JoaoJunior/formatted-java-preprocessed-code-APR

public boolean contains(JComponent c, int x, int y) { if (path == null) { return false; } else { Point loc = relationship.getLocation(); return path.intersects(x - radius + loc.x, y - radius + loc.y, radius*2, radius*2); } }

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public boolean intersects(Rectangle region) { return path.intersects(region.x, region.y, region.width, region.height); }

public boolean intersects(Rectangle region) { return containmentPath.intersects(region.x, region.y, region.width, region.height); }

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public void paint(Graphics g, JComponent c) { logger.debug("BasicRelationshipUI is painting"); Relationship r = (Relationship) c; Graphics2D g2 = (Graphics2D) g; g2.translate(c.getX() * -1, c.getY() * -1); // playpen coordinate space if (logger.isDebugEnabled()) { g2.setColor(c.getBackground()); Rectangle ...

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public void paint(Graphics g, JComponent c) { logger.debug("BasicRelationshipUI is painting"); Relationship r = (Relationship) c; Graphics2D g2 = (Graphics2D) g; g2.translate(c.getX() * -1, c.getY() * -1); // playpen coordinate space if (logger.isDebugEnabled()) { g2.setColor(c.getBackground()); Rectangle ...

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public void paint(Graphics g, JComponent c) { logger.debug("BasicRelationshipUI is painting"); Relationship r = (Relationship) c; Graphics2D g2 = (Graphics2D) g; g2.translate(c.getX() * -1, c.getY() * -1); // playpen coordinate space if (logger.isDebugEnabled()) { g2.setColor(c.getBackground()); Rectangle ...

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public void paint(Graphics g, JComponent c) { logger.debug("BasicRelationshipUI is painting"); Relationship r = (Relationship) c; Graphics2D g2 = (Graphics2D) g; g2.translate(c.getX() * -1, c.getY() * -1); // playpen coordinate space if (logger.isDebugEnabled()) { g2.setColor(c.getBackground()); Rectangle ...

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public void paint(Graphics g, JComponent c) { logger.debug("BasicRelationshipUI is painting"); Relationship r = (Relationship) c; Graphics2D g2 = (Graphics2D) g; g2.translate(c.getX() * -1, c.getY() * -1); // playpen coordinate space if (logger.isDebugEnabled()) { g2.setColor(c.getBackground()); Rectangle ...

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public void paint(Graphics g, JComponent c) { logger.debug("BasicRelationshipUI is painting"); Relationship r = (Relationship) c; Graphics2D g2 = (Graphics2D) g; g2.translate(c.getX() * -1, c.getY() * -1); // playpen coordinate space if (logger.isDebugEnabled()) { g2.setColor(c.getBackground()); Rectangle ...

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public void paint(Graphics g, JComponent c) { logger.debug("BasicRelationshipUI is painting"); Relationship r = (Relationship) c; Graphics2D g2 = (Graphics2D) g; g2.translate(c.getX() * -1, c.getY() * -1); // playpen coordinate space if (logger.isDebugEnabled()) { g2.setColor(c.getBackground()); Rectangle ...

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public void paint(Graphics g, JComponent c) { logger.debug("BasicRelationshipUI is painting"); Relationship r = (Relationship) c; Graphics2D g2 = (Graphics2D) g; g2.translate(c.getX() * -1, c.getY() * -1); // playpen coordinate space if (logger.isDebugEnabled()) { g2.setColor(c.getBackground()); Rectangle ...

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public void paint(Graphics g, JComponent c) { logger.debug("BasicRelationshipUI is painting"); Relationship r = (Relationship) c; Graphics2D g2 = (Graphics2D) g; g2.translate(c.getX() * -1, c.getY() * -1); // playpen coordinate space if (logger.isDebugEnabled()) { g2.setColor(c.getBackground()); Rectangle ...

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public void paint(Graphics g, JComponent c) { logger.debug("BasicRelationshipUI is painting"); Relationship r = (Relationship) c; Graphics2D g2 = (Graphics2D) g; g2.translate(c.getX() * -1, c.getY() * -1); // playpen coordinate space if (logger.isDebugEnabled()) { g2.setColor(c.getBackground()); Rectangle ...

