JoaoJunior/formatted-java-preprocessed-code-APR

public void actionPerformed(ActionEvent e) { File plEngine = new File(ArchitectFrame.getMainInstance().getUserSettings().getETLUserSettings().getString(ETLUserSettings.PROP_PL_ENGINE_PATH,"")); File plDir = plEngine.getParentFile(); File engineExe = new File(plDir, "PowerLoade...

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public int hashCode() { //uses idea from Long hashcode to hash position return (name.hashCode() + (int)(position ^ (position >>> 32))); }

public int hashCode() { //uses idea from Long hashcode to hash position if (name != null){ return (name.hashCode() + (int)(position ^ (position >>> 32))); }else{ return (int)position; } }

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public void trimEndWhitespace() { int index = text.length(); while (--index > 0) { char ch = text.charAt(index); if (!Character.isWhitespace(ch)) { break; } } index++; if ( index < text.length() ) { this.text = text.substr...

public void trimEndWhitespace() { int index = text.length(); while (--index >= 0) { char ch = text.charAt(index); if (!Character.isWhitespace(ch)) { break; } } index++; if ( index < text.length() ) { this.text = text.subst...

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private boolean createDatabase() { // Ask for the admin password try { PVDatabase db = new PVDatabase(); db.setName( nameFld.getText() ); PhotovaultSettings settings = PhotovaultSettings.getSettings(); settings.addDatabase( db ); String user = "";...

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private JPanel buildPanel() { FormLayout sqlLayout = new FormLayout( "4dlu, min:grow, 4dlu", //columns "pref, 4dlu, pref, 6dlu, fill:300dlu:grow,6dlu, pref, 6dlu, pref"); //rows CellConstraints cc = new CellConstraints(); sqlDoc = new DefaultStyledDocument(); SimpleAttributeSet att = new SimpleAttrib...

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public void actionPerformed(ActionEvent e) { System.out.println( "SQL_FILE_FILTER:"+ ((FileExtensionFilter) ASUtils.SQL_FILE_FILTER).toString()); SaveDocument sd = new SaveDocument(parent,sqlDoc, (FileExtensionFilter) ASUtils.SQL_FILE_FILTER ); }

public void actionPerformed(ActionEvent e) { logger.info( "SQL_FILE_FILTER:"+ ((FileExtensionFilter) ASUtils.SQL_FILE_FILTER).toString()); SaveDocument sd = new SaveDocument(parent,sqlDoc, (FileExtensionFilter) ASUtils.SQL_FILE_FILTER ); }

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public SQLObject getObjectToCompare() throws ArchitectException, IOException { SQLObject o; if (playPenRadio.isSelected()) { o = ArchitectFrame.getMainInstance().playpen.getDatabase(); } else if (physicalRadio.isSelected()) { if (schemaDropdown.getSelectedItem() != null) { o = (SQLObject) schemaDro...

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public PlinkResultsPanel(HaploView h, Vector results, Vector colNames, Vector filters){ hv = h; setLayout(new GridBagLayout()); plinkTableModel = new PlinkTableModel(colNames,results); sorter = new TableSorter(plinkTableModel); table = new JTable(sorter); table.setSelection...

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public DashboardContextImpl(WebContext webContext, DashboardConfig dashboardConfig, HttpServletRequest request){ this.webContext = webContext; this.dashboardConfig = dashboardConfig; this.request = request; setServerPath(); }

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protected void createTypeMap() throws SQLException { typeMap = new HashMap(); typeMap.put(new Integer(Types.BIGINT), new GenericTypeDescriptor("NUMERIC", Types.BIGINT, 1000, null, null, DatabaseMetaData.columnNullable, true, false)); typeMap.put(new Integer(Types.BINARY), new GenericTypeDescriptor("BYTEA", Types....

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public String toIdentifier(String name) { return name.replace(' ','_').toUpperCase(); }

public String toIdentifier(String name) { return name.replace(' ','_').toLowerCase(); }

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private void findAllMatchingTestMail(String username) throws SamplingException { try { org.apache.commons.net.pop3.POP3Client pop3Client = openConnection(username); // retrieve all messages POP3MessageInfo[] entries = null; try { entries = pop3Client...

