2) / (this.counts[0][0] + this.counts[0][1]); }else{ int N = counts[0][0] + counts[0][1] + counts[1][0] + counts[1][1]; ... | public double getChiSq(int type) { if(!this.chiSet){ if (type == ASSOC_TRIO){ this.chiSqVal = Math.pow( (this.counts[0][0] - this.counts[0][1]),2) / (this.counts[0][0] + this.counts[0][1]); }else{ int N = counts[0][0] + counts[0][1] + counts[1][0] + counts[... | 1,110,971 |
public String getOverTransmittedAllele(int type) { String[] alleleCodes = new String[5]; alleleCodes[0] = "X"; alleleCodes[1] = "A"; alleleCodes[2] = "C"; alleleCodes[3] = "G"; alleleCodes[4] = "T"; String retStr; if (this.counts[0][0] > this.counts[0][1]){ ... | public String getOverTransmittedAllele(int type) { String[] alleleCodes = new String[5]; alleleCodes[0] = "X"; alleleCodes[1] = "A"; alleleCodes[2] = "C"; alleleCodes[3] = "G"; alleleCodes[4] = "T"; String retStr; if (this.counts[0][0] > this.counts[0][1]){ ... | 1,110,972 |
public String getTURatio(int type) { if (type == 1){ if (this.counts[0][0] > this.counts[0][1]){ return this.counts[0][0] + ":" + this.counts[0][1]; }else{ return this.counts[0][1] + ":" + this.counts[0][0]; } }else{ if (this.co... | public String getTURatio(int type) { if (type == ASSOC_TRIO){ if (this.counts[0][0] > this.counts[0][1]){ return this.counts[0][0] + ":" + this.counts[0][1]; }else{ return this.counts[0][1] + ":" + this.counts[0][0]; } }else{ if... | 1,110,973 |
public final void endStatement(DDLStatement.StatementType type, SQLObject sqlObject) { ddlStatements.add(new DDLStatement(sqlObject, type, ddl.toString())); ddl = new StringBuffer(500); } | public final void endStatement(DDLStatement.StatementType type, SQLObject sqlObject) { String cat = getTargetCatalog(); if (cat != null) { cat = toIdentifier(cat); } String sch = getTargetSchema(); if (sch != null) { sch = toIdentifier(sch); } ddlStatements.add(new DDLStatement(sqlObject, type, ddl.toString(), cat,... | 1,110,975 |
private void processFile(String fileName,boolean fileType,String infoFileName){ try { int outputType; long maxDistance; long negMaxDistance; HaploData textData; File OutputFile; File inputFile; inputFile = new File(fileName); ... | private void processFile(String fileName,boolean fileType,String infoFileName){ try { int outputType; long maxDistance; long negMaxDistance; HaploData textData; File OutputFile; File inputFile; inputFile = new File(fileName); ... | 1,110,978 |
public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) throws Exception { ... | public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) throws Exception { ... | 1,110,979 |
public Dimension getPreferredSize() { //loop through table to find deepest non-null comparison PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; int count = 0; for (int x = 0; x < dPrimeTable.length-1; x++){ for (int y = x+1; y < dPrimeTable.length; y++){ ... | public Dimension getPreferredSize() { //loop through table to find deepest non-null comparison PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; int count = 0; for (int x = 0; x < dPrimeTable.length-1; x++){ for (int y = x+1; y < dPrimeTable.length; y++){ ... | 1,110,981 |
public Dimension getPreferredSize() { //loop through table to find deepest non-null comparison PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; int count = 0; for (int x = 0; x < dPrimeTable.length-1; x++){ for (int y = x+1; y < dPrimeTable.length; y++){ ... | public Dimension getPreferredSize() { //loop through table to find deepest non-null comparison PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; int count = 0; for (int x = 0; x < dPrimeTable.length-1; x++){ for (int y = x+1; y < dPrimeTable.length; y++){ ... | 1,110,982 |
public void mouseClicked(MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON1_MASK) == InputEvent.BUTTON1_MASK) { int clickX = e.getX(); int clickY = e.getY(); if (showWM && worldmapRect.contains(clickX,clickY)){ //convert a click on the wo... | public void mouseClicked(MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON1_MASK) == InputEvent.BUTTON1_MASK) { int clickX = e.getX(); int clickY = e.getY(); if (showWM && worldmapRect.contains(clickX,clickY)){ //convert a click on the wo... | 1,110,983 |