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public void paint(Graphics g, JComponent c) { logger.debug("BasicRelationshipUI is painting"); Relationship r = (Relationship) c; Graphics2D g2 = (Graphics2D) g; g2.translate(c.getX() * -1, c.getY() * -1); // playpen coordinate space if (logger.isDebugEnabled()) { g2.setColor(c.getBackground()); Rectangle ...

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public String generateToolTip(XYDataset dataset, int series, int item){ return (String)info[series].get(new Double(dataset.getXValue(series,item))); }

public String generateToolTip(XYDataset dataset, int series, int item){ return (String)info[seriesKeys[series]-1].get(new Double(dataset.getXValue(series,item))); }

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protected void handleException(Exception e) throws Exception { log.error( "Caught exception: " + e, e ); if ( e instanceof JellyException ) { e.fillInStackTrace(); throw e; } if ( e instanceof InvocationTargetException) { throw new JellyExce...

protected void handleException(JellyException e) throws Exception { log.error( "Caught exception: " + e, e ); if ( e instanceof JellyException ) { e.fillInStackTrace(); throw e; } if ( e instanceof InvocationTargetException) { throw new Jell...

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protected void handleException(Exception e) throws Exception { log.error( "Caught exception: " + e, e ); if ( e instanceof JellyException ) { e.fillInStackTrace(); throw e; } if ( e instanceof InvocationTargetException) { throw new JellyExce...

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protected void handleException(Exception e) throws Exception { log.error( "Caught exception: " + e, e ); if ( e instanceof JellyException ) { e.fillInStackTrace(); throw e; } if ( e instanceof InvocationTargetException) { throw new JellyExce...

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protected void handleException(Exception e) throws Exception { log.error( "Caught exception: " + e, e ); if ( e instanceof JellyException ) { e.fillInStackTrace(); throw e; } if ( e instanceof InvocationTargetException) { throw new JellyExce...

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public void mousePressed(MouseEvent evt) { requestFocus(); maybeShowPopup(evt); Point p = evt.getPoint(); unzoomPoint(p); PlayPenComponent c = contentPane.getComponentAt(p); if (c != null) p.translate(-c.getX(), -c.getY()); if (c instanceof Relationship) { if ((evt.getModifiersEx() & MouseEven...

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protected void createUI() { GridBagConstraints labelConstraints = new GridBagConstraints(); labelConstraints.insets = new Insets( 2, 20, 2, 2 ); labelConstraints.anchor = GridBagConstraints.EAST; labelConstraints.gridwidth = GridBagConstraints.RELATIVE; //next-to-last labelConstraints.fill = GridBagConstrain...

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public void doTag(XMLOutput output) throws Exception { task.init(); if ( "echo".equals( task.getTaskName() ) ) { Echo echoTask = (Echo) task; echoTask.addText( getBodyText() ); echoTask.perform(); echoTask.setMessage( "" ); } ...

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public Task getTask() { return task; }

public Task getTask() throws Exception { if ( task == null ) { task = (Task) taskType.newInstance(); task.setProject(project); task.setTaskName(taskName); task.init(); setDynaBean( new ConvertingWrapDynaBean(task) ); } return task; }

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public Object getTaskObject() { return task; }

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public long getMorganDistance(){ return morganDistance; }

public double getMorganDistance(){ return morganDistance; }

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protected Object createWidget(Class theClass, Widget parent, int style) throws Exception { if (theClass == null) { throw new JellyException( "No Class available to create the new widget"); } if (parent == null) { // lets try call a constructor with a single style ...

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public void drop(DropTargetDropEvent dtde) { if (tpTarget != null) { tpTarget.getDropTarget().drop(dtde); return; } Transferable t = dtde.getTransferable(); PlayPen c = (PlayPen) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if...

