JoaoJunior/formatted-java-preprocessed-code-APR

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

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

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

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

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

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

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

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public void setUp() { String volumeRoot = "c:\\temp\\photoVaultVolumeTest"; volume = new Volume( "testVolume", volumeRoot ); extVol = new ExternalVolume( "extVolume", extvolRoot.getAbsolutePath() ); PhotovaultSettings settings = PhotovaultSettings.getSettings(); PVDatabase curDb = settings.getCurrent...

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public PresentationObject getTopicsOverView(IWContext iwc){ Table T = new Table(); int row = 1; T.add(getTopicLink(-1,iwrb.getLocalizedString("new_topic","New topic")),1,row); row++; T.add(tf.format(iwrb.getLocalizedString("name","Name"),tf.HEADER),1,row); T.add(tf.format(iwrb.getLocalizedString("category",...

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private Query<S> applyFilterValues(FilterValues<S> values) { // FIXME: figure out how to transfer values directly to query. Query<S> query = mQuery; Filter<S> filter = query.getFilter(); // FIXME: this code can get confused if filter has constants. if (values != null && filter != ...

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public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command.equals(BROWSE_GENO)){ browse(GENO_FILE); }else if (command.equals(BROWSE_HAPS)){ browse(HAPS_FILE); }else if (command.equals(BROWSE_HMP)){ browse(HMP_FILE); ...

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protected XMLParser getXMLParser() { XMLParser parser = (XMLParser) parserPool.get(); if (parser == null) { parser = createXMLParser(); parserPool.set(parser); } return parser; }

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public void buildPage(String template, JellyContext ctx) { // try {// // Embedded embedded = new Embedded();// embedded.setOutputStream(new FileOutputStream("out.html"));// //embedded.setVariable("some-var","some-object");// // embedded.setScript("file:///anoncvs/jakarta-commons-sandbox/jelly/sample.jell...

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public TDTPanel(Vector chromosomes) { JTable table; TDT theTDT = new TDT(); Vector result = theTDT.calcTDT(chromosomes); Vector tableColumnNames = new Vector(); tableColumnNames.add("Name"); tableColumnNames.add("Chi Squared"); tableColumnNames.add("T/U Ratio"); ...

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public TDTPanel(Vector chromosomes) { JTable table; TDT theTDT = new TDT(); Vector result = theTDT.calcTDT(chromosomes); Vector tableColumnNames = new Vector(); tableColumnNames.add("Name"); tableColumnNames.add("Chi Squared"); tableColumnNames.add("T/U Ratio"); ...

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protected void createFolderPaneUI() { JPanel pane = new JPanel(); tabPane.addTab( "Folders", pane ); folderTreePane = new FolderTreePane( ctrl.getFolderController() ); pane.add( folderTreePane, BorderLayout.NORTH ); }

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public SQLTable(SQLObject parent, String name, String remarks, String objectType, boolean startPopulated) throws ArchitectException { logger.debug("NEW TABLE "+name+"@"+hashCode()); this.parent = parent; setName(name); this.remarks = remarks; this.objectType = objectType; this.children = new ArrayList(); initFo...

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public HaplotypeDisplayController(HaplotypeDisplay parent){ this.parent = parent; setLayout(new BoxLayout(this, BoxLayout.Y_AXIS)); JPanel leftPanel = new JPanel(); leftPanel.setLayout(new BoxLayout(leftPanel, BoxLayout.Y_AXIS)); JPanel rightPanel = new JPanel(); rightPanel...

