bugged stringlengths 6 599k | fixed stringlengths 10 599k | __index_level_0__ int64 0 1.13M |
|---|---|---|
public void doTag(XMLOutput output) throws Exception { // Try find find the body from the reserved 'org.apache.commons.jelly.body' variable Script script = (Script) context.getVariable("org.apache.commons.jelly.body"); if (script != null) { script.run(context, output); } ... | public void doTag(XMLOutput output) throws Exception { // Try find find the body from the reserved 'org.apache.commons.jelly.body' variable Script script = (Script) context.getVariable("org.apache.commons.jelly.body"); if (script != null) { script.run(context, output); } ... | 1,108,599 |
public void doTag(final XMLOutput output) throws Exception { getGoal(getName()).addPostActionCallback( new PostActionCallback() { public void firePostAction(Goal goal) throws Exception { // lets run the body log.info( "Running post actio... | public void doTag(final XMLOutput output) throws Exception { getGoal(getName()).addPostActionCallback( new PostActionCallback() { public void firePostAction(Goal goal) throws Exception { // lets run the body log.info( "Running post actio... | 1,108,600 |
public void firePostAction(Goal goal) throws Exception { // lets run the body log.info( "Running post action: " + getName() ); getBody().run( context, output); } | public void firePostAction(Goal goal) throws Exception { // lets run the body log.info( "Running post action: " + getName() ); invokeBody( output); } | 1,108,601 |
HandlerContext(Command command, boolean isAuthRequired){ this.command = command; this.serviceContext = getServiceContext(command, isAuthRequired); } | HandlerContext(Command command, boolean isAuthRequired){ this.command = command; this.serviceContext = getServiceContext(command, isAuthRequired); } | 1,108,602 |
public void writeHeader() { out.println("-- Created by SQLPower Oracle 8i/9i DDL Generator "+GENERATOR_VERSION+" --"); } | public void writeHeader() { println("-- Created by SQLPower Oracle 8i/9i DDL Generator "+GENERATOR_VERSION+" --"); } | 1,108,605 |
public void doTag(XMLOutput output) throws Exception { String message = getBodyText(); Object expectedValue = expected.evaluate(context); Object actualValue = actual.evaluate(context); if (expectedValue == null && actualValue == null) { ... | public void doTag(XMLOutput output) throws JellyTagException { String message = getBodyText(); Object expectedValue = expected.evaluate(context); Object actualValue = actual.evaluate(context); if (expectedValue == null && actualValue == nul... | 1,108,606 |
public static void writeKey(EncryptedKey encryptedKey) throws FileNotFoundException, IOException { File file = new File(KEY_FILE_PATH); if(file.exists()){ file.delete(); } file.createNewFile(); FileOutputStream fos = new FileOutputStream(file); fos.write(e... | public static void writeKey(EncryptedKey encryptedKey) throws FileNotFoundException, IOException { File file = new File(KEY_FILE_PATH); if(file.exists()){ file.renameTo(new File(KEY_FILE_PATH + ".bak")); } file.createNewFile(); FileOutputStream fos = new FileOutp... | 1,108,607 |
private boolean isRotHandleAt( int x, int y ) { int accuracy = 10; int dx = x - rotHandleX[1]; int dy = y - rotHandleY[1]; boolean isHandle = ( dx*dx + dy*dy < accuracy * accuracy ); System.err.println( "Is rot handle? " + isHandle ); return isHandle; } | private boolean isRotHandleAt( int x, int y ) { int accuracy = 10; int dx = x - rotHandleX[1]; int dy = y - rotHandleY[1]; boolean isHandle = ( dx*dx + dy*dy < accuracy * accuracy ); log.debug( "Is rot handle? " + isHandle ); return isHandle; } | 1,108,609 |
public void mousePressed(MouseEvent mouseEvent) { if ( !drawCropped ) { // Check if we clicked on a handle handleMoving = getHandleAt( mouseEvent.getX(), mouseEvent.getY() ); System.err.println( "Moving handle " + handleMoving ); if ( handleMoving < 0 ) { ... | public void mousePressed(MouseEvent mouseEvent) { if ( !drawCropped ) { // Check if we clicked on a handle handleMoving = getHandleAt( mouseEvent.getX(), mouseEvent.getY() ); log.debug( "Moving handle " + handleMoving ); if ( handleMoving < 0 ) { is... | 1,108,610 |
private void rotateCrop( int newx, int newy ) { // Calculate new rotation double dx = newx-imgX-cropBorderX; double dy = newy-imgY-cropBorderY; if ( Math.abs( dy ) > 0.0001 ) { cropBorderRot = -Math.atan( dx/dy ); } else { cropBorderRot = 0; } ... | private void rotateCrop( int newx, int newy ) { // Calculate new rotation double dx = newx-imgX-cropBorderX; double dy = newy-imgY-cropBorderY; if ( Math.abs( dy ) > 0.0001 ) { cropBorderRot = -Math.atan( dx/dy ); } else { cropBorderRot = 0; } ... | 1,108,611 |
public TagLibrary resolveTagLibrary(String uri) { ServiceDiscovery discovery = getServiceDiscovery(); String name = uri; if ( uri.startsWith( "jelly:" ) ) { name = "jelly." + uri.substring(6); } log.info( "Looking up service name: " + name ); Serv... | public TagLibrary resolveTagLibrary(String uri) { DiscoverClasses discovery = getDiscoverClasses(); String name = uri; if ( uri.startsWith( "jelly:" ) ) { name = "jelly." + uri.substring(6); } log.info( "Looking up service name: " + name ); Servic... | 1,108,612 |