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public void drop(DropTargetDropEvent dtde) { if (tpTarget != null) { tpTarget.getDropTarget().drop(dtde); return; } Transferable t = dtde.getTransferable(); PlayPen c = (PlayPen) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if...

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public void compile() throws Exception { TaskTag tag = (TaskTag) findAncestorWithClass( TaskTag.class ); if ( tag == null ) { throw new JellyException( "You should only use Ant DataType tags within an Ant Task" ); } Task task = tag.getTask(); Class taskC...

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private void buildCCSet(PedFile pf, Vector affectedStatus, TreeSet snpsToBeTested){ ArrayList results = new ArrayList(); int numMarkers = Chromosome.getUnfilteredSize(); Vector indList = pf.getUnrelatedIndividuals(); int numInds = indList.size(); if(affectedStatus == null || affec...

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public void doTag(XMLOutput xmlOutput) throws Exception { HttpContextTag httpContext = (HttpContextTag) findAncestorWithClass( HttpContextTag.class); if ( httpContext == null ) { throw new JellyTagException( "<notFoundHandler> tag must be enclosed inside a <httpContext> tag" ); ...

public void doTag(XMLOutput xmlOutput) throws JellyTagException { HttpContextTag httpContext = (HttpContextTag) findAncestorWithClass( HttpContextTag.class); if ( httpContext == null ) { throw new JellyTagException( "<notFoundHandler> tag must be enclosed inside a <httpContext> t...

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public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); /...

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public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); /...

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public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); /...

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public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); /...

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public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); /...

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public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); /...

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public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); /...

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public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); /...

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public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); /...

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public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); /...

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public void writeHeader() { out.println("-- Created by SQLPower DB2 DDL Generator "+GENERATOR_VERSION+" --"); }

public void writeHeader() { println("-- Created by SQLPower DB2 DDL Generator "+GENERATOR_VERSION+" --"); }

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public void actionPerformed(ActionEvent e) { // ArchitectPanelBuilder cannot handle this because of the // wizard-style buttons (right-justified FlowLayout). final JDialog d = new JDialog(frame,title ); JPanel plr = new JPanel(new BorderLayout(12,12)); plr.setBorder(BorderFactory.createEmptyBorder(12,12,12,12...

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protected Project getProject() { ProjectTag tag = (ProjectTag) findAncestorWithClass(ProjectTag.class); if ( tag != null) { return tag.getProject(); } return (Project) context.getVariable( "org.apache.commons.jelly.werkz.Project" ); }

protected Project getProject() { ProjectTag tag = (ProjectTag) findAncestorWithClass(ProjectTag.class); if ( tag != null) { return tag.getProject(); } return (Project) context.findVariable( "org.apache.commons.jelly.werkz.Project" ); }

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public void actionPerformed(ActionEvent e) { TreePath p = getSelectionPath(); if (p == null) { return; } Object [] pathArray = p.getPath(); int ii = 0; SQLDatabase sd = null; while (ii < pathArray.length && sd == null) { if (pathArray[ii] instanceof SQLDatabase) { sd = (SQLDatabase) pathArr...

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public void actionPerformed(ActionEvent e) { TreePath p = getSelectionPath(); if (p == null) { return; } Object [] pathArray = p.getPath(); int ii = 0; SQLDatabase sd = null; while (ii < pathArray.length && sd == null) { if (pathArray[ii] instanceof SQLDatabase) { sd = (SQLDatabase) pathArr...

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public void run(JellyContext context, XMLOutput output) throws Exception { Tag tag = getTag(); if ( tag == null ) { return; } tag.setContext(context); // initialize all the properties of the tag before its used // if there is a problem abort this tag ...

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void prepareMarkerInput(File infile, 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 maxdist ...