public void mouseReleased(MouseEvent e) { //remove popped up window if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK){ popupExists = false; repaint(); //resize window once user has ceased dragging } else if ((e.getModifiers(... | public void mouseReleased(MouseEvent e) { //remove popped up window if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK){ popupExists = false; repaint(); //resize window once user has ceased dragging } else if ((e.getModifiers(... | 1,110,984 |
public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | 1,110,985 |
public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | 1,110,986 |
public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | 1,110,987 |
public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | 1,110,988 |
public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | 1,110,989 |
public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | 1,110,990 |
public void refresh(){ noImage = true; repaint(); } | public void refresh(int scheme){ if (scheme != 0){ colorDPrime(scheme); } noImage = true; repaint(); } | 1,110,991 |
public void dataSet(byte[] data) { dataSet(data, 0, this.base_offset, Math.min(this.data_length, data.length)); } | public void dataSet(byte[] data) { dataSet(data, 0, 0, Math.min(this.data_length, data.length)); } | 1,110,992 |
public void execute() { finished = false; stmtsTried = 0; stmtsCompleted = 0; SQLDatabase target = architectFrame.playpen.getDatabase(); Connection con; Statement stmt; try { con = target.getConnection(); } catch (ArchitectException ex) { final Exception fex = ex; SwingUtilities.invo... | public void execute() { finished = false; stmtsTried = 0; stmtsCompleted = 0; SQLDatabase target = architectFrame.playpen.getDatabase(); Connection con; Statement stmt; try { con = target.getConnection(); } catch (ArchitectException ex) { final Exception fex = ex; SwingUtilities.invo... | 1,110,993 |
public void execute() { finished = false; stmtsTried = 0; stmtsCompleted = 0; SQLDatabase target = architectFrame.playpen.getDatabase(); Connection con; Statement stmt; try { con = target.getConnection(); } catch (ArchitectException ex) { final Exception fex = ex; SwingUtilities.invo... | public void execute() { finished = false; stmtsTried = 0; stmtsCompleted = 0; SQLDatabase target = architectFrame.playpen.getDatabase(); Connection con; Statement stmt; try { con = target.getConnection(); } catch (ArchitectException ex) { final Exception fex = ex; SwingUtilities.invo... | 1,110,994 |
public void execute() { finished = false; stmtsTried = 0; stmtsCompleted = 0; SQLDatabase target = architectFrame.playpen.getDatabase(); Connection con; Statement stmt; try { con = target.getConnection(); } catch (ArchitectException ex) { final Exception fex = ex; SwingUtilities.invo... | public void execute() { finished = false; stmtsTried = 0; stmtsCompleted = 0; SQLDatabase target = architectFrame.playpen.getDatabase(); Connection con; Statement stmt; try { con = target.getConnection(); } catch (ArchitectException ex) { final Exception fex = ex; SwingUtilities.invo... | 1,110,995 |
public void execute() { finished = false; stmtsTried = 0; stmtsCompleted = 0; SQLDatabase target = architectFrame.playpen.getDatabase(); Connection con; Statement stmt; try { con = target.getConnection(); } catch (ArchitectException ex) { final Exception fex = ex; SwingUtilities.invo... | public void execute() { finished = false; stmtsTried = 0; stmtsCompleted = 0; SQLDatabase target = architectFrame.playpen.getDatabase(); Connection con; Statement stmt; try { con = target.getConnection(); } catch (ArchitectException ex) { final Exception fex = ex; SwingUtilities.invo... | 1,110,996 |
public void run() { JOptionPane.showMessageDialog (dialog, "You have to specify a target database connection" +"\nbefore executing this script."); ArchitectFrame.getMainInstance().playpen.showDbcsDialog(); } | public void run() { JOptionPane.showMessageDialog (dialog, "You have to specify a target database connection" +"\nbefore executing this script."); ArchitectFrame.getMainInstance().playpen.showDbcsDialog(); } | 1,110,997 |