public TagLibrary resolveTagLibrary(String uri) { ServiceDiscovery discovery = getServiceDiscovery(); String name = uri; if ( uri.startsWith( "jelly:" ) ) { name = "jelly." + uri.substring(6); } log.info( "Looking up service name: " + name ); Serv... | public TagLibrary resolveTagLibrary(String uri) { ServiceDiscovery discovery = getServiceDiscovery(); String name = uri; if ( uri.startsWith( "jelly:" ) ) { name = "jelly." + uri.substring(6); } log.info( "Looking up service name: " + name ); Serv... | 1,108,613 |
public TagLibrary resolveTagLibrary(String uri) { ServiceDiscovery discovery = getServiceDiscovery(); String name = uri; if ( uri.startsWith( "jelly:" ) ) { name = "jelly." + uri.substring(6); } log.info( "Looking up service name: " + name ); Serv... | public TagLibrary resolveTagLibrary(String uri) { ServiceDiscovery discovery = getServiceDiscovery(); String name = uri; if ( uri.startsWith( "jelly:" ) ) { name = "jelly." + uri.substring(6); } log.info( "Looking up service name: " + name ); Serv... | 1,108,614 |
private ArchitectFrame() throws ArchitectException { synchronized (ArchitectFrame.class) { mainInstance = this; } setIconImage(new ImageIcon(getClass().getResource("/icons/Architect16.png")).getImage()); // close handled by window listener setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE); ar... | private ArchitectFrame() throws ArchitectException { synchronized (ArchitectFrame.class) { mainInstance = this; } setIconImage(new ImageIcon(getClass().getResource("/icons/Architect16.png")).getImage()); // close handled by window listener setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE); ar... | 1,108,615 |
public CoreUserSettings getUserSettings() { return this.userSettings; } | public CoreUserSettings getUserSettings() { return this.userSettings; } | 1,108,616 |
public UserSettings read(ArchitectSession session) throws IOException { logger.debug("reading UserSettings from java.util.prefs."); Preferences prefs = ArchitectFrame.getMainInstance().getPrefs(); UserSettings userSettings = new UserSettings(); int i; for (i = 0; i <= 99; i++) { String jarName = prefs.get(j... | public UserSettings read(ArchitectSession session) throws IOException { logger.debug("reading UserSettings from java.util.prefs."); Preferences prefs = ArchitectFrame.getMainInstance().getPrefs(); UserSettings userSettings = new UserSettings(); int i; for (i = 0; i <= 99; i++) { String jarName = prefs.get(j... | 1,108,617 |
public void setUserSettings(CoreUserSettings argUserSettings) { this.userSettings = argUserSettings; } | public void setUserSettings(CoreUserSettings argUserSettings) { this.userSettings = argUserSettings; } | 1,108,618 |
public HelpAction() { super("Help",ASUtils.createJLFIcon( "general/Help", "Help", ArchitectFrame.getMainInstance().getSprefs().getInt(SwingUserSettings.ICON_SIZE, 24))); putValue(AbstractAction.SHORT_DESCRIP... | public HelpAction() { super("Help",ASUtils.createJLFIcon( "general/Help", "Help", ArchitectFrame.getMainInstance().getSprefs().getInt(SwingUserSettings.ICON_SIZE, 24))); putValue(AbstractAction.SHORT_DESCRIP... | 1,108,619 |
public Dimension drawHighLevelReport(Graphics2D g, Dimension pageSize) throws ArchitectException { int y = 0; for (Map.Entry<SQLTable, Collection<SQLTable>> entry : mappings.entrySet()) { SQLTable st = entry.getKey(); Collection<SQLTable> targets = entry.getValue(); if... | public Dimension drawHighLevelReport(Graphics2D g, Dimension pageSize) throws ArchitectException { int y = 0; for (Map.Entry<SQLTable, Collection<SQLTable>> entry : mappings.entrySet()) { SQLTable st = entry.getKey(); Collection<SQLTable> targets = entry.getValue(); if... | 1,108,620 |
public void setPlayPen(PlayPen newPP) { if (pp != null) { pp.removeSelectionListener(this); } pp = newPP; pp.addSelectionListener(this); } | public void setPlayPen(PlayPen newPP) throws ArchitectException { if (pp != null) { pp.removeSelectionListener(this); } pp = newPP; pp.addSelectionListener(this); } | 1,108,621 |
public void setPlayPen(PlayPen pp) { if (pp != null) { pp.removeSelectionListener(this); } this.pp = pp; this.pp.addSelectionListener(this); } | public void setPlayPen(PlayPen pp) { if (pp != null) { pp.removeSelectionListener(this); } this.pp = pp; this.pp.addSelectionListener(this); } | 1,108,623 |
public void setPlayPen(PlayPen pp) { if (pp != null) { pp.removeSelectionListener(this); } this.pp = pp; this.pp.addSelectionListener(this); } | public void setPlayPen(PlayPen pp) { if (pp != null) { pp.removeSelectionListener(this); } this.pp = pp; this.pp.addSelectionListener(this); } | 1,108,624 |
public void photoCollectionChanged( PhotoCollectionChangeEvent e ) { repaint(); } | public void photoCollectionChanged( PhotoCollectionChangeEvent e ) { repaint(); } | 1,108,627 |
public void setCollection(PhotoCollection v) { if ( photoCollection != null ) { photoCollection.removePhotoCollectionChangeListener( this ); } photoCollection = v; photoCollection.addPhotoCollectionChangeListener( this ); revalidate(); } | public void setCollection(PhotoCollection v) { if ( photoCollection != null ) { photoCollection.removePhotoCollectionChangeListener( this ); } photoCollection = v; photoCollection.addPhotoCollectionChangeListener( this ); revalidate(); } | 1,108,628 |