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public void setDisplayThresh(int amount){ if (parent.displayThresh != amount){ parent.adjustDisplay(amount); } }

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protected int countSourceTables(int count, SQLObject o) throws ArchitectException { if (o instanceof SQLTable) { return count + 1; } else { Iterator it = o.getChildren().iterator(); while (it.hasNext()) { count += countSourceTables(count, (SQLObject) it.next()); } } return count; }

protected int countSourceTables(SQLObject o) throws ArchitectException { if (o instanceof SQLTable) { return count + 1; } else { Iterator it = o.getChildren().iterator(); while (it.hasNext()) { count += countSourceTables(count, (SQLObject) it.next()); } } return count; }

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protected int countSourceTables(int count, SQLObject o) throws ArchitectException { if (o instanceof SQLTable) { return count + 1; } else { Iterator it = o.getChildren().iterator(); while (it.hasNext()) { count += countSourceTables(count, (SQLObject) it.next()); } } return count; }

protected int countSourceTables(int count, SQLObject o) throws ArchitectException { if (o instanceof SQLTable) { return 1; } else if (o == playPen.getDatabase()) { return 0; } else { Iterator it = o.getChildren().iterator(); while (it.hasNext()) { count += countSourceTables(count, (SQLObject) it.next()); ...

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protected int countSourceTables(int count, SQLObject o) throws ArchitectException { if (o instanceof SQLTable) { return count + 1; } else { Iterator it = o.getChildren().iterator(); while (it.hasNext()) { count += countSourceTables(count, (SQLObject) it.next()); } } return count; }

protected int countSourceTables(int count, SQLObject o) throws ArchitectException { if (o instanceof SQLTable) { return count + 1; } else { Iterator it = o.getChildren().iterator(); while (it.hasNext()) { myCount += countSourceTables((SQLObject) it.next()); } } return count; }

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protected int countSourceTables(int count, SQLObject o) throws ArchitectException { if (o instanceof SQLTable) { return count + 1; } else { Iterator it = o.getChildren().iterator(); while (it.hasNext()) { count += countSourceTables(count, (SQLObject) it.next()); } } return count; }

protected int countSourceTables(int count, SQLObject o) throws ArchitectException { if (o instanceof SQLTable) { return count + 1; } else { Iterator it = o.getChildren().iterator(); while (it.hasNext()) { count += countSourceTables(count, (SQLObject) it.next()); } } }

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public void save(ProgressMonitor pm) throws IOException, ArchitectException { out = new PrintWriter(new BufferedWriter(new FileWriter(file))); objectIdMap = new HashMap(); dbcsIdMap = new HashMap(); indent = 0; this.pm = pm; pm.setMinimum(0); pm.setMaximum(countSourceTables(0, (SQLObject) sourceDatabases.getMod...

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protected void saveSQLObject(SQLObject o) throws IOException, ArchitectException { String id = (String) objectIdMap.get(o); if (id != null) { println("<reference ref-id=\""+id+"\" />"); return; } String type; Map propNames = new TreeMap(); if (o instanceof SQLDatabase) { id = "DB"+objectIdMap.size(); ...

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

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

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

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public TagScript createCustomTagScript(final String name, Attributes attributes) throws Exception { // custom Ant tags if ( name.equals("fileScanner") ) { return new BeanTagScript( new TagFactory() { public Tag createTag() throws Exception { ...

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public Tag createTag() throws Exception { return new FileScannerTag(new FileScanner(getProject())); }

public Tag createTag() throws Exception { return new FileScannerTag(new FileScanner()); }

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public static Project createProject() { Project project = new Project(); BuildLogger logger = new NoBannerLogger(); logger.setMessageOutputLevel( org.apache.tools.ant.Project.MSG_INFO ); logger.setOutputPrintStream( System.out ); logger.setErrorPrintStream( System.err); pro...

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public Tag createTag(String name) throws Exception { AntTag tag = new AntTag( getProject(), name ); if ( name.equals( "echo" ) ) { tag.setTrim(false); } return tag; }

public Tag createTag(String name) throws Exception { AntTag tag = new AntTag( name ); if ( name.equals( "echo" ) ) { tag.setTrim(false); } return tag; }

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public static Project getProject(JellyContext context) { Project project = (Project) context.findVariable( "org.apache.commons.jelly.ant.Project" ); if ( project == null ) { project = createProject(); context.setVariable( "org.apache.commons.jelly.ant.Project", project ); ...

public static Project getProject(JellyContext context) { Project project = (Project) context.findVariable( PROJECT_CONTEXT_HANDLE ); if ( project == null ) { project = createProject(); context.setVariable( "org.apache.commons.jelly.ant.Project", project ); } return ...