public void run() { JOptionPane.showMessageDialog (dialog, "Couldn't generate DDL statements: "+fex.getMessage() +"\nThe problem was reported by the target database."); } | public void run() { JOptionPane.showMessageDialog (dialog, "Couldn't generate DDL statements: "+fex.getMessage() +"\nThe problem was reported by the target database."); } | 1,110,998 |
public void run() { JOptionPane.showMessageDialog (dialog, "Couldn't generate DDL statements: "+fex.getMessage() +"\nThe problem was detected internally to the Architect."); } | public void run() { JOptionPane.showMessageDialog (dialog, "Couldn't generate DDL statements: "+fex.getMessage() +"\nThe problem was reported by the target database."); } | 1,110,999 |
public void run() { JOptionPane.showMessageDialog (dialog, "Couldn't connect to target database: "+fex.getMessage() +"\nPlease check the connection settings and try again."); ArchitectFrame.getMainInstance().playpen.showDbcsDialog(); } | public void run() { JOptionPane.showMessageDialog (dialog, "Couldn't connect to target database: "+fex.getMessage() +"\nPlease check the connection settings and try again."); ArchitectFrame.getMainInstance().playpen.showDbcsDialog(); } | 1,111,001 |
public static List findConflicting(Connection con, DDLStatement ddlStmt) throws SQLException { List conflicts = new ArrayList(); SQLObject so = ddlStmt.getObject(); Class clazz = so.getClass(); if (clazz.equals(SQLTable.class)) { SQLTable t = (SQLTable) so; DatabaseMetaData dbmd = con.getMetaData(); if (logg... | public static List findConflicting(Connection con, DDLStatement ddlStmt) throws SQLException { List conflicts = new ArrayList(); SQLObject so = ddlStmt.getObject(); Class clazz = so.getClass(); if (clazz.equals(SQLTable.class)) { SQLTable t = (SQLTable) so; DatabaseMetaData dbmd = con.getMetaData(); if (logg... | 1,111,002 |
public static List findConflicting(Connection con, DDLStatement ddlStmt) throws SQLException { List conflicts = new ArrayList(); SQLObject so = ddlStmt.getObject(); Class clazz = so.getClass(); if (clazz.equals(SQLTable.class)) { SQLTable t = (SQLTable) so; DatabaseMetaData dbmd = con.getMetaData(); if (logg... | public static List findConflicting(Connection con, DDLStatement ddlStmt) throws SQLException { List conflicts = new ArrayList(); SQLObject so = ddlStmt.getObject(); Class clazz = so.getClass(); if (clazz.equals(SQLTable.class)) { SQLTable t = (SQLTable) so; DatabaseMetaData dbmd = con.getMetaData(); if (logg... | 1,111,003 |
public static List findConflicting(Connection con, DDLStatement ddlStmt) throws SQLException { List conflicts = new ArrayList(); SQLObject so = ddlStmt.getObject(); Class clazz = so.getClass(); if (clazz.equals(SQLTable.class)) { SQLTable t = (SQLTable) so; DatabaseMetaData dbmd = con.getMetaData(); if (logg... | public static List findConflicting(Connection con, DDLStatement ddlStmt) throws SQLException { List conflicts = new ArrayList(); SQLObject so = ddlStmt.getObject(); Class clazz = so.getClass(); if (clazz.equals(SQLTable.class)) { SQLTable t = (SQLTable) so; DatabaseMetaData dbmd = con.getMetaData(); if (logg... | 1,111,004 |
public static void dropConflicting(Connection con, List objectNames) throws SQLException { Iterator it = objectNames.iterator(); Statement stmt = null; try { while (it.hasNext()) { String objectName = (String) it.next(); stmt = con.createStatement(); stmt.executeUpdate("DROP "+objectName); } } finally... | public static void dropConflicting(Connection con, Collection objectNames) throws SQLException { Iterator it = objectNames.iterator(); Statement stmt = null; try { while (it.hasNext()) { String objectName = (String) it.next(); stmt = con.createStatement(); stmt.executeUpdate("DROP "+objectName); } } f... | 1,111,006 |
public void testAllSettersGenerateEvents() throws IllegalArgumentException, IllegalAccessException, InvocationTargetException, NoSuchMethodException { SQLObject so = getSQLObjectUnderTest(); Set<String>propertiesToIgnore = new HashSet<String>(); propertiesToIgnore.add("populated"); propertiesToIgnore.add("S... | public void testAllSettersGenerateEvents() throws IllegalArgumentException, IllegalAccessException, InvocationTargetException, NoSuchMethodException { SQLObject so = getSQLObjectUnderTest(); Set<String>propertiesToIgnore = new HashSet<String>(); propertiesToIgnore.add("populated"); propertiesToIgnore.add("S... | 1,111,008 |