public WLServerConnection(MBeanServer mbeanServer){ assert mbeanServer != null; this.mbeanServer = mbeanServer; } | public WLServerConnection(MBeanServer mbeanServer){ assert mbeanServer != null; this.mbeanServer = (RemoteMBeanServer)mbeanServer; } | 1,108,629 |
public static void setMaxDistance(int maxDistance) { Options.maxDistance = maxDistance; } | public static void setMaxDistance(int maxDistance) { Options.maxDistance = maxDistance*1000; } | 1,108,630 |
public void appendTo(Appendable app, FilterValues<S> values) throws IOException { mProperty.appendTo(app); app.append(' '); app.append(mOp.toString()); app.append(' '); if (values != null) { Object value = values.getValue(this); if (value != null || values.is... | public void appendTo(Appendable app, FilterValues<S> values) throws IOException { mProperty.appendTo(app); app.append(' '); app.append(mOp.toString()); app.append(' '); if (values != null) { Object value = values.getValue(this); if (value != null || values.is... | 1,108,632 |
public void appendTo(Appendable app, FilterValues<S> values) throws IOException { mProperty.appendTo(app); app.append(' '); app.append(mOp.toString()); app.append(' '); if (values != null) { Object value = values.getValue(this); if (value != null || values.is... | public void appendTo(Appendable app, FilterValues<S> values) throws IOException { mProperty.appendTo(app); app.append(' '); app.append(mOp.toString()); app.append(' '); if (values != null) { Object value = values.getValue(this); if (value != null || values.is... | 1,108,633 |
protected void writeDDLUserSettings(DDLUserSettings ddlprefs) { println("<ddl-user-settings>"); indent++; Properties props = ddlprefs.toPropList(); Iterator it = props.keySet().iterator(); while (it.hasNext()) { String prefName = (String) it.next(); println("<setting name=\""+escape(prefName) +"\" value=\... | protected void writeDDLUserSettings(DDLUserSettings ddlprefs) { println("<ddl-user-settings>"); indent++; Properties props = ddlprefs.toPropList(); Iterator it = props.keySet().iterator(); while (it.hasNext()) { String prefName = (String) it.next(); println("<setting name=\""+escape(prefName) +"\" value=\... | 1,108,634 |
protected void writeETLUserSettings(ETLUserSettings etlprefs) { println("<etl-user-settings>"); indent++; Properties props = etlprefs.toPropList(); Iterator it = props.keySet().iterator(); while (it.hasNext()) { String prefName = (String) it.next(); println("<setting name=\""+escape(prefName) +"\" value=\... | protected void writeETLUserSettings(ETLUserSettings etlprefs) { println("<etl-user-settings>"); indent++; Properties props = etlprefs.toPropList(); Iterator it = props.keySet().iterator(); while (it.hasNext()) { String prefName = (String) it.next(); println("<setting name=\""+escape(prefName) +"\" value=\... | 1,108,635 |
protected void writePrintUserSettings(PrintUserSettings printPrefs) { println("<print-user-settings>"); indent++; Properties props = printPrefs.toPropList(); Iterator it = props.keySet().iterator(); while (it.hasNext()) { String prefName = (String) it.next(); println("<setting name=\""+escape(prefName) +"... | protected void writePrintUserSettings(PrintUserSettings printPrefs) { println("<print-user-settings>"); indent++; Properties props = printPrefs.toPropList(); Iterator it = props.keySet().iterator(); while (it.hasNext()) { String prefName = (String) it.next(); println("<setting name=\""+escape(prefName) +"... | 1,108,636 |
protected void writeSwingSettings(SwingUserSettings sprefs) { println("<swing-gui-settings>"); indent++; Iterator it = sprefs.getSettingNames().iterator(); while (it.hasNext()) { String prefName = (String) it.next(); Object pref = sprefs.getObject(prefName, ""); println("<setting name=\""+escape(prefName) ... | protected void writeSwingSettings(SwingUserSettings sprefs) { println("<swing-gui-settings>"); indent++; Iterator it = sprefs.getSettingNames().iterator(); while (it.hasNext()) { String prefName = (String) it.next(); Object pref = sprefs.getObject(prefName, ""); println("<setting name=\""+escape(prefName) ... | 1,108,637 |
public List<String> getDriverJarList() { return Collections.unmodifiableList(driverJarList); } | public List<String> getDriverJarList() { return Collections.unmodifiableList(driverJarList); } | 1,108,639 |
public XWikiStoreInterface getStore() { return store; } | public XWikiStoreInterface getStore() { return store; } | 1,108,640 |
public String toXML(XWikiContext context) throws XWikiException { Document doc = toXMLDocument(context); return toXML(doc, context); } | public String toXML(XWikiContext context) throws XWikiException { Document doc = toXMLDocument(context); return toXML(doc, context); } | 1,108,641 |
public XWikiDocumentArchive getDocumentArchive() { // We are using a SoftReference which will allow the archive to be // discarded by the Garbage collector as long as the context is closed (usually during the request) if (archive==null) return null; else return (XWikiDocu... | public XWikiDocumentArchive getDocumentArchive() { // We are using a SoftReference which will allow the archive to be // discarded by the Garbage collector as long as the context is closed (usually during the request) if (archive==null) return null; else return (XWikiDocu... | 1,108,642 |