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public static Project getProject(JellyContext context) { Project project = (Project) context.findVariable( "org.apache.commons.jelly.ant.Project" ); if ( project == null ) { project = createProject(); context.setVariable( "org.apache.commons.jelly.ant.Project", project ); ...

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public void dbChildrenRemoved(SQLObjectEvent e) { logger.debug("SQLObject children got removed: "+e); boolean fireEvent = false; SQLObject o = e.getSQLSource(); SQLObject[] c = e.getChildren(); for (int i = 0; i < c.length; i++) { try { ArchitectUtils.unlistenToHierarchy(this, c[i]); } catch (ArchitectExce...

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public void dbChildrenRemoved(SQLObjectEvent e) { logger.debug("SQLObject children got removed: "+e); boolean fireEvent = false; SQLObject o = e.getSQLSource(); SQLObject[] c = e.getChildren(); for (int i = 0; i < c.length; i++) { try { ArchitectUtils.unlistenToHierarchy(this, c[i]); } catch (ArchitectExce...

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public void itemSelected(SelectionEvent e) { selectedChild = e.getSelectedItem(); fireSelectionEvent(e.getSelectedItem()); }

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void setupTablePanePopup() { ArchitectFrame af = ArchitectFrame.getMainInstance(); tablePanePopup = new JPopupMenu(); JMenuItem mi; mi = new JMenuItem(); mi.setAction(af.editColumnAction); tablePanePopup.add(mi); mi = new JMenuItem(); mi.setAction(af.insertColumnAction); tablePanePopup.add(mi); mi = new JMen...

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public void mouseClicked(MouseEvent e) { JTableHeader h = (JTableHeader) e.getSource(); TableColumnModel columnModel = h.getColumnModel(); int viewColumn = columnModel.getColumnIndexAtX(e.getX()); //XXX: Should change to a better condition for size editting ...

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public TableModelColumnAutofit(TableModel tableModel, ProfileTable table){ this.tableModel = tableModel; this.table = table; mouseListener = new MouseListener(); }

public TableModelColumnAutofit(TableModel tableModel, JTable table){ this.tableModel = tableModel; this.table = table; mouseListener = new MouseListener(); }

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protected void fireTreeNodesChanged(TreeModelEvent e) { final TreeModelEvent ev =e; Runnable notifier = new Runnable(){ public void run() { Iterator it = treeModelListeners.iterator(); while (it.hasNext()) { ((TreeModelListener) it.next()).treeNodesChanged(ev); } } }; if (SwingUtilities.isEventDi...

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protected void fireTreeNodesInserted(TreeModelEvent e) { if (logger.isDebugEnabled()) logger.debug("Firing treeNodesInserted event: "+e); final TreeModelEvent ev =e; Runnable notifier = new Runnable(){ public void run() { Iterator it = treeModelListeners.iterator(); while (it.hasNext()) { ((TreeModelLi...

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protected void fireTreeNodesInserted(TreeModelEvent e) { if (logger.isDebugEnabled()) logger.debug("Firing treeNodesInserted event: "+e); final TreeModelEvent ev =e; Runnable notifier = new Runnable(){ public void run() { Iterator it = treeModelListeners.iterator(); while (it.hasNext()) { ((TreeModelLi...

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protected void fireTreeNodesRemoved(TreeModelEvent e) { if (logger.isDebugEnabled()) logger.debug("Firing treeNodesRemoved event "+e); final TreeModelEvent ev =e; Runnable notifier = new Runnable(){ public void run() { Iterator it = treeModelListeners.iterator(); while (it.hasNext()) { ((TreeModelListe...

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protected void fireTreeStructureChanged(TreeModelEvent e) { final TreeModelEvent ev =e; Runnable notifier = new Runnable(){ public void run() { Iterator it = treeModelListeners.iterator(); while (it.hasNext()) { ((TreeModelListener) it.next()).treeStructureChanged(ev); } } }; if (SwingUtilities.i...

protected void fireTreeStructureChanged(TreeModelEvent e) { final TreeModelEvent ev =e; Runnable notifier = new Runnable(){ public void run() { Iterator it = treeModelListeners.iterator(); while (it.hasNext()) { ((TreeModelListener) it.next()).treeStructureChanged(ev); } } }; notifier.run(); ...

