rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k |
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getBody().run( context, output); | invokeBody( output); | 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... |
getBody().run( context, output); | invokeBody( output); | public void firePostAction(Goal goal) throws Exception { // lets run the body log.info( "Running post action: " + getName() ); getBody().run( context, output); } |
HandlerContext(Command command, boolean isAuthRequired){ this.command = command; this.serviceContext = getServiceContext(command, isAuthRequired); | HandlerContext(Command command){ this(command, true); | HandlerContext(Command command, boolean isAuthRequired){ this.command = command; this.serviceContext = getServiceContext(command, isAuthRequired); } |
if (o == null) return false; | public boolean equals(Object o) { ArchitectDataSource other = (ArchitectDataSource) o; return this.properties.equals(other.properties); } | |
if(metaAppConfig.isDisplayURL()) appForm.setURL(config.getURL()); | public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) { ApplicationConfig config =... | |
out.println("-- Created by SQLPower Oracle 8i/9i DDL Generator "+GENERATOR_VERSION+" --"); | println("-- Created by SQLPower Oracle 8i/9i DDL Generator "+GENERATOR_VERSION+" --"); | public void writeHeader() { out.println("-- Created by SQLPower Oracle 8i/9i DDL Generator "+GENERATOR_VERSION+" --"); } |
public void doTag(XMLOutput output) throws Exception { | public void doTag(XMLOutput output) throws JellyTagException { | 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) { ... |
file.delete(); | file.renameTo(new File(KEY_FILE_PATH + ".bak")); | 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... |
if(password == null){ assert plaintextPassword != null; password = Crypto.hash(plaintextPassword); } | public String getPassword() { return password; } | |
System.err.println( "Is rot handle? " + isHandle ); | log.debug( "Is rot handle? " + 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 ); System.err.println( "Is rot handle? " + isHandle ); return isHandle; } |
System.err.println( "Moving handle " + handleMoving ); | log.debug( "Moving handle " + handleMoving ); | 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 ) { ... |
System.err.println( "New rotation " + cropBorderRot ); | log.debug( "New rotation " + cropBorderRot ); | 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; } ... |
ServiceDiscovery discovery = getServiceDiscovery(); | DiscoverClasses discovery = getDiscoverClasses(); | 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... |
ServiceInfo[] infoArray = discovery.findServices(name); if ( infoArray != null && infoArray.length > 0 ) { for (int i = 0; i < infoArray.length; i++ ) { ServiceInfo info = infoArray[i]; try { Class typeClass = info.getLoader().loadClass( info.getImplName() ); if ( typeClass != null ) { return newInstance(uri, typeClas... | ResourceClassIterator iter = discovery.findResourceClasses(name); while (iter.hasNext()) { ResourceClass resource = iter.nextResourceClass(); try { Class typeClass = resource.loadClass(); if ( typeClass != null ) { return newInstance(uri, typeClass); | 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... |
else { log.info( "Could not find any services for name: " + name ); } | log.info( "Could not find any services for name: " + name ); | 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... |
architectSession = ArchitectSession.getInstance(); | architectSession = ArchitectSessionImpl.getInstance(); | 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... |
public CoreUserSettings getUserSettings() { return this.userSettings; } | public CoreUserSettings getUserSettings(); | public CoreUserSettings getUserSettings() { return this.userSettings; } |
logger.debug("Pruning dead jar entry " + i); | 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 void setUserSettings(CoreUserSettings argUserSettings) { this.userSettings = argUserSettings; } | public void setUserSettings(CoreUserSettings argUserSettings); | public void setUserSettings(CoreUserSettings argUserSettings) { this.userSettings = argUserSettings; } |