public void actionPerformed(ActionEvent e) { logger.debug("event was fired"); ASUtils.LabelValueBean lvb = (ASUtils.LabelValueBean) connectionsBox.getSelectedItem(); if (lvb.getValue() == null) { runPLEngine.setSelected(false); runPLEngine.setEnabled(false); plRepOwner.setText(null); plUserName.s... | public void actionPerformed(ActionEvent e) { logger.debug("event was fired"); ASUtils.LabelValueBean lvb = (ASUtils.LabelValueBean) connectionsBox.getSelectedItem(); if (lvb.getValue() == null) { runPLEngine.setSelected(false); runPLEngine.setEnabled(false); plRepOwner.setText(null); plUserName.s... | 1,108,643 |
public void actionPerformed(ActionEvent e) { logger.debug("event was fired"); ASUtils.LabelValueBean lvb = (ASUtils.LabelValueBean) connectionsBox.getSelectedItem(); if (lvb.getValue() == null) { runPLEngine.setSelected(false); runPLEngine.setEnabled(false); plRepOwner.setText(null); plUserName.s... | public void actionPerformed(ActionEvent e) { logger.debug("event was fired"); ASUtils.LabelValueBean lvb = (ASUtils.LabelValueBean) connectionsBox.getSelectedItem(); if (lvb.getValue() == null) { runPLEngine.setSelected(false); runPLEngine.setEnabled(false); plRepOwner.setText(null); plUserName.s... | 1,108,644 |
private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus, Vector kidAffStatus) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_blocks = block_size.len... | private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus, Vector kidAffStatus) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_blocks = block_size.len... | 1,108,645 |
private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus, Vector kidAffStatus) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_blocks = block_size.len... | private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus, Vector kidAffStatus) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_blocks = block_size.len... | 1,108,646 |
private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus, Vector kidAffStatus) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_blocks = block_size.len... | private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus, Vector kidAffStatus) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_blocks = block_size.len... | 1,108,647 |
private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus, Vector kidAffStatus) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_blocks = block_size.len... | private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus, Vector kidAffStatus) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_blocks = block_size.len... | 1,108,648 |
private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus, Vector kidAffStatus) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_blocks = block_size.len... | private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus, Vector kidAffStatus) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_blocks = block_size.len... | 1,108,649 |
public String getAttachmentURL(String filename, String action, XWikiContext context) { URL url = context.getURLFactory().createAttachmentURL(filename, getWeb(), getName(), action, null, getDatabase(), context); return context.getURLFactory().getURL(url, context); } | public String getAttachmentURL(String filename, String action, XWikiContext context) { URL url = context.getURLFactory().createAttachmentURL(filename, getWeb(), getName(), action, null, getDatabase(), context); return context.getURLFactory().getURL(url, context); } | 1,108,651 |
public String getURL(String action, XWikiContext context) { return getURL(action, false, context); } | public String getURL(String action, XWikiContext context) { return getURL(action, false, context); } | 1,108,652 |
public XWikiPluginManager(String classList, XWikiContext context) { String[] classNames = StringUtils.split(classList, " ,"); addPlugins(classNames, context); } | public XWikiPluginManager(String classList, XWikiContext context) { String[] classNames = StringUtils.split(classList, " ,"); addPlugins(classNames, context); } | 1,108,653 |
public String toIdentifier(String name) { if (name == null) return null; else return name.replace(' ', '_'); } | public String toIdentifier(String name) { if (name == null) return null; else return name.replace(' ', '_'); } | 1,108,655 |
public PLExportPanel() { setLayout(new GridLayout(1,2)); ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); projName = new String(project.getName()); newConnButton= new JButton("New"); newConnButton.addActionListener(new NewConnectionListener()); List connectionHisto... | public PLExportPanel() { setLayout(new GridLayout(1,2)); ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); projName = new String(project.getName()); newConnButton= new JButton("New"); newConnButton.addActionListener(new NewConnectionListener()); String plIniPath =... | 1,108,656 |
public PLExportPanel() { setLayout(new GridLayout(1,2)); ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); projName = new String(project.getName()); newConnButton= new JButton("New"); newConnButton.addActionListener(new NewConnectionListener()); List connectionHisto... | public PLExportPanel() { setLayout(new GridLayout(1,2)); ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); projName = new String(project.getName()); newConnButton= new JButton("New"); newConnButton.addActionListener(new NewConnectionListener()); List connectionHisto... | 1,108,657 |