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private void processFile(String fileName,int fileType,String infoFileName){ try { int outputType; long maxDistance; long negMaxDistance; HaploData textData; File OutputFile; File inputFile; inputFile = new File(fileName); ...

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private void processFile(String fileName,int fileType,String infoFileName){ try { int outputType; long maxDistance; long negMaxDistance; HaploData textData; File OutputFile; File inputFile; inputFile = new File(fileName); ...

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public void run() { synchronized ( this ) { while ( true ) { try { log.debug( "Waiting..." ); wait(); log.debug( "Waited..." ); if ( photo != null ) { log.debug( "Creating thumbnail for " + photo.getUid() ); Thumbnail thumb = photo.getThumbnail(); log.debug( "Done!" ); final PhotoIn...

public void run() { synchronized ( this ) { while ( true ) { try { log.debug( "Waiting..." ); wait(); log.debug( "Waited..." ); if ( photo != null ) { log.debug( "Creating thumbnail for " + photo.getUid() ); Thumbnail thumb = null; while ( thumb == null ) { try { thumb = photo.getThumbn...

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public CoreUserSettings read(ArchitectSession session) throws IOException { logger.debug("reading UserSettings from java.util.prefs."); if ( prefs == null ) { prefs = ArchitectFrame.getMainInstance().getPrefs(); } logger.debug("Preferences class = " + prefs.getClass()); CoreUserSettings use...

public CoreUserSettings read(ArchitectSession session) throws IOException { logger.debug("loading UserSettings from java.util.prefs."); if ( prefs == null ) { prefs = ArchitectFrame.getMainInstance().getPrefs(); } logger.debug("Preferences class = " + prefs.getClass()); CoreUserSettings use...

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public CoreUserSettings read(ArchitectSession session) throws IOException { logger.debug("reading UserSettings from java.util.prefs."); if ( prefs == null ) { prefs = ArchitectFrame.getMainInstance().getPrefs(); } logger.debug("Preferences class = " + prefs.getClass()); CoreUserSettings use...

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private List<DashboardConfig> getDashboardConfigList(List dashboards){ final List<DashboardConfig> dashboardConfigList = new LinkedList<DashboardConfig>(); for(Iterator it = dashboards.iterator(); it.hasNext();){ Element dashboard = (Element)it.next(); DashboardConfig dashboardCo...

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public void removeAllFromFolder( PhotoFolder f ) { addedToFolders.remove( f ); removedFromFolders.add( f ); // Remove the folder from the tree DefaultMutableTreeNode treeNode = (DefaultMutableTreeNode) folderNodes.get( f ); DefaultMutableTreeNode parentNode = (DefaultMutableTreeNode) treeNode.getParent(); ...

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public TablePane(SQLTable m) { setOpaque(true); setModel(m); setMinimumSize(new Dimension(100,200)); setPreferredSize(new Dimension(100,200)); dt = new DropTarget(this, new TablePaneDropListener()); dgl = new TablePaneDragGestureListener(); ds = new DragSource(); dgr = getToolkit().createDragGestureRecognizer(...

public TablePane() { setOpaque(true); setModel(m); setMinimumSize(new Dimension(100,200)); setPreferredSize(new Dimension(100,200)); dt = new DropTarget(this, new TablePaneDropListener()); dgl = new TablePaneDragGestureListener(); ds = new DragSource(); dgr = getToolkit().createDragGestureRecognizer(MouseDragG...

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public TablePane(SQLTable m) { setOpaque(true); setModel(m); setMinimumSize(new Dimension(100,200)); setPreferredSize(new Dimension(100,200)); dt = new DropTarget(this, new TablePaneDropListener()); dgl = new TablePaneDragGestureListener(); ds = new DragSource(); dgr = getToolkit().createDragGestureRecognizer(...

public TablePane(SQLTable m) { setOpaque(true); setMinimumSize(new Dimension(100,200)); setPreferredSize(new Dimension(100,200)); dt = new DropTarget(this, new TablePaneDropListener()); dgl = new TablePaneDragGestureListener(); ds = new DragSource(); dgr = getToolkit().createDragGestureRecognizer(MouseDragGes...