kit = new HTMLEditorKit(); editorPane.setEditorKit(kit); | public HelpAction() { super("Help",ASUtils.createJLFIcon( "general/Help", "Help", ArchitectFrame.getMainInstance().getSprefs().getInt(SwingUserSettings.ICON_SIZE, 24))); putValue(AbstractAction.SHORT_DESCRIP... | |
return new Dimension(maxSourceWidth + sourceTargetGap + maxTargetWidth, y - unrelatedSourcesGap); | return new Dimension(maxSourceWidth + sourceTargetGap + maxTargetWidth, y ); | 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 void setPlayPen(PlayPen newPP) { | public void setPlayPen(PlayPen newPP) throws ArchitectException { | public void setPlayPen(PlayPen newPP) { if (pp != null) { pp.removeSelectionListener(this); } pp = newPP; pp.addSelectionListener(this); } |
setupAction(pp.getSelectedItems()); | public void setPlayPen(PlayPen newPP) { if (pp != null) { pp.removeSelectionListener(this); } pp = newPP; pp.addSelectionListener(this); } | |
if (pp != null) { pp.removeSelectionListener(this); } this.pp = pp; this.pp.addSelectionListener(this); | setupAction(pp.getSelectedItems()); | public void setPlayPen(PlayPen pp) { if (pp != null) { pp.removeSelectionListener(this); } this.pp = pp; this.pp.addSelectionListener(this); } |
if (pp != null) { pp.removeSelectionListener(this); } this.pp = pp; this.pp.addSelectionListener(this); | if (this.pp != null) { this.pp.removeSelectionListener(this); } this.pp=pp; pp.addSelectionListener(this); setupAction(pp.getSelectedItems()); | public void setPlayPen(PlayPen pp) { if (pp != null) { pp.removeSelectionListener(this); } this.pp = pp; this.pp.addSelectionListener(this); } |
firstMouseEvent = mouseEvent; | public void mousePressed(MouseEvent mouseEvent) { } | |
firstMouseEvent = null; | public void mouseReleased(MouseEvent mouseEvent) { } | |
repaint(); } | revalidate(); repaint(); } | public void photoCollectionChanged( PhotoCollectionChangeEvent e ) { repaint(); } |
photoCollection = v; photoCollection.addPhotoCollectionChangeListener( this ); revalidate(); | photoCollection = v; photoCollection.addPhotoCollectionChangeListener( this ); revalidate(); repaint(); | public void setCollection(PhotoCollection v) { if ( photoCollection != null ) { photoCollection.removePhotoCollectionChangeListener( this ); } photoCollection = v; photoCollection.addPhotoCollectionChangeListener( this ); revalidate(); } |
this.mbeanServer = mbeanServer; | this.mbeanServer = (RemoteMBeanServer)mbeanServer; | public WLServerConnection(MBeanServer mbeanServer){ assert mbeanServer != null; this.mbeanServer = mbeanServer; } |
Options.maxDistance = maxDistance; | Options.maxDistance = maxDistance*1000; | public static void setMaxDistance(int maxDistance) { Options.maxDistance = maxDistance; } |
if (filter == null) { return Filter.getOpenFilter(getStorableType()); } | public Filter<S> getFilter() { Filter<S> filter = mIdentityFilter; for (PropertyFilter<S> p : mExclusiveRangeStartFilters) { filter = filter == null ? p : filter.and(p); } for (PropertyFilter<S> p : mInclusiveRangeStartFilters) { filter = filter == null ? p : filter... | |
/* Uncomment for testing if (mBindID != 0) { | if (mBindID > 1) { | 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... | |
println("<setting name=\""+escape(prefName) +"\" value=\""+escape(props.getProperty(prefName))+"\" />"); | println("<setting name=\""+ArchitectUtils.escapeXML(prefName) +"\" value=\""+ArchitectUtils.escapeXML(props.getProperty(prefName))+"\" />"); | 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=\... |
println("<setting name=\""+escape(prefName) +"\" value=\""+escape(props.getProperty(prefName))+"\" />"); | println("<setting name=\""+ArchitectUtils.escapeXML(prefName) +"\" value=\""+ArchitectUtils.escapeXML(props.getProperty(prefName))+"\" />"); | 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=\... |
println("<setting name=\""+escape(prefName) +"\" value=\""+escape(props.getProperty(prefName))+"\" />"); | println("<setting name=\""+ArchitectUtils.escapeXML(prefName) +"\" value=\""+ArchitectUtils.escapeXML(props.getProperty(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) +"... |