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protected void fireTreeStructureChanged(TreeModelEvent e) { final TreeModelEvent ev =e; Runnable notifier = new Runnable(){ public void run() { Iterator it = treeModelListeners.iterator(); while (it.hasNext()) { ((TreeModelListener) it.next()).treeStructureChanged(ev); } } }; if (SwingUtilities.i...

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public static Vector calcTDT(Vector chromosomes) { Vector results = new Vector(); int numMarkers = Chromosome.getSize(); for(int k=0;k<numMarkers;k++){ results.add(new TDTResult(Chromosome.getMarker(k))); } for(int i=0;i<chromosomes.size()-3;i++){ Chromosome ...

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public void mouseMoved(MouseEvent e) { if (movingPk) { r.setPkConnectionPoint(translatePoint(e.getPoint())); } else { r.setFkConnectionPoint(translatePoint(e.getPoint())); } }

public void mouseMoved(MouseEvent e) { if (movingPk) { r.setPkConnectionPoint(translatePoint(p)); } else { r.setFkConnectionPoint(translatePoint(e.getPoint())); } }

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public void mouseMoved(MouseEvent e) { if (movingPk) { r.setPkConnectionPoint(translatePoint(e.getPoint())); } else { r.setFkConnectionPoint(translatePoint(e.getPoint())); } }

public void mouseMoved(MouseEvent e) { if (movingPk) { r.setPkConnectionPoint(translatePoint(e.getPoint())); } else { r.setFkConnectionPoint(translatePoint(p)); } }

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protected void setup() { pkConnectionPoint = new Point(); fkConnectionPoint = new Point(); updateUI(); setOpaque(true); setBackground(Color.green); model.addSQLObjectListener(this); setToolTipText(model.getName()); ui.bestConnectionPoints(pkTable, fkTable, pkConnectionPoint, // in pktable-space ...

protected void setup() { pkConnectionPoint = new Point(); fkConnectionPoint = new Point(); updateUI(); setOpaque(false); setBackground(Color.green); model.addSQLObjectListener(this); setToolTipText(model.getName()); ui.bestConnectionPoints(pkTable, fkTable, pkConnectionPoint, // in pktable-space ...

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Haplotype[][] generateHaplotypes(Vector blocks, int hapthresh) throws HaploViewException{ //TODO: output indiv hap estimates Haplotype[][] results = new Haplotype[blocks.size()][]; //String raw = new String(); //String currentLine; this.totalBlocks = blocks.size(); this.blo...

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Haplotype[][] generateHaplotypes(Vector blocks, int hapthresh) throws HaploViewException{ //TODO: output indiv hap estimates Haplotype[][] results = new Haplotype[blocks.size()][]; //String raw = new String(); //String currentLine; this.totalBlocks = blocks.size(); this.blo...

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public Object createObject(Attributes attributes) { SQLTable tab = new SQLTable(); String id = attributes.getValue("id"); if (id != null) { objectIdMap.put(id, tab); } else { logger.warn("No ID found in table element while loading project...

public Object createObject(Attributes attributes) throws ArchitectException{ SQLTable tab = new SQLTable(); String id = attributes.getValue("id"); if (id != null) { objectIdMap.put(id, tab); } else { logger.warn("No ID found in table elem...

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public Tag createTag() throws Exception { return (Tag) tagClass.newInstance(); }

public Tag createTag(String name, Attributes attributes) throws Exception { return (Tag) tagClass.newInstance(); }

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public void doTag(XMLOutput output) throws Exception { Object xpathContext = getXPathContext(); if (select == null) { select = createXPathFromBody(xpathContext); } String text = select.valueOf(xpathContext); if ( text != null ) { output.write(...

public void doTag(XMLOutput output) throws Exception { Object xpathContext = getXPathContext(); if (select == null) { throw new MissingAttributeException( "select" ); } String text = select.valueOf(xpathContext); if ( text != null ) { output.w...