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public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) throws Exception { ...

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public Vector check() throws PedFileException{ //before we perform the check we want to prune out individuals with too much missing data //or trios which contain individuals with too much missing data Vector indList = getOrder(); Individual currentInd; Family currentFamily; ...

public Vector check() throws PedFileException{ //before we perform the check we want to prune out individuals with too much missing data //or trios which contain individuals with too much missing data Vector indList = (Vector)order.clone(); Individual currentInd; Family currentFam...

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public Vector check() throws PedFileException{ //before we perform the check we want to prune out individuals with too much missing data //or trios which contain individuals with too much missing data Vector indList = getOrder(); Individual currentInd; Family currentFamily; ...

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ExportThread( ExportSelectedAction owner, Collection selection, String fnameFormat, int width, int height ) { this.selection = selection; this.format = fnameFormat; this.exportWidth = width; this.exportHeight = height; this.owner = owner; ...

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public void run() { Iterator iter = selection.iterator(); int n = 1; while ( iter.hasNext() ) { String fname = String.format( format, new Integer( n ) ); int percent = (n-1) * 100 / selection.size(); owner.exportingPhoto( this, fname,...

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public void run() { Iterator iter = selection.iterator(); int n = 1; while ( iter.hasNext() ) { String fname = String.format( format, new Integer( n ) ); int percent = (n-1) * 100 / selection.size(); owner.exportingPhoto( this, fname,...

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public void run() { Iterator iter = selection.iterator(); int n = 1; while ( iter.hasNext() ) { String fname = String.format( format, new Integer( n ) ); int percent = (n-1) * 100 / selection.size(); owner.exportingPhoto( this, fname,...

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public void actionPerformed( ActionEvent ev ) { File exportFile = null; if ( view.getSelectedCount() > 1 ) { exportFile = new File( "image_$n.jpg" ); } else { exportFile = new File( "image.jpg" ); } ExportDlg dlg = new ExportDlg( null, true ); dlg.setF...

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public void actionPerformed( ActionEvent ev ) { File exportFile = null; if ( view.getSelectedCount() > 1 ) { exportFile = new File( "image_$n.jpg" ); } else { exportFile = new File( "image.jpg" ); } ExportDlg dlg = new ExportDlg( null, true ); dlg.setF...

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public void doTag(XMLOutput output) throws Exception { Object xpathContext = getXPathContext(); if (select == null) { throw new MissingAttributeException("select"); } SAXWriter saxWriter = new SAXWriter(output, output); Object node = select.selectSingleNode(xpathContext); if (node instanceof Element) { Eleme...

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public void doTag(XMLOutput output) throws Exception { Object xpathContext = getXPathContext(); if (select == null) { throw new MissingAttributeException("select"); } SAXWriter saxWriter = new SAXWriter(output, output); Object node = select.selectSingleNode(xpathContext); if (node instanceof Element) { Eleme...

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public void doTag(XMLOutput output) throws Exception { Object xpathContext = getXPathContext(); if (select == null) { throw new MissingAttributeException("select"); } SAXWriter saxWriter = new SAXWriter(output, output); Object node = select.selectSingleNode(xpathContext); if (node instanceof Element) { Eleme...

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public static void main(String[] args) throws Exception { try { if (args.length <= 0) { System.out.println("Usage: Jelly scriptFile [outputFile]"); return; } Jelly jelly = new Jelly(); jelly.setScript(args[0]); ...

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public static void main(String[] args) throws Exception { try { if (args.length <= 0) { System.out.println("Usage: Jelly scriptFile [outputFile]"); return; } Jelly jelly = new Jelly(); jelly.setScript(args[0]); ...

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public void doTag(XMLOutput output) throws Exception { String localName = null; int idx = name.indexOf(':'); if (idx >= 0) { localName = name.substring(idx + 1); } else { localName = name; } output.startElement(namespace, localName, name, attrib...

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public void setAttributeValue( String name, String value ) { // ### we'll assume that all attributes are in no namespace! // ### this is severely limiting! // ### we should be namespace aware int index = attributes.getIndex("", name); if (index >= 0) { attributes.remove...