public PLExportPanel() { setLayout(new GridLayout(1,2)); ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); projName = new String(project.getName()); newConnButton= new JButton("New"); newConnButton.addActionListener(new NewConnectionListener()); List connectionHisto... | public PLExportPanel() { setLayout(new GridLayout(1,2)); ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); projName = new String(project.getName()); newConnButton= new JButton("New"); newConnButton.addActionListener(new NewConnectionListener()); List connectionHisto... | 1,108,658 |
public PLExportPanel() { setLayout(new GridLayout(1,2)); ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); projName = new String(project.getName()); newConnButton= new JButton("New"); newConnButton.addActionListener(new NewConnectionListener()); List connectionHisto... | public PLExportPanel() { setLayout(new GridLayout(1,2)); ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); projName = new String(project.getName()); newConnButton= new JButton("New"); newConnButton.addActionListener(new NewConnectionListener()); List connectionHisto... | 1,108,659 |
public PLExportPanel() { setLayout(new GridLayout(1,2)); ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); projName = new String(project.getName()); newConnButton= new JButton("New"); newConnButton.addActionListener(new NewConnectionListener()); List connectionHisto... | public PLExportPanel() { setLayout(new GridLayout(1,2)); ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); projName = new String(project.getName()); newConnButton= new JButton("New"); newConnButton.addActionListener(new NewConnectionListener()); List connectionHisto... | 1,108,660 |
public PLExportPanel() { setLayout(new GridLayout(1,2)); ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); projName = new String(project.getName()); newConnButton= new JButton("New"); newConnButton.addActionListener(new NewConnectionListener()); List connectionHisto... | public PLExportPanel() { setLayout(new GridLayout(1,2)); ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); projName = new String(project.getName()); newConnButton= new JButton("New"); newConnButton.addActionListener(new NewConnectionListener()); List connectionHisto... | 1,108,661 |
public void applyChanges() { String name = plFolderName.getText(); } | public void applyChanges() { } | 1,108,662 |
private FilterValues<S> transferValues(FilterValues<T> values) { if (values == null) { return null; } // FIXME: throws exception if not all values supplied return mOuterLoopFilterValues.withValues(values.getValuesFor(mSourceFilterAsFromTarget)); } | private FilterValues<S> transferValues(FilterValues<T> values) { if (values == null) { return null; } // FIXME: throws exception if not all values supplied return mOuterLoopFilterValues .withValues(values.getSuppliedValuesFor(mSourceFilterAsFromTarget)); } | 1,108,663 |
public static PhotoInfo addToDB( File imgFile ) throws PhotoNotFoundException { VolumeBase vol = null; try { vol = VolumeBase.getVolumeOfFile( imgFile ); } catch (IOException ex) { throw new PhotoNotFoundException(); } // Determine the fle that will ... | public static PhotoInfo addToDB( File imgFile ) throws PhotoNotFoundException { VolumeBase vol = null; try { vol = VolumeBase.getVolumeOfFile( imgFile ); } catch (IOException ex) { throw new PhotoNotFoundException(); } // Determine the fle that will ... | 1,108,665 |
static public PhotoInfo[] retrieveByOrigHash(byte[] hash) { ODMGXAWrapper txw = new ODMGXAWrapper(); Implementation odmg = ODMG.getODMGImplementation(); Transaction tx = odmg.currentTransaction(); PhotoInfo photos[] = null; try { PersistenceBroker broker = ((HasBroker) tx).getBroker(); Criteria ... | static public PhotoInfo[] retrieveByOrigHash(byte[] hash) { ODMGXAWrapper txw = new ODMGXAWrapper(); Implementation odmg = ODMG.getODMGImplementation(); Transaction tx = odmg.currentTransaction(); PhotoInfo photos[] = null; try { PersistenceBroker broker = ((HasBroker) tx).getBroker(); Criteria ... | 1,108,666 |
public void stateChanged(ChangeEvent e) { if (tabs.getSelectedIndex() != -1){ window.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ ex... | public void stateChanged(ChangeEvent e) { if (tabs.getSelectedIndex() != -1){ window.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ ex... | 1,108,667 |
public void stateChanged(ChangeEvent e) { if (tabs.getSelectedIndex() != -1){ window.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ ex... | public void stateChanged(ChangeEvent e) { if (tabs.getSelectedIndex() != -1){ window.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ ex... | 1,108,668 |
void export(int tabNum, int format, int start, int stop){ fc.setSelectedFile(new File("")); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION){ File outfile = fc.getSelectedFile(); if (format == PNG_MODE || format == COMPRESSED_PNG_MODE){ BufferedImage ima... | void export(int tabNum, int format, int start, int stop){ fc.setSelectedFile(new File("")); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION){ File outfile = fc.getSelectedFile(); if (format == PNG_MODE || format == COMPRESSED_PNG_MODE){ BufferedImage ima... | 1,108,669 |