println("<setting name=\""+escape(prefName) +"\" class=\""+escape(pref.getClass().getName()) +"\" value=\""+escape(pref.toString())+"\" />"); | println("<setting name=\""+ArchitectUtils.escapeXML(prefName) +"\" class=\""+ArchitectUtils.escapeXML(pref.getClass().getName()) +"\" value=\""+ArchitectUtils.escapeXML(pref.toString())+"\" />"); | 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) ... |
printUserSettings = new PrintUserSettings(); | public UserSettings() { super(); dbConnections = new LinkedList(); swingSettings = new SwingUserSettings(); etlUserSettings = new ETLUserSettings(); ddlUserSettings = new DDLUserSettings(); } | |
public List<String> getDriverJarList() { return Collections.unmodifiableList(driverJarList); } | public List<String> getDriverJarList(); | public List<String> getDriverJarList() { return Collections.unmodifiableList(driverJarList); } |
public XWikiStoreInterface getStore() { return store; | public XWikiStoreInterface getStore(XWikiContext context) { return context.getWiki().getStore(); | public XWikiStoreInterface getStore() { return store; } |
public String toXML(XWikiContext context) throws XWikiException { Document doc = toXMLDocument(context); return toXML(doc, context); | public String toXML(Document doc, XWikiContext context) { OutputFormat outputFormat = new OutputFormat("", true); if ((context == null) || (context.getWiki() == null)) outputFormat.setEncoding("UTF-8"); else outputFormat.setEncoding(context.getWiki().getEncoding()); StringWriter out = new StringWriter(); XMLWriter writ... | public String toXML(XWikiContext context) throws XWikiException { Document doc = toXMLDocument(context); return toXML(doc, context); } |
public XWikiDocumentArchive getDocumentArchive() { if (archive==null) return null; else return (XWikiDocumentArchive) archive.get(); | public XWikiDocumentArchive getDocumentArchive(XWikiContext context) throws XWikiException { loadArchive(context); return getDocumentArchive(); | 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... |
ASUtils.LabelValueBean lvb = (ASUtils.LabelValueBean) connectionsBox.getSelectedItem(); if (lvb.getValue() == null) { | ArchitectDataSource dataSource = (ArchitectDataSource) connectionsBox.getSelectedItem(); if (dataSource == null) { | 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... |
PLConnectionSpec pldbcon = (PLConnectionSpec) lvb.getValue(); plRepOwner.setText(pldbcon.getPlsOwner()); plUserName.setText(pldbcon.getUid()); plPassword.setText(pldbcon.getPwd()); | plRepOwner.setText(dataSource.get(ArchitectDataSource.PL_SCHEMA_OWNER)); plUserName.setText(dataSource.get(ArchitectDataSource.PL_UID)); plPassword.setText(dataSource.get(ArchitectDataSource.PL_PWD)); | 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... |
double[] prob = new double[num_poss]; | MapWrap probMap = new MapWrap(PSEUDOCOUNT); | 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... |
prob = estimateProbsSmall(num_indivs,num_poss); | total=(double)num_poss; total *= PSEUDOCOUNT; for (int i=0; i<num_indivs; i++) { if (data[i].nposs==1) { tempRec = (Recovery)data[i].poss.elementAt(0); probMap.put(new Long(tempRec.h1), probMap.get(new Long(tempRec.h1)) + 1.0); probMap.put(new Long(tempRec.h2), probMap.get(new Long(tempRec.h2)) + 1.0); total+=2.0; }... | 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... |
if(prob[((int) j)] > .001) { | if (probMap.get(new Long(j)) > .001) { | 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... |
hprob[block][m] = prob[((int) j)]; | hprob[block][m]=probMap.get(new Long(j)); | 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... |
if(poss_full < Integer.MAX_VALUE) { finishLarge(num_indivs, poss_full,kidAffStatus, num_blocks,block_size,num_hlist,hlist, num_loci); }else { finishSmall(num_indivs,(int) poss_full,kidAffStatus, num_blocks,block_size,num_hlist,hlist, num_loci); } | total = poss_full * PSEUDOCOUNT; for (int i=0; i<num_indivs; i++) { if (superdata[i].nsuper==1) { Long h1 = new Long(superdata[i].superposs[0].h1); Long h2 = new Long(superdata[i].superposs[0].h2); fullProbMap.put(h1,fullProbMap.get(h1) +1.0); fullProbMap.put(h2,fullProbMap.get(h2) +1.0); total+=2.0; } } fullPro... | 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... |