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public Test_ThumbnailView() { testRefImageDir = new File( "c:\\java\\photovault\\tests\\images\\photovault\\swingui\\TestThumbnailView\\" ); testRefImageDir.mkdirs(); }

public Test_ThumbnailView() { testRefImageDir = new File( "/home/harri/projects/photovault/tests/images/photovault/swingui/TestThumbnailView/" ); testRefImageDir.mkdirs(); }

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private boolean compareImgToFile( BufferedImage img, File file ) { if ( file.exists() ) { log.debug( "File exists" ); BufferedImage fImg = null; try { fImg = ImageIO.read( file ); log.debug( "Read image" ); } catch ( IOException e ) { log.warn( "Error reading image: " + e.getMessage() ); retu...

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protected void setUp() { // Create a frame with the test instance name as the title frame = new JFrame(getName()); pane = (JPanel)frame.getContentPane(); pane.setLayout(new FlowLayout()); pane.setBorder(new EmptyBorder(50, 50, 50, 50)); tester = ComponentTester.getT...

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public void registerBeanTag(String name, BeanTag tag) { templates.put(name, tag); }

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protected void createThumbnail( Volume volume ) { log.warn( "Creating thumbnail" ); ODMGXAWrapper txw = new ODMGXAWrapper(); txw.lock( this, Transaction.WRITE ); // Find the original image to use as a staring point ImageInstance original = null; for ( int n = 0; n < instances.size(); n++ ) { ImageInstance inst...

protected void createThumbnail( Volume volume ) { log.debug( "Creating thumbnail" ); ODMGXAWrapper txw = new ODMGXAWrapper(); txw.lock( this, Transaction.WRITE ); // Find the original image to use as a staring point ImageInstance original = null; for ( int n = 0; n < instances.size(); n++ ) { ImageInstance ins...

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public Thumbnail getThumbnail() { log.debug( "Finding thumbnail for " + uid ); if ( thumbnail == null ) { // First try to find an instance from existing instances ImageInstance original = null; for ( int n = 0; n < instances.size(); n++ ) { ImageInstance instance = (ImageInstance) instances.get( n ); ...

public Thumbnail getThumbnail() { log.debug( "getThumbnail: Finding thumbnail for " + uid ); if ( thumbnail == null ) { // First try to find an instance from existing instances ImageInstance original = null; for ( int n = 0; n < instances.size(); n++ ) { ImageInstance instance = (ImageInstance) instanc...

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public boolean hasThumbnail() { log.debug( "Finding thumbnail for " + uid ); if ( thumbnail == null ) { // First try to find an instance from existing instances ImageInstance original = null; for ( int n = 0; n < instances.size(); n++ ) { ImageInstance instance = (ImageInstance) instances.get( n ); if...

public boolean hasThumbnail() { log.debug( "hasThumbnail: Finding thumbnail for " + uid ); if ( thumbnail == null ) { // First try to find an instance from existing instances ImageInstance original = null; for ( int n = 0; n < instances.size(); n++ ) { ImageInstance instance = (ImageInstance) instances...

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public void stateChanged(ChangeEvent e) { if (tabs.getSelectedIndex() != -1){ window.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); String title = tabs.getTitleAt(tabs.getSelectedIndex()); if (title.equals(VIEW_DPRIME) || title.equals(VIEW_HAPL...

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public int getPreciseMarkerAt(double pos){ int where = Arrays.binarySearch(alignedPositions,pos); if (where >= 0){ return where; }else{ int left = -where-2; int right = -where-1; if (left < 0){ left = 0; right = 1; ...

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public void mousePressed (MouseEvent e) { Rectangle blockselector = new Rectangle(clickXShift-boxRadius,clickYShift - boxRadius, (int)alignedPositions[alignedPositions.length-1]+boxSize, boxSize); //if users right clicks & holds, pop up the info if ((e.getModifiers() & InputEvent...

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public void mousePressed (MouseEvent e) { Rectangle blockselector = new Rectangle(clickXShift-boxRadius,clickYShift - boxRadius, (int)alignedPositions[alignedPositions.length-1]+boxSize, boxSize); //if users right clicks & holds, pop up the info if ((e.getModifiers() & InputEvent...

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public void paintComponent(Graphics g){ DPrimeTable dPrimeTable = theData.dpTable; if (Chromosome.getSize() < 2){ //if there zero or only one valid marker return; } Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zoomi...