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public void actionPerformed(ActionEvent evt) { logger.debug("delete action detected!"); logger.debug("ACTION COMMAND: " + evt.getActionCommand()); if (evt.getActionCommand().equals(ArchitectSwingConstants.ACTION_COMMAND_SRC_PLAYPEN)) { logger.debug("delete action came from playpen"); List items = pp.getSelected...

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protected void createThumbnail( Volume volume ) { log.debug( "Creating thumbnail for " + uid ); 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++ ) { ImageI...

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public void testOriginalHash() { String fname = "test1.jpg"; File f = new File( testImgDir, fname ); PhotoInfo photo = null; try { photo = PhotoInfo.addToDB( f ); } catch ( PhotoNotFoundException e ) { fail( "Could not find photo: " + e.getMessage() ); } byte hash[] = photo.getOrigInstanceHas...

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public void testOriginalHash() { String fname = "test1.jpg"; File f = new File( testImgDir, fname ); PhotoInfo photo = null; try { photo = PhotoInfo.addToDB( f ); } catch ( PhotoNotFoundException e ) { fail( "Could not find photo: " + e.getMessage() ); } byte hash[] = photo.getOrigInstanceHas...

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public ServerConnection getServerConnection(ApplicationConfig config) throws ConnectionFailedException { /* Initialize the AdminClient */ Properties adminProps = new Properties(); adminProps.setProperty(AdminClient.CONNECTOR_TYPE, AdminClient.CONNECTOR_TYPE_SOAP); ...

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protected void ensureInMapping(SQLColumn pkcol) throws ArchitectException { if (!containsPkColumn(pkcol)) { SQLColumn fkcol = fkTable.getColumnByName(pkcol.getName()); if (fkcol == null) { fkcol = SQLColumn.getDerivedInstance(pkcol, fkTable); fkTable.addColumn(fkcol); if (identifying) { fkcol...

protected void ensureInMapping(SQLColumn pkcol) throws ArchitectException { if (!containsPkColumn(pkcol)) { SQLColumn fkcol = fkTable.getColumnByName(pkcol.getName()); if (fkcol == null) { fkcol = (SQLColumn) pkcol.clone(); fkTable.addColumn(fkcol); if (identifying) { fkcol.setPrimaryKeySeq(n...

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public void setIdentifying(boolean argIdentifying) { this.identifying = argIdentifying; fireDbObjectChanged("identifying"); }

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private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0, haploid = 0; Hashtable founderGenoCount = new Hashtable(); ...

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private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0, haploid = 0; Hashtable founderGenoCount = new Hashtable(); ...

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public void doTag(final XMLOutput output) throws Exception { if ( var == null ) { throw new MissingAttributeException("var"); } if ( factory == null ) { factory = new com.sun.msv.verifier.jarv.TheFactoryImpl(); } InputStream in = null; if ( uri != ...

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public HaploView(){ fc = new JFileChooser(System.getProperty("user.dir")); //menu setup JMenuBar menuBar = new JMenuBar(); setJMenuBar(menuBar); JMenuItem menuItem; //file menu JMenu fileMenu = new JMenu("File"); menuBar.add(fileMenu); menuItem = new JM...

public HaploView(){ try{ fc = new JFileChooser(System.getProperty("user.dir")); }catch(NullPointerException n){ try{ UIManager.setLookAndFeel(UIManager.getCrossPlatformLookAndFeelClassName()); fc = new JFileChooser(System.getProperty("user.dir")); UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassN...

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public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == READ_GENOTYPES){ ReadDataDialog readDialog = new ReadDataDialog("Open new data", this); readDialog.pack(); readDialog.setVisible(true); } else if (command == READ_...

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private static ResourceBundle findMatch(String basename, Locale pref) { ResourceBundle match = null; try { ResourceBundle bundle = ResourceBundle.getBundle(basename, pref, Thread.currentThread().getContextClassLoader()); Locale avail = bundle.getLocale(); if (pref.equals(avail)) { // Exact match ma...

private static ResourceBundle findMatch(String basename, Locale pref, ClassLoader cl) { ResourceBundle match = null; try { ResourceBundle bundle = ResourceBundle.getBundle(basename, pref, Thread.currentThread().getContextClassLoader()); Locale avail = bundle.getLocale(); if (pref.equals(avail)) { // E...