Vector haplos_present = new Vector(); Vector haplo_freq= new Vector(); ArrayList keys = new ArrayList(fullProbMap.theMap.keySet()); Collections.sort(keys); Iterator kitr = keys.iterator(); while(kitr.hasNext()) { Object key = kitr.next(); long keyLong = ((Long)key).longValue(); if(fullProbMap.get(key) > .001) { haplo... | 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... | |
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, XWikiContext context) { return getAttachmentURL(filename, "download", 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); } |
public String getURL(String action, XWikiContext context) { return getURL(action, false, context); | public String getURL(String action, boolean redirect, XWikiContext context) { URL url = context.getURLFactory().createURL(getWeb(), getName(), action, null, null, getDatabase(), context); if (redirect) { if (url == null) return null; else return url.toString(); } else return context.getURLFactory().getURL(url, context)... | public String getURL(String action, XWikiContext context) { return getURL(action, false, context); } |
public XWikiPluginManager(String classList, XWikiContext context) { String[] classNames = StringUtils.split(classList, " ,"); addPlugins(classNames, context); | public XWikiPluginManager() { | public XWikiPluginManager(String classList, XWikiContext context) { String[] classNames = StringUtils.split(classList, " ,"); addPlugins(classNames, context); } |
dbmd = null; | protected String checkTargetTable(SQLTable t) throws SQLException, ArchitectException { GenericDDLGenerator ddlg = ArchitectFrame.getMainInstance().getProject().getDDLGenerator(); logger.debug("DDLG class is: " + ddlg.getClass().getName()); String tableName = ddlg.toIdentifier(t.getName()); List ourColumns = new A... | |
public String toIdentifier(String name) { if (name == null) return null; else return name.replace(' ', '_'); | public String toIdentifier(String logicalName, String physicalName) { if (logicalName == null) return null; else return logicalName.replace(' ', '_'); | public String toIdentifier(String name) { if (name == null) return null; else return name.replace(' ', '_'); } |
List connectionHistory = af.getUserSettings().getConnections(); | 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... | |
plOdbcCon = getPLDBConnection(plIniPath); | plOdbcCon = parsePlDotIni(plIniPath); | 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... |
history = new Vector(); history.add(ASUtils.lvb("(Select PL Connection)", null)); Iterator it = connectionHistory.iterator(); | connections = new Vector(); connections.add(ASUtils.lvb("(Select PL Connection)", null)); Iterator it = af.getUserSettings().getConnections().iterator(); | 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... |
history.add(ASUtils.lvb(spec.getDisplayName(), spec)); | connections.add(ASUtils.lvb(spec.getDisplayName(), spec)); | 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... |
historyBox = new JComboBox(history); historyBox.addActionListener(new HistoryBoxListener()); | connectionsBox = new JComboBox(connections); | 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... |
jdbcPanel.add(historyBox); | jdbcPanel.add(connectionsBox); | 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... |
String name = plFolderName.getText(); | public void applyChanges() { String name = plFolderName.getText(); } | |
return mOuterLoopFilterValues.withValues(values.getValuesFor(mSourceFilterAsFromTarget)); | return mOuterLoopFilterValues .withValues(values.getSuppliedValuesFor(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.getValuesFor(mSourceFilterAsFromTarget)); } |
log.debug( "Using config file " + configFile.getAbsolutePath() ); | protected PhotovaultSettings() { // Load XML configuration file String confFileName = System.getProperty( "photovault.configfile" ); if ( confFileName != null ) { System.out.println( "photovault.configfile " + confFileName ); configFile = new File( confFileName ); ... | |
FileInputStream in = new FileInputStream( imgFile ); FileOutputStream out = new FileOutputStream( instanceFile ); byte buf[] = new byte[1024]; int nRead = 0; int offset = 0; while ( (nRead = in.read( buf )) > 0 ) { out.write( buf, 0, nRead ); offset += nRead; } out.close(); in.close(); } catch ( Exception e ) { log.war... | FileUtils.copyFile( imgFile, instanceFile ); } catch (IOException ex) { log.warn( "Error copying file: " + ex.getMessage() ); | 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 ... |