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public void doTag(XMLOutput output) throws Exception { Object xpathContext = getXPathContext(); if (select == null) { select = createXPathFromBody(xpathContext); } String text = select.valueOf(xpathContext); if ( text != null ) { output.write(...

public void doTag(XMLOutput output) throws Exception { Object xpathContext = getXPathContext(); if (select == null) { select = createXPathFromBody(xpathContext); } String text = select.stringValueOf(xpathContext); if ( text != null ) { output....

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public void doTag(final XMLOutput output) throws Exception { if ( xmlOutput == null ) { // lets default to system.out xmlOutput = XMLOutput.createXMLOutput( System.out ); } Thread thread = new Thread( new Runnable() { public void run() { ...

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public void run() { try { invokeBody(xmlOutput); xmlOutput.close(); } catch (Exception e) { e.printStackTrace(); } }

public void run() { try { getBody().run(newContext, xmlOutput); xmlOutput.close(); } catch (Exception e) { e.printStackTrace(); } }

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public void actionPerformed(ActionEvent e) { if (configFile == null) configFile = ConfigFile.getDefaultInstance(); try { sprefs.setInt(SwingUserSettings.DIVIDER_LOCATION, splitPane.getDividerLocation()); sprefs.setInt(SwingUserSettings.MAIN_FRAME_X, getLocation().x); sprefs.setInt(SwingUserSettings...

public void actionPerformed(ActionEvent e) { try { sprefs.setInt(SwingUserSettings.DIVIDER_LOCATION, splitPane.getDividerLocation()); sprefs.setInt(SwingUserSettings.MAIN_FRAME_X, getLocation().x); sprefs.setInt(SwingUserSettings.MAIN_FRAME_Y, getLocation().y); sprefs.setInt(SwingUserSettings....

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public void actionPerformed(ActionEvent e) { if (configFile == null) configFile = ConfigFile.getDefaultInstance(); try { sprefs.setInt(SwingUserSettings.DIVIDER_LOCATION, splitPane.getDividerLocation()); sprefs.setInt(SwingUserSettings.MAIN_FRAME_X, getLocation().x); sprefs.setInt(SwingUserSettings...

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public ArchitectFrame() throws ArchitectException { mainInstance = this; try { ConfigFile cf = ConfigFile.getDefaultInstance(); prefs = cf.read(); sprefs = prefs.getSwingSettings(); } catch (IOException e) { throw new ArchitectException("prefs.read", e); } project = new SwingUIProject("New Project"); set...

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public ArchitectFrame() throws ArchitectException { mainInstance = this; try { ConfigFile cf = ConfigFile.getDefaultInstance(); prefs = cf.read(); sprefs = prefs.getSwingSettings(); } catch (IOException e) { throw new ArchitectException("prefs.read", e); } project = new SwingUIProject("New Project"); set...

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public ArchitectFrame() throws ArchitectException { mainInstance = this; try { ConfigFile cf = ConfigFile.getDefaultInstance(); prefs = cf.read(); sprefs = prefs.getSwingSettings(); } catch (IOException e) { throw new ArchitectException("prefs.read", e); } project = new SwingUIProject("New Project"); set...

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void browse(int browseType){ String name; String markerInfoName = ""; JFileChooser fc = new JFileChooser(System.getProperty("user.dir")); fc.setSelectedFile(null); int returned = fc.showOpenDialog(this); if (returned != JFileChooser.APPROVE_OPTION) return; File file ...

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void browse(int browseType){ String name; String markerInfoName = ""; JFileChooser fc = new JFileChooser(System.getProperty("user.dir")); fc.setSelectedFile(null); int returned = fc.showOpenDialog(this); if (returned != JFileChooser.APPROVE_OPTION) return; File file ...

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public void mouseClicked(MouseEvent evt) { if ((evt.getModifiers() & MouseEvent.BUTTON1_MASK) != 0) { TablePane tp = (TablePane) evt.getSource(); if (evt.getClickCount() == 2) { // double click if (tp.isSelected()) { ArchitectFrame af = ArchitectFrame.getMainInstance(); int selectedColIndex = tp.getSel...