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private static ResourceBundle findMatch(String basename, Locale pref) { ResourceBundle match = null; try { ResourceBundle bundle = ResourceBundle.getBundle(basename, pref, Thread.currentThread().getContextClassLoader()); Locale avail = bundle.getLocale(); if (pref.equals(avail)) { // Exact match ma...

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public String getDescription() { if(description == null) return "No description available."; return description; }

public String getDescription() { if(description == null || description.trim().length() == 0) return "No description available."; return description; }

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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...

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public Object construct(){ for (int i = 0; i < viewMenuItems.length; i++){ viewMenuItems[i].setEnabled(false); } dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); ...

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public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ...

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public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ...

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public MarkerAssociationResult(Haplotype[] locusHaplos, String n, SNP snp) { nf.setGroupingUsed(false); for (int i = 0; i < locusHaplos.length; i++){ alleles.add(locusHaplos[i]); } setFrequencyCutoff(0); name = n; this.snp = snp; }

public MarkerAssociationResult(Haplotype[] locusHaplos, String n, SNP snp) { nf.setGroupingUsed(false); for (int i = 0; i < locusHaplos.length; i++){ alleles.add(locusHaplos[i]); } filterByFrequency(0); name = n; this.snp = snp; }

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protected void createThumbnail( VolumeBase volume ) { log.debug( "Creating thumbnail for " + uid ); ODMGXAWrapper txw = new ODMGXAWrapper(); txw.lock( this, Transaction.WRITE ); // Maximum size of the thumbnail int maxThumbWidth = 100; int maxThumbHeight = 1...

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protected void createThumbnail( VolumeBase volume ) { log.debug( "Creating thumbnail for " + uid ); ODMGXAWrapper txw = new ODMGXAWrapper(); txw.lock( this, Transaction.WRITE ); // Maximum size of the thumbnail int maxThumbWidth = 100; int maxThumbHeight = 1...

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void generateDPrimeTable(long maxdist){ //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset dPrimeTable = new PairwiseLinkage[Chromosome.getSize()][Chromosome.getSize()]; int doublehet; long negMaxdist = -1*maxdist; int[][] twoMark...

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void guessBlocks(int method){ Vector returnVec = new Vector(); switch(method){ case 0: returnVec = FindBlocks.doSFS(filteredDPrimeTable); break; case 1: returnVec = FindBlocks.do4Gamete(filteredDPrimeTable,0.01); break; case 2: returnVec = FindBlocks.doMJD(filteredDPri...

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void prepareMarkerInput(File infile, long maxdist) 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 is //...

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public void saveDprimeToText(PairwiseLinkage[][] dPrimeTable, File dumpDprimeFile, boolean info) throws IOException{ FileWriter saveDprimeWriter = new FileWriter(dumpDprimeFile); if (info){ saveDprimeWriter.write("L1\tL2\tD'\tLOD\tr^2\tCIlow\tCIhi\tDist\n"); long dist; ...

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private void realizeMapping() throws ArchitectException { for (ColumnMapping m : getMappings()) { SQLColumn fkCol = m.getFkColumn(); try { fkCol.setMagicEnabled(false); if (fkCol.getReferenceCount() == 0) fkCol.addReference(); // This might bump up the reference count (which would be correct) fkTable....

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public void setUp() { context = new Context(); context.setVariable( "foo", "abc" ); context.setVariable( "bar", new Integer( 123 ) ); factory = new BeanShellExpressionFactory(); }

public void setUp() { context = new JellyContext(); context.setVariable( "foo", "abc" ); context.setVariable( "bar", new Integer( 123 ) ); factory = new BeanShellExpressionFactory(); }

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public void doTag(XMLOutput output) throws Exception { if (select != null) { Iterator iter = select.selectNodes( getXPathContext() ).iterator(); while (iter.hasNext()) { iterationValue = iter.next(); if (var != null) { context.setVariable...

public void doTag(XMLOutput output) throws Exception { if (select != null) { List nodes = select.selectNodes( getXPathContext() ); if (xpCmp != null && (xpCmp.getXpath() != null)) { Collections.sort(nodes, xpCmp); } Iterator iter = nodes.iterator(); while (iter.hasNext()) { ...