photos = (PhotoInfo[]) result.toArray( new PhotoInfo[0] ); | photos = (PhotoInfo[]) result.toArray( new PhotoInfo[result.size()] ); | 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 ... |
/* JTabbedPane metaAssoc= (JTabbedPane)tabs.getComponentAt(tabNum); | JTabbedPane metaAssoc= (JTabbedPane)tabs.getComponentAt(tabNum); | 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... |
StringBuffer header = new StringBuffer(); | 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... | |
taggerConfigPanel = new TaggerConfigPanel(theData); JPanel metaTagPanel = new JPanel(); metaTagPanel.setLayout(new BoxLayout(metaTagPanel,BoxLayout.Y_AXIS)); metaTagPanel.add(taggerConfigPanel); JTabbedPane tagTabs = new JTabbedPane(); tagTabs.add("Configuration",metaTagPanel); JPanel resMetaPanel = new JPanel(); ... | 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... | |
taggerConfigPanel = new TaggerConfigPanel(theData); JPanel metaTagPanel = new JPanel(); metaTagPanel.setLayout(new BoxLayout(metaTagPanel,BoxLayout.Y_AXIS)); metaTagPanel.add(taggerConfigPanel); JTabbedPane tagTabs = new JTabbedPane(); tagTabs.add("Configuration",metaTagPanel); JPanel resMetaPanel = new JPanel(); ... | public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ... | |
if (taggerConfigPanel != null){ taggerConfigPanel.refreshTable(); } | void readMarkers(File inputFile, String[][] hminfo){ try { theData.prepareMarkerInput(inputFile, hminfo); if (theData.infoKnown){ analysisItem.setEnabled(true); gbrowseItem.setEnabled(true); spacingItem.setEnabled(true); }else{ ... | |
long minpos = Chromosome.getMarker(0).getPosition(); long maxpos = Chromosome.getMarker(Chromosome.getSize()-1).getPosition(); | long minpos = Chromosome.getFilteredMarker(0).getPosition(); long maxpos = Chromosome.getFilteredMarker(Chromosome.getFilteredSize()-1).getPosition(); | 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... |
float scale = 1.0f; imgRot = newRotDegrees; if ( fitSize ) { log.debug( "fitSize" ); float widthScale = ((float)maxWidth)/origImage.getWidth(); float heightScale = ((float)maxHeight)/origImage.getHeight(); scale = widthScale; if ( heightScale < scale ) { scale = heightScale; } log.debug( "scale: " + scale ); } else {... | Cursor oldCursor = getCursor(); try { float scale = 1.0f; imgRot = newRotDegrees; if ( fitSize ) { log.debug( "fitSize" ); float widthScale = ((float)maxWidth)/origImage.getWidth(); float heightScale = ((float)maxHeight)/origImage.getHeight(); scale = widthScale; if ( heightScale < scale ) { scale = heightScale; } l... | 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; ... |
AffineTransform at = null; if ( fitSize ) { at = org.photovault.image.ImageXform.getFittingXform( (int)maxWidth, (int)maxHeight, imgRot, (int)( origImage.getWidth() * cropUsed.getWidth() ), (int)(( cropUsed.getHeight()* origImage.getHeight() ) ) ); } else { at = org.photovault.image.ImageXform.getScaleXform( imgScale, ... | setCursor( oldCursor ); | 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; ... |
if ( getTrim() | if ( isTrim() | public Script getBody() { if ( getTrim() && ! hasTrimmed ) { trimBody(); } return body; } |
if(context.getUser().isAdmin()){ EncryptedKey encryptedKey = KeyManager.readKey(changePasswordForm.getOldPassword().toCharArray()); encryptedKey.setPassword(changePasswordForm.getNewPassword().toCharArray()); KeyManager.writeKey(encryptedKey); } | public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) throws Exception { ... | |
public Tag createTag() { | public Tag createTag(String name, Attributes attributes) { | 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 Tag createTag() throws Exception { | public Tag createTag(String name, Attributes attributes) throws Exception { | 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... |
Tag tag = JeezTagLibrary.this.createTag(name); | Tag tag = JeezTagLibrary.this.createTag(name, attributes); | 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... |
return antTagLib.createTag( name ); | return antTagLib.createTag( name, attributes ); | 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 Tag createTag() { | public Tag createTag(String name, Attributes attributes) { | public Tag createTag() { return new TagDefTag( JeezTagLibrary.this ); } |