public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == "Open Haplotype File" || command == "Open Linkage File"){ fc.setSelectedFile(null); int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { File inputFile = fc.getSelected... | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); String shortHapInputFileName; if (command == "Open Linkage File"){ fc.setSelectedFile(null); int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { File inputFile = fc.getSelectedFile()... | 1,111,010 |
public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == "Open Haplotype File" || command == "Open Linkage File"){ fc.setSelectedFile(null); int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { File inputFile = fc.getSelected... | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == "Open Haplotype File" || command == "Open Linkage File"){ fc.setSelectedFile(null); int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { File inputFile = fc.getSelected... | 1,111,011 |
public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == "Open Haplotype File" || command == "Open Linkage File"){ fc.setSelectedFile(null); int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { File inputFile = fc.getSelected... | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == "Open Haplotype File" || command == "Open Linkage File"){ fc.setSelectedFile(null); int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { File inputFile = fc.getSelected... | 1,111,012 |
public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == "Open Haplotype File" || command == "Open Linkage File"){ fc.setSelectedFile(null); int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { File inputFile = fc.getSelected... | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == "Open Haplotype File" || command == "Open Linkage File"){ fc.setSelectedFile(null); int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { File inputFile = fc.getSelected... | 1,111,013 |
public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == "Open Haplotype File" || command == "Open Linkage File"){ fc.setSelectedFile(null); int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { File inputFile = fc.getSelected... | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == "Open Haplotype File" || command == "Open Linkage File"){ fc.setSelectedFile(null); int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { File inputFile = fc.getSelected... | 1,111,014 |
public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == "Open Haplotype File" || command == "Open Linkage File"){ fc.setSelectedFile(null); int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { File inputFile = fc.getSelected... | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == "Open Haplotype File" || command == "Open Linkage File"){ fc.setSelectedFile(null); int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { File inputFile = fc.getSelected... | 1,111,015 |
void readGenotypes(String[] inputOptions, int type){ //input is a 3 element array with //inputOptions[0] = ped file //inputOptions[1] = info file ("" if none) //inputOptions[2] = max comparison distance (don't compute d' if markers are greater than this dist apart) //type is eithe... | void readGenotypes(String[] inputOptions, int type){ //input is a 3 element array with //inputOptions[0] = ped file //inputOptions[1] = info file ("" if none) //inputOptions[2] = max comparison distance (don't compute d' if markers are greater than this dist apart) //type is eithe... | 1,111,017 |
void readMarkers(File inputFile, String[][] hminfo){ try { theData.prepareMarkerInput(inputFile, maxCompDist, hminfo); if (theData.infoKnown){ analysisItem.setEnabled(true); }else{ analysisItem.setEnabled(false); } if (check... | void readMarkers(File inputFile, String[][] hminfo){ try { theData.prepareMarkerInput(inputFile, maxCompDist, hminfo); if (theData.infoKnown){ analysisItem.setEnabled(true); }else{ analysisItem.setEnabled(false); } if (check... | 1,111,018 |