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public void paintComponent(Graphics g){ DPrimeTable dPrimeTable = theData.dpTable; if (Chromosome.getSize() < 2){ //if there zero or only one valid marker return; } Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zoomi...

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public void paintComponent(Graphics g){ DPrimeTable dPrimeTable = theData.dpTable; if (Chromosome.getSize() < 2){ //if there zero or only one valid marker return; } Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zoomi...

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public void paintComponent(Graphics g){ DPrimeTable dPrimeTable = theData.dpTable; if (Chromosome.getSize() < 2){ //if there zero or only one valid marker return; } Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zoomi...

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public void actionPerformed(ActionEvent evt) { if (evt.getActionCommand().equals(ArchitectSwingConstants.ACTION_COMMAND_SRC_PLAYPEN)) { List items = pp.getSelectedItems(); if (items.size() > 1) { int decision = JOptionPane.showConfirmDialog(pp, "Are you sure you want to delete the " ...

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public void actionPerformed(ActionEvent evt) { if (evt.getActionCommand().equals(ArchitectSwingConstants.ACTION_COMMAND_SRC_PLAYPEN)) { List items = pp.getSelectedItems(); if (items.size() > 1) { int decision = JOptionPane.showConfirmDialog(pp, "Are you sure you want to delete the " ...

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public void actionPerformed(ActionEvent evt) { if (evt.getActionCommand().equals(ArchitectSwingConstants.ACTION_COMMAND_SRC_PLAYPEN)) { List items = pp.getSelectedItems(); if (items.size() > 1) { int decision = JOptionPane.showConfirmDialog(pp, "Are you sure you want to delete the " ...

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public void actionPerformed(ActionEvent evt) { if (evt.getActionCommand().equals(ArchitectSwingConstants.ACTION_COMMAND_SRC_PLAYPEN)) { List items = pp.getSelectedItems(); if (items.size() > 1) { int decision = JOptionPane.showConfirmDialog(pp, "Are you sure you want to delete the " ...

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public double chsoneCalculate(double[] bins, double[] ebins, int nbins, int knstrn) throws CheckDataException{ double prob, df, chsq, temp; df = nbins - knstrn ; chsq = 0.0 ; for (int j = 1 ; j <= nbins ; j ++ ) { if (ebins [j ]<= 0.0 ) throw new CheckDataException("Bad expected number in chsone" ); temp = ...

public double chsoneCalculate(double[] bins, double[] ebins, int nbins, int knstrn){ double prob, df, chsq, temp; df = nbins - knstrn ; chsq = 0.0 ; for (int j = 1 ; j <= nbins ; j ++ ) { if (ebins [j ]<= 0.0 ) throw new CheckDataException("Bad expected number in chsone" ); temp = bins[j]- ebins[j]; chsq ...

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public double chsoneCalculate(double[] bins, double[] ebins, int nbins, int knstrn) throws CheckDataException{ double prob, df, chsq, temp; df = nbins - knstrn ; chsq = 0.0 ; for (int j = 1 ; j <= nbins ; j ++ ) { if (ebins [j ]<= 0.0 ) throw new CheckDataException("Bad expected number in chsone" ); temp = ...

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private double getObsHET(int het, int hom){ double obsHET = het/(het+hom+0.0); return obsHET; }

private double getObsHET(int het, int hom){ double obsHET; if (het+hom == 0){ obsHET = 0; }else{ obsHET = het/(het+hom+0.0); } return obsHET; }

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private double getPValue(Hashtable parentHom, int parentHet){ //ie: 11 13 31 33 -> homA =1 homB = 1 parentHet=2 int homA=0, homB=0, num; double pvalue=0; Enumeration enu = parentHom.elements(); while(enu.hasMoreElements()){ num = Integer.parseInt((String)enu.nextElement()); if(homA>0) homB = num; else homA ...