public Tag createTag() { | public Tag createTag(String name, Attributes attributes) { | public Tag createTag() { return new TargetTag(); } |
public Tag createTag() throws Exception { | public Tag createTag(String name, Attributes attributes) throws Exception { | public Tag createTag() throws Exception { // lets try create a dynamic tag first Tag tag = JeezTagLibrary.this.createTag(name); if ( tag != null ) { return tag; ... |
Tag tag = JeezTagLibrary.this.createTag(name); | Tag tag = JeezTagLibrary.this.createTag(name, attributes); | public Tag createTag() throws Exception { // lets try create a dynamic tag first Tag tag = JeezTagLibrary.this.createTag(name); if ( tag != null ) { return tag; ... |
return antTagLib.createTag( name ); | return antTagLib.createTag( name, attributes ); | public Tag createTag() throws Exception { // lets try create a dynamic tag first Tag tag = JeezTagLibrary.this.createTag(name); if ( tag != null ) { return tag; ... |
public TagDefTag() { | public TagDefTag(DynamicTagLibrary tagLibrary) { this.tagLibrary = tagLibrary; | public TagDefTag() { } |
g.fillRect(clickX+1,clickY+1,strlen+leftMargin+4,5*metrics.getHeight()+9); | g.fillRect(clickX+1-rightEdgeShift, clickY+1-botEdgeShift, strlen+leftMargin+4, 5*metrics.getHeight()+9); | 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... |
g.drawRect(clickX,clickY,strlen+leftMargin+5,5*metrics.getHeight()+10); | g.drawRect(clickX-rightEdgeShift, clickY-botEdgeShift, strlen+leftMargin+5, 5*metrics.getHeight()+10); | 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... |
g.drawString(displayStrings[x],clickX + leftMargin, clickY+5+((x+1)*metrics.getHeight())); | g.drawString(displayStrings[x],clickX + leftMargin - rightEdgeShift, clickY+5+((x+1)*metrics.getHeight())-botEdgeShift); | 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... |
g.fillRect(clickX+1,clickY+1,strlen+leftMargin+4,5*metrics.getHeight()+9); | g.fillRect(clickX+1-rightEdgeShift, clickY+1-botEdgeShift, strlen+leftMargin+4, 5*metrics.getHeight()+9); | public Object construct(){ final int leftMargin = 12; String[] displayStrings = new String[5]; if (markersLoaded){ displayStrings[0] = new String ("(" +((SNP)marker... |
g.drawRect(clickX,clickY,strlen+leftMargin+5,5*metrics.getHeight()+10); | g.drawRect(clickX-rightEdgeShift, clickY-botEdgeShift, strlen+leftMargin+5, 5*metrics.getHeight()+10); | public Object construct(){ final int leftMargin = 12; String[] displayStrings = new String[5]; if (markersLoaded){ displayStrings[0] = new String ("(" +((SNP)marker... |
g.drawString(displayStrings[x],clickX + leftMargin, clickY+5+((x+1)*metrics.getHeight())); | g.drawString(displayStrings[x],clickX + leftMargin - rightEdgeShift, clickY+5+((x+1)*metrics.getHeight())-botEdgeShift); | public Object construct(){ final int leftMargin = 12; String[] displayStrings = new String[5]; if (markersLoaded){ displayStrings[0] = new String ("(" +((SNP)marker... |
Rectangle clipRect = (Rectangle)g.getClip(); | clipRect = (Rectangle)g.getClip(); | 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... |
/** if (pref.getWidth() > viewRect.width){ | 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... | |
httpResponse.setContentLength(writer.length()); | httpResponse.setContentLength(writer.size()); | 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")... |
MBeanServer server = MBeanServerFactory.createMBeanServer(DOMAIN_CONNECTOR); String objName = ":appType=connector,appName=" + config.getName() | MBeanServer server = MBeanServerFactory.newMBeanServer(DOMAIN_CONNECTOR); String objName = ":appId=" + appId + ",appType=connector,appName=" + config.getName() | 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... |
markerResults[i] = ((Boolean)table.getValueAt(i,9)).booleanValue(); | markerResults[i] = ((Boolean)table.getValueAt(i,CheckDataPanel.STATUS_COL)).booleanValue(); | 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... |
window.readPhasedGenotypes(inputArray); | window.readGenotypes(inputArray, HAPS); | 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... |
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