public static Test suite() { TestSuite suite = new TestSuite("Test for regress"); //$JUnit-BEGIN$ suite.addTestSuite(TestSQLDatabase.class); suite.addTestSuite(ArchitectExceptionTest.class); suite.addTestSuite(SaveLoadTest.class); suite.addTestSuite(PLDotIniTest.class); suite.addTestSuite(TestSQLColumn.class); ... | public static Test suite() { TestSuite suite = new TestSuite("Test for regress"); //$JUnit-BEGIN$ suite.addTestSuite(TestSQLDatabase.class); suite.addTestSuite(ArchitectExceptionTest.class); suite.addTestSuite(SaveLoadTest.class); suite.addTestSuite(PLDotIniTest.class); suite.addTest(TestSQLColumn.suite()); su... | 1,111,019 |
public void doTag(XMLOutput output) throws Exception { invokeBody(output); if (name == null) { throw new MissingAttributeException("name"); } if (className == null) { throw new MissingAttributeException("className"); } Class theClass = null; try { ClassLoader classLoader = getClas... | public void doTag(XMLOutput output) throws Exception { invokeBody(output); if (name == null) { throw new MissingAttributeException("name"); } if (className == null) { throw new MissingAttributeException("className"); } Class theClass = null; try { ClassLoader classLoader = getClas... | 1,111,022 |
public Tag createTag() { return new DynamicBeanTag(beanClass, beanAttributes, varAttribute, invokeMethod); } | public Tag createTag(String name, Attributes attributes) { return new DynamicBeanTag(beanClass, beanAttributes, varAttribute, invokeMethod); } | 1,111,023 |
public void testArgs() throws Exception { InputStream in = getClass().getResourceAsStream( "testing123.jelly" ); XMLParser parser = new XMLParser(); Script script = parser.parse( in ); script = script.compile(); log.debug( "Found: " + script ); assertTrue( "Script i... | public void testArgs() throws Exception { InputStream in = getClass().getResourceAsStream( "testing123.jelly" ); XMLParser parser = new XMLParser(); Script script = parser.parse( in ); script = script.compile(); log.debug( "Found: " + script ); assertTrue( "Script i... | 1,111,024 |
public void addDriverJarPath(String path) { ArchitectSession.getInstance().addDriverJar(path); } | public void addDriverJarPath(String path) { ArchitectSessionImpl.getInstance().addDriverJar(path); } | 1,111,025 |
void load(int ft){ fileType = ft; JPanel contents = new JPanel(); contents.setLayout(new BoxLayout(contents, BoxLayout.Y_AXIS)); JPanel filePanel = new JPanel(); filePanel.setLayout(new BoxLayout(filePanel, BoxLayout.Y_AXIS)); JPanel topFilePanel = new JPanel(); JPan... | void load(int ft){ fileType = ft; JPanel contents = new JPanel(); contents.setLayout(new BoxLayout(contents, BoxLayout.Y_AXIS)); JPanel filePanel = new JPanel(); filePanel.setLayout(new BoxLayout(filePanel, BoxLayout.Y_AXIS)); JPanel topFilePanel = new JPanel(); JPan... | 1,111,026 |
public BufferedImage export(int start, int stop, boolean compress){ forExport = true; exportStart = start; if (exportStart < 0){ exportStart = 0; } exportStop = stop; if (exportStop > Chromosome.getSize()){ exportStop = Chromosome.getSize(); } ... | public BufferedImage export(int start, int stop, boolean compress){ forExport = true; exportStart = start; if (exportStart < 0){ exportStart = 0; } exportStop = stop; if (exportStop > Chromosome.getSize()){ exportStop = Chromosome.getSize(); } ... | 1,111,027 |
public BufferedImage export(int start, int stop, boolean compress){ forExport = true; exportStart = start; if (exportStart < 0){ exportStart = 0; } exportStop = stop; if (exportStop > Chromosome.getSize()){ exportStop = Chromosome.getSize(); } ... | public BufferedImage export(int start, int stop, boolean compress){ forExport = true; exportStart = start; if (exportStart < 0){ exportStart = 0; } exportStop = stop; if (exportStop > Chromosome.getSize()){ exportStop = Chromosome.getSize(); } ... | 1,111,028 |