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void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //type is either 3 or 4 for ped and hapmap files respectively final File inFile = new File(inputOptions[0]); try ...

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public Object construct(){ dPrimeDisplay=null; changeKey(1); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ...

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public TagScript createTagScript(String name, Attributes attributes) throws Exception { Class type = (Class) tags.get(name); if ( type != null ) { return TagScript.newInstance(type); } return null; }

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private void addHeaderRow(ProfileManager pm, SQLTable sqlTable, PdfPTable table, BaseFont bf, float titleFSize, float colHeadingFSize, float[] widths) throws DocumentException, IOException, ArchitectException { int ncols =...

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private void addHeaderRow(ProfileManager pm, SQLTable sqlTable, PdfPTable table, BaseFont bf, float titleFSize, float colHeadingFSize, float[] widths) throws DocumentException, IOException, ArchitectException { int ncols =...

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public void createPdf(OutputStream out, java.util.List<SQLTable> tables, ProfileManager pm) throws DocumentException, IOException, SQLException, ArchitectException, InstantiationException, IllegalAccessException { ...

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public void createPdf(OutputStream out, java.util.List<SQLTable> tables, ProfileManager pm) throws DocumentException, IOException, SQLException, ArchitectException, InstantiationException, IllegalAccessException { ...

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public void createPdf(OutputStream out, java.util.List<SQLTable> tables, ProfileManager pm) throws DocumentException, IOException, SQLException, ArchitectException, InstantiationException, IllegalAccessException { ...

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private void processFile(String fileName, int fileType, String infoFileName){ try { //int outputType; HaploData textData; File OutputFile; File inputFile; if(!HaploText.quietMode && fileName != null){ System.out.println("Using data file " ...

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public static Vector calcTrioTDT(PedFile pf) throws PedFileException{ Vector results = new Vector(); int numMarkers = Chromosome.getUnfilteredSize(); for (int i = 0; i < numMarkers; i++){ TDTResult thisResult = new TDTResult(Chromosome.getUnfilteredMarker(i)); Vector indLi...

public static Vector calcTrioTDT(PedFile pf){ Vector results = new Vector(); int numMarkers = Chromosome.getUnfilteredSize(); for (int i = 0; i < numMarkers; i++){ TDTResult thisResult = new TDTResult(Chromosome.getUnfilteredMarker(i)); Vector indList = pf.getOrder(); ...

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public static Vector calcTrioTDT(PedFile pf) throws PedFileException{ Vector results = new Vector(); int numMarkers = Chromosome.getUnfilteredSize(); for (int i = 0; i < numMarkers; i++){ TDTResult thisResult = new TDTResult(Chromosome.getUnfilteredMarker(i)); Vector indLi...

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void run() { PhotovaultSettings settings = PhotovaultSettings.getSettings(); Collection databases = settings.getDatabases(); if ( databases.size() == 0 ) { // No known database exists, so create new Object options[] = { "Create", "Exit" }; int retval = JOptionPa...

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private void processFile(String fileName,boolean fileType,String infoFileName){ try { int outputType; long maxDistance; HaploData textData; File OutputFile; File inputFile; inputFile = new File(fileName); if(!inputFile.exists()){ ...

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public void modifyColumn(SQLColumn c) throws ArchitectDiffException { Map colNameMap = new HashMap(); SQLTable t = c.getParentTable(); print("\n ALTER TABLE "); printQualified(t.getPhysicalName()); print(" MODIFY "); print(columnDefinition(c,colNameMap)); endStatement(DDLStatement.StatementType.MODIFY, c); ...

public void modifyColumn(SQLColumn c) throws ArchitectDiffException { Map colNameMap = new HashMap(); SQLTable t = c.getParentTable(); print("\n ALTER TABLE "); print( DDLUtils.toQualifiedName(t.getCatalogName(),t.getSchemaName(),t.getPhysicalName()) ); print(" MODIFY "); print(columnDefinition(c,colNameMap)...