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public CompareSchemaWorker (SQLSchema source, SQLSchema target ) throws ArchitectException { this.source = source; this.target = target; jobSize = source.getChildren().size(); progress = 0; finished = false; }

public CompareSchemaWorker (SQLSchema source, SQLSchema target, GenericDDLGenerator gen ) throws ArchitectException { this.source = source; this.target = target; jobSize = source.getChildren().size(); progress = 0; finished = false; }

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public void run() { // FIXME: this should not be hardwired to oracle! OracleDDLGenerator od = new OracleDDLGenerator(); final DefaultStyledDocument output = new DefaultStyledDocument(); SimpleAttributeSet attrsSource = new SimpleAttributeSet(); SimpleAttributeSet attrsTarget = new SimpleAttri...

public void run() { // FIXME: this should not be hardwired to oracle! final DefaultStyledDocument output = new DefaultStyledDocument(); SimpleAttributeSet attrsSource = new SimpleAttributeSet(); SimpleAttributeSet attrsTarget = new SimpleAttributeSet(); SimpleAttributeSet attrsSame = new S...

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public void run() { if ( sourceInd ) { sourceSchemaDropdown.removeAllItems(); sourceSchemaDropdown.setVisible(true); Iterator it = schema.iterator(); while (it.hasNext()) { sourceSchemaDropdown.addItem((String)it.next()); } // If it has a schema set this enabled ...

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public Integer getJobSize() throws ArchitectException { return progressMonitor.getJobSize(); }

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public int getProgress() throws ArchitectException { return progressMonitor.getProgress(); }

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public boolean isFinished() throws ArchitectException { return progressMonitor.isFinished(); }

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public void actionPerformed(ActionEvent e) { try { startCompareAction.setEnabled(false); SimpleAttributeSet attrsMsg = new SimpleAttributeSet(); StyleConstants.setFontFamily(attrsMsg, "Courier New"); StyleConstants.setFontSize(attrsMsg, 12); StyleConstants.setForeground(attr...

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public void actionPerformed(ActionEvent e) { try { startCompareAction.setEnabled(false); SimpleAttributeSet attrsMsg = new SimpleAttributeSet(); StyleConstants.setFontFamily(attrsMsg, "Courier New"); StyleConstants.setFontSize(attrsMsg, 12); StyleConstants.setForeground(attr...

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private void buildUI() { ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); // layout source database option/combox target combox JRadioButton sourcePlayPenRadio = new JRadioButton(); sourcePlayPenRadio.setName("sourcePlayPenRadio"); sourcePlayPenRadio.setActionComman...

private void buildUI() { ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); // layout source database option/combox target combox sourcePlayPenRadio = new JRadioButton(); sourcePlayPenRadio.setName("sourcePlayPenRadio"); sourcePlayPenRadio.setActionCommand("Project");...

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private void buildUI() { ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); // layout source database option/combox target combox JRadioButton sourcePlayPenRadio = new JRadioButton(); sourcePlayPenRadio.setName("sourcePlayPenRadio"); sourcePlayPenRadio.setActionComman...

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private void buildUI() { ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); // layout source database option/combox target combox JRadioButton sourcePlayPenRadio = new JRadioButton(); sourcePlayPenRadio.setName("sourcePlayPenRadio"); sourcePlayPenRadio.setActionComman...

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private void buildUI() { ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); // layout source database option/combox target combox JRadioButton sourcePlayPenRadio = new JRadioButton(); sourcePlayPenRadio.setName("sourcePlayPenRadio"); sourcePlayPenRadio.setActionComman...

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private void buildUI() { ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); // layout source database option/combox target combox JRadioButton sourcePlayPenRadio = new JRadioButton(); sourcePlayPenRadio.setName("sourcePlayPenRadio"); sourcePlayPenRadio.setActionComman...