void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files re... | void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files re... | 1,108,670 |
public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ... | public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ... | 1,108,671 |
public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; if (dPrimeTable.length == 0){ //if there are no valid markers, but info is known we don't want //to paint any of that stuff. printDPrimeValues = false; pri... | public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; if (dPrimeTable.length == 0){ //if there are no valid markers, but info is known we don't want //to paint any of that stuff. printDPrimeValues = false; pri... | 1,108,673 |
private void buildXformImage() { // ParameterBlock pbRen = new ParameterBlock();// pbRen.addSource( origImage );// pbRen.add(null).add(null).add(null).add(null).add(null); // RenderableImage renSrc = JAI.createRenderable( "renderable", pbRen ); float scale = 1.0f; ... | private void buildXformImage() { // ParameterBlock pbRen = new ParameterBlock();// pbRen.addSource( origImage );// pbRen.add(null).add(null).add(null).add(null).add(null); // RenderableImage renSrc = JAI.createRenderable( "renderable", pbRen ); float scale = 1.0f; ... | 1,108,674 |
private void buildXformImage() { // ParameterBlock pbRen = new ParameterBlock();// pbRen.addSource( origImage );// pbRen.add(null).add(null).add(null).add(null).add(null); // RenderableImage renSrc = JAI.createRenderable( "renderable", pbRen ); float scale = 1.0f; ... | private void buildXformImage() { // ParameterBlock pbRen = new ParameterBlock();// pbRen.addSource( origImage );// pbRen.add(null).add(null).add(null).add(null).add(null); // RenderableImage renSrc = JAI.createRenderable( "renderable", pbRen ); float scale = 1.0f; ... | 1,108,675 |
public Script getBody() { if ( getTrim() && ! hasTrimmed ) { trimBody(); } return body; } | public Script getBody() { if ( isTrim() && ! hasTrimmed ) { trimBody(); } return body; } | 1,108,676 |
public TagScript createTagScript( final String name, Attributes attrs ) throws Exception { if ( name.equals( "tagdef" ) ) { return new TagScript( new TagFactory() { public Tag createTag() { return new TagDefTag( JeezTagLibra... | public TagScript createTagScript( final String name, Attributes attrs ) throws Exception { if ( name.equals( "tagdef" ) ) { return new TagScript( new TagFactory() { public Tag createTag(String name, Attributes attributes) { ... | 1,108,678 |
public TagScript createTagScript( final String name, Attributes attrs ) throws Exception { if ( name.equals( "tagdef" ) ) { return new TagScript( new TagFactory() { public Tag createTag() { return new TagDefTag( JeezTagLibra... | public TagScript createTagScript( final String name, Attributes attrs ) throws Exception { if ( name.equals( "tagdef" ) ) { return new TagScript( new TagFactory() { public Tag createTag() { return new TagDefTag( JeezTagLibra... | 1,108,679 |
public TagScript createTagScript( final String name, Attributes attrs ) throws Exception { if ( name.equals( "tagdef" ) ) { return new TagScript( new TagFactory() { public Tag createTag() { return new TagDefTag( JeezTagLibra... | public TagScript createTagScript( final String name, Attributes attrs ) throws Exception { if ( name.equals( "tagdef" ) ) { return new TagScript( new TagFactory() { public Tag createTag() { return new TagDefTag( JeezTagLibra... | 1,108,680 |
public TagScript createTagScript( final String name, Attributes attrs ) throws Exception { if ( name.equals( "tagdef" ) ) { return new TagScript( new TagFactory() { public Tag createTag() { return new TagDefTag( JeezTagLibra... | public TagScript createTagScript( final String name, Attributes attrs ) throws Exception { if ( name.equals( "tagdef" ) ) { return new TagScript( new TagFactory() { public Tag createTag() { return new TagDefTag( JeezTagLibra... | 1,108,681 |
public Tag createTag() { return new TagDefTag( JeezTagLibrary.this ); } | public Tag createTag(String name, Attributes attributes) { return new TagDefTag( JeezTagLibrary.this ); } | 1,108,682 |
public Tag createTag() { return new TargetTag(); } | public Tag createTag(String name, Attributes attributes) { return new TargetTag(); } | 1,108,683 |
public Tag createTag() throws Exception { // lets try create a dynamic tag first Tag tag = JeezTagLibrary.this.createTag(name); if ( tag != null ) { return tag; ... | public Tag createTag(String name, Attributes attributes) throws Exception { // lets try create a dynamic tag first Tag tag = JeezTagLibrary.this.createTag(name); if ( tag != null ) { r... | 1,108,684 |
public Tag createTag() throws Exception { // lets try create a dynamic tag first Tag tag = JeezTagLibrary.this.createTag(name); if ( tag != null ) { return tag; ... | public Tag createTag() throws Exception { // lets try create a dynamic tag first Tag tag = JeezTagLibrary.this.createTag(name, attributes); if ( tag != null ) { return tag; ... | 1,108,685 |
public Tag createTag() throws Exception { // lets try create a dynamic tag first Tag tag = JeezTagLibrary.this.createTag(name); if ( tag != null ) { return tag; ... | public Tag createTag() throws Exception { // lets try create a dynamic tag first Tag tag = JeezTagLibrary.this.createTag(name); if ( tag != null ) { return tag; ... | 1,108,686 |