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private double getPValue(Hashtable parentHom, int parentHet){ //ie: 11 13 31 33 -> homA =1 homB = 1 parentHet=2 int homA=0, homB=0, num; double pvalue=0; Enumeration enu = parentHom.elements(); while(enu.hasMoreElements()){ num = Integer.parseInt((String)enu.nextElement()); if(homA>0) homB = num; else homA ...

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private double getPreHET(Hashtable count){ int sumsq=0, sum=0, num=0; Enumeration enu = count.elements(); while(enu.hasMoreElements()){ num = Integer.parseInt((String)enu.nextElement()); sumsq += num*num; sum += num; } double preHet = 1.0 - (sumsq/((sum*sum)+0.0)); return preHet; }

private double getPreHET(Hashtable count){ int sumsq=0, sum=0, num=0; Enumeration enu = count.elements(); while(enu.hasMoreElements()){ num = Integer.parseInt((String)enu.nextElement()); sumsq += num*num; sum += num; } double preHet; if (sum == 0){ preHet = 0; }else{ preHet = 1.0 - (sumsq/((sum*sum)+0.0)); ...

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private double hwCalculate(double obsAA, double obsAB, double obsBB) throws CheckDataException{ double obs[]={0.0, obsAA, obsAB, obsBB}; double expect[]={0.0, 0.0, 0.0, 0.0}; double sum_obs; //double csq, df, sum_expect; double prob, p, start, end; double best_prob =-1.0; double best_p=0; sum_obs = obs [...

private double hwCalculate(double obsAA, double obsAB, double obsBB){ double obs[]={0.0, obsAA, obsAB, obsBB}; double expect[]={0.0, 0.0, 0.0, 0.0}; double sum_obs; //double csq, df, sum_expect; double prob, p, start, end; double best_prob =-1.0; double best_p=0; sum_obs = obs [1 ]+ obs [2 ]+ obs [3 ]; ...

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public void runUnitTest(String name) throws Exception { // parse script InputStream in = new FileInputStream(name); XMLParser parser = new XMLParser(); Script script = parser.parse(in); script = script.compile(); assertTrue("Parsed a Script", script instanceof Script); ...

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public void runUnitTest(String name) throws Exception { // parse script InputStream in = new FileInputStream(name); XMLParser parser = new XMLParser(); Script script = parser.parse(in); script = script.compile(); assertTrue("Parsed a Script", script instanceof Script); ...

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public IndividualDialog (HaploView h, String title) { super(h,title); JPanel contents = new JPanel(); JTable table; contents.setLayout(new BoxLayout(contents,BoxLayout.Y_AXIS)); Vector people = h.theData.getPedFile().getAllIndividuals(); Vector excludedPeople = h.theData.ge...

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private static void dropTableNoFail(Connection con, String tableName) throws SQLException { Statement stmt = null; try { stmt = con.createStatement(); stmt.executeUpdate("DROP TABLE "+tableName); } catch (SQLException e) { System.out.println("Ignoring SQLException. Assuming it means the table we tried to dro...

private static void dropTableNoFail(Connection con, String tableName) throws SQLException { Statement stmt = null; try { stmt = con.createStatement(); stmt.executeUpdate("DROP TABLE "+tableName); } catch (SQLException e) { System.out.println("Ignoring SQLException. Assume "+tableName+" didn't exist."); e.p...

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public static void oneTimeSetUp() throws Exception { System.out.println("TestSQLColumn.oneTimeSetUp()"); SQLDatabase mydb = new SQLDatabase(getDataSource()); Connection con = mydb.getConnection(); Statement stmt = con.createStatement(); dropTableNoFail(con, "SQL_COLUMN_TEST_1PK"); dropTableNoFail(con, "SQL_C...

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public static void oneTimeSetUp() throws Exception { System.out.println("TestSQLColumn.oneTimeSetUp()"); SQLDatabase mydb = new SQLDatabase(getDataSource()); Connection con = mydb.getConnection(); Statement stmt = con.createStatement(); dropTableNoFail(con, "SQL_COLUMN_TEST_1PK"); dropTableNoFail(con, "SQL_C...