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private void buildUI() { ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); // layout source database option/combox target combox JRadioButton sourcePlayPenRadio = new JRadioButton(); sourcePlayPenRadio.setName("sourcePlayPenRadio"); sourcePlayPenRadio.setActionComman...

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private void buildUI() { ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); // layout source database option/combox target combox JRadioButton sourcePlayPenRadio = new JRadioButton(); sourcePlayPenRadio.setName("sourcePlayPenRadio"); sourcePlayPenRadio.setActionComman...

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public void run() { outputTextPane.setDocument(output); }

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public void doTag(XMLOutput output) throws Exception { // evaluate body as it may contain a <destination> tag getBody().run(context, output); Destination destination = getDestination(); if ( destination == null ) { throw new JellyException( "No destination specified. E...

public void doTag(XMLOutput output) throws Exception { // evaluate body as it may contain a <destination> tag invokeBody(output); Destination destination = getDestination(); if ( destination == null ) { throw new JellyException( "No destination specified. Either specif...

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private void paintThumbnail( Graphics2D g2, PhotoInfo photo, int startx, int starty, boolean isSelected ) { log.debug( "paintThumbnail entry " + photo.getUid() ); long startTime = System.currentTimeMillis(); long thumbReadyTime = 0; long thumbDrawnTime = 0; long endTime = 0; ...

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public void removeAllFromFolder( PhotoFolder f ) { addedToFolders.remove( f ); removedFromFolders.add( f ); DefaultMutableTreeNode treeNode = (DefaultMutableTreeNode) folderNodes.get( f ); FolderNode fn = (FolderNode) treeNode.getUserObject(); fn.removeAllPhotos(); // If this folder has n...

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protected URL createRelativeURL(URL rootURL, String relativeURI) throws MalformedURLException { if (rootURL == null) { File file = new File(System.getProperty("user.dir")); rootURL = file.toURL(); } String urlText = rootURL.toString() + relativeURI; if ( log....

protected URL createRelativeURL(URL rootURL, String relativeURI) throws MalformedURLException { URL url = rootURL; if (url == null) { File file = new File(System.getProperty("user.dir")); rootURL = file.toURL(); } String urlText = rootURL.toString() + relativeURI; ...

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protected URL createRelativeURL(URL rootURL, String relativeURI) throws MalformedURLException { if (rootURL == null) { File file = new File(System.getProperty("user.dir")); rootURL = file.toURL(); } String urlText = rootURL.toString() + relativeURI; if ( log....

protected URL createRelativeURL(URL rootURL, String relativeURI) throws MalformedURLException { if (rootURL == null) { File file = new File(System.getProperty("user.dir")); url = file.toURL(); } String urlText = rootURL.toString() + relativeURI; if ( log.isDe...

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protected URL createRelativeURL(URL rootURL, String relativeURI) throws MalformedURLException { if (rootURL == null) { File file = new File(System.getProperty("user.dir")); rootURL = file.toURL(); } String urlText = rootURL.toString() + relativeURI; if ( log....

protected URL createRelativeURL(URL rootURL, String relativeURI) throws MalformedURLException { if (rootURL == null) { File file = new File(System.getProperty("user.dir")); rootURL = file.toURL(); } String urlText = url.toString() + relativeURI; if ( log.isDe...

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public ClassLoader getClassLoader() { if (this.classLoader != null) { return (this.classLoader); } if (this.useContextClassLoader) { ClassLoader classLoader = Thread.currentThread().getContextClassLoader(); if (classLoader != null) { return (class...

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public Object getVariable(String name) { Object value = variables.get(name); boolean definedHere = value != null || variables.containsKey(name); if (definedHere) return value; if ( value == null && isInherit() ) { JellyContext parent = getParent(); if (parent != nul...