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void renameSelectedFolder() { if ( selected != null ) { String origName = selected.getName(); String newName = (String) JOptionPane.showInputDialog( this, "Enter new name", "Rename folder", JOptionPane.PLAIN_MESSAGE, null, null, origName ); if ( newName != null ) { PhotoFolder f = s...

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public Script compile() throws Exception { if (tag instanceof CompilableTag) { ((CompilableTag) tag).compile(); } List typeList = new ArrayList(); List methodList = new ArrayList(); List expressionList = new ArrayList(); BeanInfo info = Introspector.getBeanInfo(t...

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public void run(JellyContext context, XMLOutput output) throws Exception { tag.setContext(context); // initialize all the properties of the tag before its used // if there is a problem abort this tag for (int i = 0, size = expressions.length; i < size; i++) { Expressio...

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public void run(JellyContext context, XMLOutput output) throws Exception { tag.setContext(context); // initialize all the properties of the tag before its used // if there is a problem abort this tag for (int i = 0, size = expressions.length; i < size; i++) { Expressio...

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private JFrame createMenuTest(int max) throws HeadlessException { JFrame jf = new JFrame(); final JMenuBar jb = new JMenuBar(); jf.setJMenuBar(jb); fileMenu = new JMenu("File"); for (int i = 0; i <= max; i++) { fileMenu.add(new JMenuItem(Integer.toString(i))); } jf.setSize(400, 600); jb.add(fileMenu); ASUti...

private JFrame createMenuTest(int max) throws HeadlessException { final JFrame jf = new JFrame(); jf.setSize(400, 600); final JMenuBar jb = new JMenuBar(); jf.setJMenuBar(jb); fileMenu = new JMenu("File"); for (int i = 0; i <= max; i++) { fileMenu.add(new JMenuItem(Integer.toString(i))); } jf.setSize(400, 600...

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private JFrame createMenuTest(int max) throws HeadlessException { JFrame jf = new JFrame(); final JMenuBar jb = new JMenuBar(); jf.setJMenuBar(jb); fileMenu = new JMenu("File"); for (int i = 0; i <= max; i++) { fileMenu.add(new JMenuItem(Integer.toString(i))); } jf.setSize(400, 600); jb.add(fileMenu); ASUti...

private JFrame createMenuTest(int max) throws HeadlessException { JFrame jf = new JFrame(); final JMenuBar jb = new JMenuBar(); jf.setJMenuBar(jb); fileMenu = new JMenu("File"); for (int i = 0; i <= max; i++) { if ( i==10 || i == 9 ) { final JMenuItem jmi = new JMenuItem(Integer.toString(i)); fileMenu.add(jmi);...

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private JFrame createMenuTest(int max) throws HeadlessException { JFrame jf = new JFrame(); final JMenuBar jb = new JMenuBar(); jf.setJMenuBar(jb); fileMenu = new JMenu("File"); for (int i = 0; i <= max; i++) { fileMenu.add(new JMenuItem(Integer.toString(i))); } jf.setSize(400, 600); jb.add(fileMenu); ASUti...

private JFrame createMenuTest(int max) throws HeadlessException { JFrame jf = new JFrame(); final JMenuBar jb = new JMenuBar(); jf.setJMenuBar(jb); fileMenu = new JMenu("File"); for (int i = 0; i <= max; i++) { fileMenu.add(new JMenuItem(Integer.toString(i))); } jb.add(fileMenu); ASUtils.breakLongMenu(jf, ...

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public static void main(String[] args) { for (int i = 69; i <= 71; i++) new TestASUtilsMenu().createMenuTest(i); }

public static void main(String[] args) { for (int i = 48; i <= 51; i++) new TestASUtilsMenu().createMenuTest(i); }

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private void makeDialog(SQLTable table) { final TableEditPanel editPanel = new TableEditPanel(table); Action okAction = new AbstractAction() { public void actionPerformed(ActionEvent evt) { editPanel.applyChanges(); // XXX: also apply changes on mapping tab d.setVisible(false); } }; Action cancelActio...

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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 Task in...

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public void tallyInd(byte alleleT, byte alleleU) { if(alleleT == 5 && alleleU == 5) { if(tallyHet){ counts[0][0]++; counts[1][1]++; this.tallyHet = false; } else { counts[0][1]++; counts[1][0]++; ...