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public void dbStructureChanged(SQLObjectEvent e) { throw new UnsupportedOperationException("not yet"); }

public void dbStructureChanged(SQLObjectEvent e) { if (!SwingUtilities.isEventDispatchThread()) return; try { ArchitectUtils.listenToHierarchy(this, e.getSQLSource()); TreeModelEvent tme = new TreeModelEvent(this, getPathToNode(e.getSQLSource())); fireTreeStructureChanged(tme); } catch (ArchitectException ex) { logge...

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private void maybeShowPopup(MouseEvent e) { if (e.isPopupTrigger()) { TreePath p = getPathForLocation(e.getX(), e.getY()); popup = refreshMenu(p); setSelectionPath(p); popup.show(e.getComponent(), e.getX(), e.getY()); } }

private void maybeShowPopup(MouseEvent e) { if (e.isPopupTrigger()) { TreePath p = getPathForLocation(e.getX(), e.getY()); popup = refreshMenu(p); if (!isTargetDatabaseChild(p)) { setSelectionPath(p); } popup.show(e.getComponent(), e.getX(), e...

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protected JPopupMenu refreshMenu(TreePath p) { logger.debug("refreshMenu is being called."); JPopupMenu newMenu = new JPopupMenu(); if (isTargetDatabaseNode(p)) { // two menu items: "Set Target Database" and "Connection Properties newMenu.add(popupDBCSMenu = new JMenu("Set Target Database")); if (Architec...

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void saveHapsToText(){ fc.setSelctedFile(null); try{ fc.setSelectedFile(null); int returnVal = fc.showSaveDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { new TextMethods().saveHapsToText(finishedHaplos, fc.getSelectedFile()); } }catch (IOException ioexec){ JOptionPane.showMessageD...

void saveHapsToText(){ fc.setSelectedFile(null); try{ fc.setSelectedFile(null); int returnVal = fc.showSaveDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { new TextMethods().saveHapsToText(finishedHaplos, fc.getSelectedFile()); } }catch (IOException ioexec){ JOptionPane.showMessage...

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public void actionPerformed(ActionEvent e) { TreePath p = getSelectionPath(); if (p == null) { return; } Object [] pathArray = p.getPath(); int ii = 0; SQLDatabase sd = null; while (ii < pathArray.length && sd == null) { if (pathArray[ii] instanceof SQLDatabase) { sd = (SQLDatabase) pathArr...

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protected void setup() { GenericDDLGenerator ddlg = project.getDDLGenerator(); setLayout(new FormLayout()); Vector dbTypeList = new Vector(); dbTypeList.add(ASUtils.lvb("Generic JDBC", GenericDDLGenerator.class)); dbTypeList.add(ASUtils.lvb("DB2", DB2DDLGenerator.class)); dbTypeList.add(ASUtils.lvb("Oracle 8i/9i...

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protected void setup() { GenericDDLGenerator ddlg = project.getDDLGenerator(); setLayout(new FormLayout()); Vector dbTypeList = new Vector(); dbTypeList.add(ASUtils.lvb("Generic JDBC", GenericDDLGenerator.class)); dbTypeList.add(ASUtils.lvb("DB2", DB2DDLGenerator.class)); dbTypeList.add(ASUtils.lvb("Oracle 8i/9i...

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public Object createDataType(String name) { Object dataType = null; Class type = (Class) getAntProject().getDataTypeDefinitions().get(name); if ( type != null ) { Constructor ctor = null; boolean noArg = false; // DataType can have a "no arg" constructor or take...

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public Object createNestedObject(Object object, String name) { Object dataType = null; if ( object != null ) { IntrospectionHelper ih = IntrospectionHelper.getHelper( object.getClass() ); if ( ih != null ) { try { dataType = ih.createElement( get...

public Object createNestedObject(Object object, String name) { Object dataType = null; if ( object != null ) { IntrospectionHelper ih = IntrospectionHelper.getHelper( object.getClass() ); if ( ih != null && ! (object instanceof AntTag)) { try { d...