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public Object getVariable(String name) { if ( getInherit() ) { return getParent().findVariable( name ); } return variables.get(name); }

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public Object getVariable(String name) { if ( getInherit() ) { return getParent().findVariable( name ); } return variables.get(name); }

public Object getVariable(String name) { if ( getInherit() ) { return getParent().findVariable( name ); } return value; }

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public void setScopedVariable(String name, Object value) { if ( getExport() ) { getParent().setScopedVariable( name, value ); } }

public void setScopedVariable(String name, Object value) { if ( getExport() && getParent() != null ) { getParent().setScopedVariable( name, value ); } }

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public void databaseAdded(DatabaseListChangeEvent e) { connections = plini.getConnections(); for (int i = listenerList.size() -1 ; i>=0; i--) { listenerList.get(i).contentsChanged(new ListDataEvent(this,ListDataEvent.INTERVAL_ADDED,e.getListIndex(),e.getListIndex())); } }

public void databaseAdded(DatabaseListChangeEvent e) { connections = plini.getConnections(); for (int i = listenerList.size() - 1; i >= 0; i--) { listenerList.get(i).contentsChanged( new ListDataEvent(this, ListDataEvent.INTERVAL_ADDED, e.getListIndex(), e.getListIndex())); } for (int i = listenerList.size() -1 ; i>...

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public void databaseAdded(DatabaseListChangeEvent e) { connections = plini.getConnections(); for (int i = listenerList.size() -1 ; i>=0; i--) { listenerList.get(i).contentsChanged(new ListDataEvent(this,ListDataEvent.INTERVAL_ADDED,e.getListIndex(),e.getListIndex())); } }

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public TDTPanel(Vector chromosomes, int t) { type = t; if (type == 1){ result = TDT.calcTrioTDT(chromosomes); }else{ result = TDT.calcCCTDT(chromosomes); } tableColumnNames.add("#"); tableColumnNames.add("Name"); if (type == 1){ table...

public TDTPanel(PedFile pf, int t) { type = t; if (type == 1){ result = TDT.calcTrioTDT(chromosomes); }else{ result = TDT.calcCCTDT(chromosomes); } tableColumnNames.add("#"); tableColumnNames.add("Name"); if (type == 1){ tableColumnNa...

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public TDTPanel(Vector chromosomes, int t) { type = t; if (type == 1){ result = TDT.calcTrioTDT(chromosomes); }else{ result = TDT.calcCCTDT(chromosomes); } tableColumnNames.add("#"); tableColumnNames.add("Name"); if (type == 1){ table...

public TDTPanel(Vector chromosomes, int t) { type = t; if (type == 1){ result = TDT.calcTrioTDT(pf); }else{ result = TDT.calcCCTDT(chromosomes); } tableColumnNames.add("#"); tableColumnNames.add("Name"); if (type == 1){ tableColumnNam...

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public TDTPanel(Vector chromosomes, int t) { type = t; if (type == 1){ result = TDT.calcTrioTDT(chromosomes); }else{ result = TDT.calcCCTDT(chromosomes); } tableColumnNames.add("#"); tableColumnNames.add("Name"); if (type == 1){ table...

public TDTPanel(Vector chromosomes, int t) { type = t; if (type == 1){ result = TDT.calcTrioTDT(chromosomes); }else{ result = TDT.calcCCTDT(pf); } tableColumnNames.add("#"); tableColumnNames.add("Name"); if (type == 1){ tableColumnNam...

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public void doTag(XMLOutput output) throws Exception { Map attributes = getAttributes(); Object bean = attributes.remove( "object" ); if ( bean == null ) { throw new MissingAttributeException("bean"); } setBeanProperties(bean, attributes); }

public void doTag(XMLOutput output) throws Exception { Map attributes = getAttributes(); Object bean = attributes.remove( "object" ); if ( bean == null ) { BeanSource tag = (BeanSource) findAncestorWithClass(BeanSource.class); if (tag != null) { bean = tag.getBean(); } if (bean == nu...

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public void add(PlayPenComponent c, int i) { children.add(i,c); c.addPlayPenComponentListener(playPenComponentEventPassthrough); c.addSelectionListener(getOwner()); c.revalidate(); }

public void add(PlayPenComponent c, int i) { if (c instanceof Relationship) { relations.add(i-children.size(),(Relationship)c); } else { children.add(i,c); } c.addPlayPenComponentListener(playPenComponentEventPassthrough); c.addSelectionListener(getOwner()); c.revalidate(); }

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