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private void saveProfiles(PrintWriter out) { println(out, "<profiles>"); indent++; ProfileManager profmgr = getProfileManager(); Map<SQLObject, ProfileResult> results = profmgr.getResults(); for (Map.Entry<SQLObject, ProfileResult> e : results.entrySet()) { SQLObject so...

private void saveProfiles(PrintWriter out) { ProfileManager profmgr = getProfileManager(); println(out, "<profiles topNCount=\""+profmgr.getTopNCount()+"\">"); indent++; ProfileManager profmgr = getProfileManager(); Map<SQLObject, ProfileResult> results = profmgr.getResults(); for...

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private void saveProfiles(PrintWriter out) { println(out, "<profiles>"); indent++; ProfileManager profmgr = getProfileManager(); Map<SQLObject, ProfileResult> results = profmgr.getResults(); for (Map.Entry<SQLObject, ProfileResult> e : results.entrySet()) { SQLObject so...

private void saveProfiles(PrintWriter out) { println(out, "<profiles>"); indent++; Map<SQLObject, ProfileResult> results = profmgr.getResults(); for (Map.Entry<SQLObject, ProfileResult> e : results.entrySet()) { SQLObject so = e.getKey(); ProfileResult profi...

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public void testIndexing() { int n; ExternalVolume v = new ExternalVolume( "extVol", extVolDir.getAbsolutePath() ); PhotovaultSettings settings = PhotovaultSettings.getSettings(); PVDatabase db = settings.getDatabase( "pv_junit" ); db.addVolume( v ); ExtVolIndexer indexer =...

public void testIndexing() { int n; ExternalVolume v = new ExternalVolume( "extVol", extVolDir.getAbsolutePath() ); PhotovaultSettings settings = PhotovaultSettings.getSettings(); PVDatabase db = settings.getDatabase( "pv_junit" ); try { db.addVolume( v ); } catch (PhotovaultExcep...

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public Expression createExpression(String text) throws Exception { return new JexlExpression( org.apache.commons.jexl.ExpressionFactory.createExpression( text ) ); }

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public void testAllSettersGenerateEvents() throws IllegalArgumentException, IllegalAccessException, InvocationTargetException, NoSuchMethodException { SQLObject so = getSQLObjectUnderTest(); Set<String>propertiesToIgnore = new HashSet<String>(); propertiesToIgnore.add("populated"); propertiesToIgnore.add("S...

public void testAllSettersGenerateEvents() throws IllegalArgumentException, IllegalAccessException, InvocationTargetException, NoSuchMethodException, ArchitectException { SQLObject so = getSQLObjectUnderTest(); Set<String>propertiesToIgnore = new HashSet<String>(); propertiesToIgnore.add("populated"); prope...

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public void doTag(XMLOutput output) throws Exception { if (uri == null) { throw new MissingAttributeException( "uri" ); } // we need to create a new JellyContext of the URI // take off the script name from the URL context.runScript(uri, output, getExport(), getInherit()...

public void doTag(XMLOutput output) throws Exception { if (uri == null) { throw new MissingAttributeException( "uri" ); } // we need to create a new JellyContext of the URI // take off the script name from the URL context.runScript(uri, output, isExport(), isInherit() )...

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public void run() { try { while(testSet.getPermutationCount() - testSet.getPermutationsPerformed() != 0) { permProgressBar.setValue(testSet.getPermutationsPerformed()); scoreBoardNumTotalLabel.setText(String.valueOf(testSet.getPermutationsPerformed...

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public void finishedPerms() { scoreBoardNumTotalLabel.setText(String.valueOf(testSet.getPermutationsPerformed())); scoreBoardNumPassLabel.setText(String.valueOf(testSet.getBestExceededCount())); doPermutationsButton.setEnabled(true); stopPermutationsButton.setEnabled(false); this....

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public void finishedPerms() { scoreBoardNumTotalLabel.setText(String.valueOf(testSet.getPermutationsPerformed())); scoreBoardNumPassLabel.setText(String.valueOf(testSet.getBestExceededCount())); doPermutationsButton.setEnabled(true); stopPermutationsButton.setEnabled(false); this....

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