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public void doTag(XMLOutput output) throws JellyTagException { Project project = getAntProject(); String tagName = getTagName(); Object parentObject = findBeanAncestor(); Object parentTask = findParentTaskObject(); // lets assume that Task instances are not nested inside other Tas...

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public void doTag(XMLOutput output) throws JellyTagException { Project project = getAntProject(); String tagName = getTagName(); Object parentObject = findBeanAncestor(); Object parentTask = findParentTaskObject(); // lets assume that Task instances are not nested inside other Tas...

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public void setBeanProperty(Object object, String name, Object value) throws JellyTagException { if ( log.isDebugEnabled() ) { log.debug( "Setting bean property on: "+ object + " name: " + name + " value: " + value ); } IntrospectionHelper ih = IntrospectionHelper.getHelper( object....

public void setBeanProperty(Object object, String name, Object value) throws JellyTagException { if ( log.isDebugEnabled() ) { log.debug( "Setting bean property on: "+ safeToString(object )+ " name: " + name + " value: " + safeToString(value)); } IntrospectionHelper ih = Introspecti...

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private void doBatch() { Vector files; File batchFile; File dataFile; String line; StringTokenizer tok; String infoMaybe =null; files = new Vector(); if(batchFileName == null) { return; } batchFile = new File(this.batchFileName); ...

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protected void updateModel() { logger.debug("Updating model"); try { SQLColumn col = model.getColumn(index); col.setName(colName.getText()); col.setType(((SQLType) colType.getSelectedItem()).type); col.setScale(((Integer) colScale.getValue()).intValue()); col.setPrecision(((Integer) colPrec.getValue()).int...

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public void adjustDisplay(int dt){ //this is called when the controller wants to change the haps //displayed, instead of directly repainting so that none of this math //is done when the screen repaints for other reasons (resizing, focus change, etc) //first filter haps on displaythresh ...

public void adjustDisplay(){ //this is called when the controller wants to change the haps //displayed, instead of directly repainting so that none of this math //is done when the screen repaints for other reasons (resizing, focus change, etc) //first filter haps on displaythresh ...

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public void adjustDisplay(int dt){ //this is called when the controller wants to change the haps //displayed, instead of directly repainting so that none of this math //is done when the screen repaints for other reasons (resizing, focus change, etc) //first filter haps on displaythresh ...

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public void adjustDisplay(int dt){ //this is called when the controller wants to change the haps //displayed, instead of directly repainting so that none of this math //is done when the screen repaints for other reasons (resizing, focus change, etc) //first filter haps on displaythresh ...

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public void adjustDisplay(int dt){ //this is called when the controller wants to change the haps //displayed, instead of directly repainting so that none of this math //is done when the screen repaints for other reasons (resizing, focus change, etc) //first filter haps on displaythresh ...

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public void getHaps() throws HaploViewException{ if (theData.blocks == null) {return;} Haplotype[][] haplos = theData.generateHaplotypes(theData.blocks, 0); orderedHaplos = new Haplotype[haplos.length][]; for (int i = 0; i < haplos.length; i++) { Vector orderedHaps = new Vecto...

public void getHaps() throws HaploViewException{ if (theData.blocks == null) {return;} Haplotype[][] haplos = theData.generateHaplotypes(theData.blocks, 0,false); orderedHaplos = new Haplotype[haplos.length][]; for (int i = 0; i < haplos.length; i++) { Vector orderedHaps = new...

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public void getHaps() throws HaploViewException{ if (theData.blocks == null) {return;} Haplotype[][] haplos = theData.generateHaplotypes(theData.blocks, 0); orderedHaplos = new Haplotype[haplos.length][]; for (int i = 0; i < haplos.length; i++) { Vector orderedHaps = new Vecto...

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public void removeDataSource(ArchitectDataSource dbcs) { int where = fileSections.indexOf(dbcs); if (where < 0) throw new IllegalArgumentException("dbcs not in list"); fileSections.remove(dbcs); fireRemoveEvent(where, dbcs); }

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