public TagDefTag() { } | public TagDefTag(DynamicTagLibrary tagLibrary) { this.tagLibrary = tagLibrary; } | 1,108,687 |
public void mousePressed (MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK){ final int clickX = e.getX(); final int clickY = e.getY(); double dboxX = (double)(clickX - clickXShift - (clickY-clic... | public void mousePressed (MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK){ final int clickX = e.getX(); final int clickY = e.getY(); double dboxX = (double)(clickX - clickXShift - (clickY-clic... | 1,108,688 |
public void mousePressed (MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK){ final int clickX = e.getX(); final int clickY = e.getY(); double dboxX = (double)(clickX - clickXShift - (clickY-clic... | public void mousePressed (MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK){ final int clickX = e.getX(); final int clickY = e.getY(); double dboxX = (double)(clickX - clickXShift - (clickY-clic... | 1,108,689 |
public void mousePressed (MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK){ final int clickX = e.getX(); final int clickY = e.getY(); double dboxX = (double)(clickX - clickXShift - (clickY-clic... | public void mousePressed (MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK){ final int clickX = e.getX(); final int clickY = e.getY(); double dboxX = (double)(clickX - clickXShift - (clickY-clic... | 1,108,690 |
public Object construct(){ final int leftMargin = 12; String[] displayStrings = new String[5]; if (markersLoaded){ displayStrings[0] = new String ("(" +((SNP)marker... | public Object construct(){ final int leftMargin = 12; String[] displayStrings = new String[5]; if (markersLoaded){ displayStrings[0] = new String ("(" +((SNP)marker... | 1,108,691 |
public Object construct(){ final int leftMargin = 12; String[] displayStrings = new String[5]; if (markersLoaded){ displayStrings[0] = new String ("(" +((SNP)marker... | public Object construct(){ final int leftMargin = 12; String[] displayStrings = new String[5]; if (markersLoaded){ displayStrings[0] = new String ("(" +((SNP)marker... | 1,108,692 |
public Object construct(){ final int leftMargin = 12; String[] displayStrings = new String[5]; if (markersLoaded){ displayStrings[0] = new String ("(" +((SNP)marker... | public Object construct(){ final int leftMargin = 12; String[] displayStrings = new String[5]; if (markersLoaded){ displayStrings[0] = new String ("(" +((SNP)marker... | 1,108,693 |
public void paintComponent(Graphics g){ Graphics2D g2 = (Graphics2D) g; Dimension size = getSize(); Dimension pref = getPreferredSize(); Rectangle clipRect = (Rectangle)g.getClip(); //first paint grab the cliprect for the whole viewport if (viewRect.width == 0){viewRect=cli... | public void paintComponent(Graphics g){ Graphics2D g2 = (Graphics2D) g; Dimension size = getSize(); Dimension pref = getPreferredSize(); clipRect = (Rectangle)g.getClip(); //first paint grab the cliprect for the whole viewport if (viewRect.width == 0){viewRect=clipRect;} ... | 1,108,694 |
public void doTag(XMLOutput xmlOutput) throws Exception { // get the response from the context HttpResponse httpResponse = (HttpResponse) getContext().getVariable("response"); if (null == httpResponse) { throw new JellyException("HttpResponse variable not available in Jelly context")... | public void doTag(XMLOutput xmlOutput) throws Exception { // get the response from the context HttpResponse httpResponse = (HttpResponse) getContext().getVariable("response"); if (null == httpResponse) { throw new JellyException("HttpResponse variable not available in Jelly context")... | 1,108,696 |
private static ConnectorRegistry create(ApplicationConfig config) throws Exception { Map paramValues = config.getParamValues(); String appId = config.getApplicationId(); String connectorId = (String) paramValues.get("connectorId"); File file1 = new File(CoreUtils.getConnectorDir() + File... | private static ConnectorRegistry create(ApplicationConfig config) throws Exception { Map paramValues = config.getParamValues(); String appId = config.getApplicationId(); String connectorId = (String) paramValues.get("connectorId"); File file1 = new File(CoreUtils.getConnectorDir() + File... | 1,108,697 |
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... | 1,108,698 |
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") || args[i].equals("-help")) { nogui = true; } } if(nogui) { HaploT... | 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") || args[i].equals("-help")) { nogui = true; } } if(nogui) { HaploT... | 1,108,699 |
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") || args[i].equals("-help")) { nogui = true; } } if(nogui) { HaploT... | 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") || args[i].equals("-help")) { nogui = true; } } if(nogui) { HaploT... | 1,108,700 |
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") || args[i].equals("-help")) { nogui = true; } } if(nogui) { HaploT... | 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") || args[i].equals("-help")) { nogui = true; } } if(nogui) { HaploT... | 1,108,701 |