private UserActivityLogger(){ super(); activities = new Vector(); activityBuffer = new Vector(); /* Open the file to write, and set it to append all new entries */ try{ logWriter = new PrintWriter(new FileWriter(USER_ACTIVITY_LOG_FILE_NAME, ... | private UserActivityLogger(){ super(); activities = new Vector(); activityBuffer = new Vector(); /* Open the file to write, and set it to append all new entries */ try{ logWriter = new PrintWriter(new FileWriter(USER_ACTIVITY_LOG_FILE_NAME, ... | 1,111,030 |
public void doStuff() { if (isCancelled()) return; // now implements Monitorable, so we can ask it how it's doing try { plExport.export(playpen.getDatabase()); // if the user requested, try running the PL Job afterwards if (plExport.getRunPLEngine()) { logger.debug("Running PL Engine"); File... | public void doStuff() { if (isCancelled()) return; // now implements Monitorable, so we can ask it how it's doing try { plExport.export(playpen.getDatabase()); // if the user requested, try running the PL Job afterwards if (plExport.getRunPLEngine()) { logger.debug("Running PL Engine"); File... | 1,111,031 |
public void run() { try { final Process proc = Runtime.getRuntime().exec(commandLine.toString()); // Could in theory make this use ArchitectPanelBuilder, by creating // a JPanel subclass, but may not be worthwhile as it has both an // Abort and a Close button... final JDia... | public void run() { try { final Process proc = Runtime.getRuntime().exec(commandLine.toString()); // Could in theory make this use ArchitectPanelBuilder, by creating // a JPanel subclass, but may not be worthwhile as it has both an // Abort and a Close button... final JDia... | 1,111,032 |
public void doTag(XMLOutput output) throws MissingAttributeException { if (var != null) { context.removeVariable(var); } else { throw new MissingAttributeException("var"); } } | public void doTag(XMLOutput output) throws MissingAttributeException { if (var != null) { context.removeVariable( var.evaluateAsString(context) ); } else { throw new MissingAttributeException("var"); } } | 1,111,033 |
public void setVar(String var) { this.var = var; } | public void setVar(Expression var) { this.var = var; } | 1,111,034 |
public void run(JellyContext context, XMLOutput output) throws Exception { startNamespacePrefixes(output); Tag tag = getTag(); if ( firstRun ) { firstRun = false; // lets see if we have a dynamic tag tag = findDynamicTag(c... | public void run(JellyContext context, XMLOutput output) throws Exception { startNamespacePrefixes(output); Tag tag = getTag(); if ( firstRun ) { firstRun = false; // lets see if we have a dynamic tag tag = findDynamicTag(c... | 1,111,035 |
public void login(ServiceContext context, String username, String password) throws ServiceException{ LoginCallbackHandler callbackHandler = new LoginCallbackHandler(); callbackHandler.setUsername(username); callbackHandler.setPassword(password); ... | public void login(ServiceContext context, String username, String password) throws ServiceException{ LoginCallbackHandler callbackHandler = new LoginCallbackHandler(); callbackHandler.setUsername(username); callbackHandler.setPassword(password); ... | 1,111,036 |
public void login(ServiceContext context, String username, String password) throws ServiceException{ LoginCallbackHandler callbackHandler = new LoginCallbackHandler(); callbackHandler.setUsername(username); callbackHandler.setPassword(password); ... | public void login(ServiceContext context, String username, String password) throws ServiceException{ LoginCallbackHandler callbackHandler = new LoginCallbackHandler(); callbackHandler.setUsername(username); callbackHandler.setPassword(password); ... | 1,111,037 |
public void login(ServiceContext context, String username, String password) throws ServiceException{ LoginCallbackHandler callbackHandler = new LoginCallbackHandler(); callbackHandler.setUsername(username); callbackHandler.setPassword(password); ... | public void login(ServiceContext context, String username, String password) throws ServiceException{ LoginCallbackHandler callbackHandler = new LoginCallbackHandler(); callbackHandler.setUsername(username); callbackHandler.setPassword(password); ... | 1,111,038 |
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