public Object construct(){ dPrimeDisplay=null; theData.infoKnown = false; File markerFile; if (inputOptions[1].equals("")){ markerFile = null; }else{ markerFile = new File(inputOptions[1]); ... | public Object construct(){ dPrimeDisplay=null; theData.infoKnown = false; File markerFile; if (inputOptions[1].equals("")){ markerFile = null; }else{ markerFile = new File(inputOptions[1]); ... | 1,108,702 |
public Object construct(){ dPrimeDisplay=null; theData.infoKnown = false; File markerFile; if (inputOptions[1].equals("")){ markerFile = null; }else{ markerFile = new File(inputOptions[1]); ... | public Object construct(){ dPrimeDisplay=null; theData.infoKnown = false; File markerFile; if (inputOptions[1].equals("")){ markerFile = null; }else{ markerFile = new File(inputOptions[1]); ... | 1,108,703 |
void readMarkers(File inputFile, String[][] hminfo){ try { theData.prepareMarkerInput(inputFile,maxCompDist,hminfo); if (checkPanel != null){ checkPanel.refreshNames(); } if (tdtPanel != null){ tdtPanel.refreshNames(); } ... | void readMarkers(File inputFile, String[][] hminfo){ try { theData.prepareMarkerInput(inputFile,maxCompDist,hminfo); if (checkPanel != null){ checkPanel = new CheckDataPanel(theData); Container checkTab = (Container)tabs.getComponentAt(VIEW_CHECK_NUM); checkTab.removeAll(... | 1,108,704 |
public static double gammq (double a, double x) throws CheckDataException { double gamser, gammcf; //, gln; if ((x < 0.0 )|| (a <= 0.0 )) throw new CheckDataException("Invalid arguments in routine gammq" ); if (x < (a + 1.0) ) { gamser = gser(a , x); return (1.0 - gamser) ; } else { gammcf = gcf (a , x); ... | public static double gammq (double a, double x) { double gamser, gammcf; //, gln; if ((x < 0.0 )|| (a <= 0.0 )) throw new CheckDataException("Invalid arguments in routine gammq" ); if (x < (a + 1.0) ) { gamser = gser(a , x); return (1.0 - gamser) ; } else { gammcf = gcf (a , x); return gammcf ; } } | 1,108,707 |
public static double gammq (double a, double x) throws CheckDataException { double gamser, gammcf; //, gln; if ((x < 0.0 )|| (a <= 0.0 )) throw new CheckDataException("Invalid arguments in routine gammq" ); if (x < (a + 1.0) ) { gamser = gser(a , x); return (1.0 - gamser) ; } else { gammcf = gcf (a , x); ... | public static double gammq (double a, double x) throws CheckDataException { double gamser, gammcf; //, gln; if ((x < 0.0 )|| (a <= 0.0 )) throw new CheckDataException("Invalid arguments in routine gammq" ); if (x < (a + 1.0) ) { gamser = gser(a , x); return (1.0 - gamser) ; } else { gammcf = gcf (a , x); ... | 1,108,708 |
public HaplotypeAssociationNode(String name) { this.name = name; this.freq = ""; this.chisq = -1; this.pval = ""; } | public HaplotypeAssociationNode(String name) { this.name = name; this.freq = ""; this.chisq = -1; this.pval = new Double(0); } | 1,108,710 |
public void writeTable(SQLTable t) throws SQLException, ArchitectException { Map colNameMap = new HashMap(); // for detecting duplicate column names String origTableName = t.getName(); if (topLevelNames.get(t.getName()) != null) { int i = 1; String newName = origTableName+"_"+i; while (topLevelNames.get(newN... | public void writeTable(SQLTable t) throws SQLException, ArchitectException { Map colNameMap = new HashMap(); // for detecting duplicate column names String origTableName = t.getName(); if (topLevelNames.get(t.getName()) != null) { int i = 1; String newName = origTableName+"_"+i; while (topLevelNames.get(newN... | 1,108,711 |
public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); Object parentObject = findBeanAncestor(); // lets assume that Task instances are not nested inside other Task instances // for example <manifest> inside a <jar>... | public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); Object parentObject = findBeanAncestor(); // lets assume that Task instances are not nested inside other Task instances // for example <manifest> inside a <jar>... | 1,108,712 |
public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command.equals(READ_GENOTYPES)){ ReadDataDialog readDialog = new ReadDataDialog("Open new data", this); readDialog.pack(); readDialog.setVisible(true); } else if (command.equ... | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command.equals(READ_GENOTYPES)){ ReadDataDialog readDialog = new ReadDataDialog("Open new data", this); readDialog.pack(); readDialog.setVisible(true); } else if (command.equ... | 1,108,714 |
public void finished() { if(uc != null) { if(uc.isNewVersionAvailable()) { UpdateDisplayDialog udp = new UpdateDisplayDialog(window,"Update Check",uc); udp.pack(); udp.setVisible(tr... | public void finished() { if(uc != null) { if(uc.isNewVersionAvailable()) { UpdateDisplayDialog udp = new UpdateDisplayDialog(window,"Update Check",uc); udp.pack(); udp.setVisible(tr... | 1,108,715 |
public void actionPerformed(ActionEvent e) { final JDialog d = new JDialog(ArchitectFrame.getMainInstance(), "New PL Repository Connection"); JPanel plr = new JPanel(new BorderLayout(12,12)); plr.setBorder(BorderFactory.createEmptyBorder(12,12,12,12)); final DBCSPanel dbcsPanel = new DBCSPanel()... | public void actionPerformed(ActionEvent e) { final JDialog d = new JDialog(ArchitectFrame.getMainInstance(), "New PL Repository Connection"); JPanel plr = new JPanel(new BorderLayout(12,12)); plr.setBorder(BorderFactory.createEmptyBorder(12,12,12,12)); final DBCSPanel dbcsPanel = new DBCSPanel()... | 1,108,716 |
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