JoaoJunior/formatted-java-preprocessed-code-APR

protected TagScript createStaticTag( String namespaceURI, String localName, String qName, Attributes list) throws SAXException { try { StaticTag tag = new StaticTag( namespaceURI, localName, qName); StaticTagScript script = new StaticTagScript(tag); ...

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public void endElement(String namespaceURI, String localName, String qName) throws SAXException { try { tagScript = (TagScript) tagScriptStack.remove(tagScriptStack.size() - 1); if (tagScript != null) { if (textBuffer.length() > 0) { addTextScrip...

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public void startDocument() throws SAXException { script = new ScriptBlock(); textBuffer = new StringBuffer(); tagScript = null; parentTag = null; scriptStack.clear(); tagScriptStack.clear(); }

public void startDocument() throws SAXException { script = new ScriptBlock(); textBuffer = new StringBuffer(); tagScript = null; scriptStack.clear(); tagScriptStack.clear(); }

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public void startElement( String namespaceURI, String localName, String qName, Attributes list) throws SAXException { try { // add check to ensure namespace URI is "" for no namespace if ( namespaceURI == null ) { ...

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public void startElement( String namespaceURI, String localName, String qName, Attributes list) throws SAXException { try { // add check to ensure namespace URI is "" for no namespace if ( namespaceURI == null ) { ...

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public void startElement( String namespaceURI, String localName, String qName, Attributes list) throws SAXException { try { // add check to ensure namespace URI is "" for no namespace if ( namespaceURI == null ) { ...

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protected void processBean(String var, Object bean) throws Exception { super.processBean(var, bean); List list = getList(); System.out.println( "Created list: " + list + " with items: " + items ); // if the items variable is specified lets append all the items ...

protected void processBean(String var, Object bean) throws Exception { super.processBean(var, bean); List list = getList(); // if the items variable is specified lets append all the items if (items != null) { Iterator iter = items.evaluateAsIter...

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protected void setBeanProperties(Object bean, Map attributes) throws Exception { Object value = attributes.remove("items"); System.out.println( "value: " + value ); super.setBeanProperties(bean, attributes); // #### @todo use same algorithm as evaluateAsIterator() List lis...

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protected void setBeanProperties(Object bean, Map attributes) throws Exception { Object value = attributes.remove("items"); System.out.println( "value: " + value ); super.setBeanProperties(bean, attributes); // #### @todo use same algorithm as evaluateAsIterator() List lis...

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protected void registerFactories() { registerBeanFactory( "button", JButton.class ); registerBeanFactory( "checkBox", JCheckBox.class ); registerBeanFactory( "checkBoxMenuItem", JCheckBoxMenuItem.class ); registerBeanFactory( "comboBox", JComboBox.class ); // how to add content there...

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public void actionPerformed(ActionEvent e) { SQLObject root = (SQLObject) getModel().getRoot(); try { root.addChild(root.getChildCount(), new SQLDatabase(dbcs)); } catch (ArchitectException ex) { logger.warn("Couldn't add new database to tree", ex); JOptionPane.showMessageDialog(DBTree.this, "Couldn't ...

public void actionPerformed(ActionEvent e) { SQLObject root = (SQLObject) getModel().getRoot(); try { if (dbcsAlreadyExists(dbcs)) { logger.warn("database already exists in this project."); JOptionPane.showMessageDialog(DBTree.this, "Can't add connection, connection already exists in this project.", "Warning",...

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private void maybeShowPopup(MouseEvent e) { if (e.isPopupTrigger()) { refreshDBCSMenu(); TreePath p = getPathForLocation(e.getX(), e.getY()); if (p == null) { popup.getComponent(0).setVisible(true); popup.getComponent(1).setVisible(false); popup.getComponent(2).setVisible(false);...

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private void maybeShowPopup(MouseEvent e) { if (e.isPopupTrigger()) { refreshDBCSMenu(); TreePath p = getPathForLocation(e.getX(), e.getY()); if (p == null) { popup.getComponent(0).setVisible(true); popup.getComponent(1).setVisible(false); popup.getComponent(2).setVisible(false);...

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private void maybeShowPopup(MouseEvent e) { if (e.isPopupTrigger()) { refreshDBCSMenu(); TreePath p = getPathForLocation(e.getX(), e.getY()); if (p == null) { popup.getComponent(0).setVisible(true); popup.getComponent(1).setVisible(false); popup.getComponent(2).setVisible(false);...

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protected void refreshDBCSMenu() { popupDBCSMenu.removeAll(); popupDBCSMenu.add(new JMenuItem(newDBCSAction)); popupDBCSMenu.addSeparator(); Iterator it = ArchitectFrame.getMainInstance().getUserSettings().getConnections().iterator(); while(it.hasNext()) { DBConnectionSpec dbcs = (DBConnectionSpec) it.next(); ...

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protected void refreshDBCSMenu() { popupDBCSMenu.removeAll(); popupDBCSMenu.add(new JMenuItem(newDBCSAction)); popupDBCSMenu.addSeparator(); Iterator it = ArchitectFrame.getMainInstance().getUserSettings().getConnections().iterator(); while(it.hasNext()) { DBConnectionSpec dbcs = (DBConnectionSpec) it.next(); ...

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protected JPopupMenu setupPopupMenu() { JPopupMenu newMenu = new JPopupMenu(); newMenu.add(popupDBCSMenu = new JMenu("Add Connection")); newMenu.addSeparator(); // index 1 JMenuItem popupProperties = new JMenuItem(new DBCSPropertiesAction()); newMenu.add(popupProperties); // index 2 if (logger.isDebu...

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public void testDisableSourceDatabaseComponents() { JFrame frame = new JFrame(); frame.setContentPane(panel); frame.pack(); frame.setVisible(true); assertFalse(sourceDatabaseDropdown.isEnabled()); assertFalse(sourceNewConnButton.isEnabled()); assertFalse(sourceCatalogDropdown.isEnabled()); assertFalse(source...

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

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

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

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public Object findVariable(String name) { Object answer = variables.get(name); if ( answer == null && parent != null ) { answer = parent.findVariable(name); // ### this is a hack - remove this when we have support for pluggable Scopes if ( answer == null ) ...

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public JUnitTagLibrary() { registerTag("assert", AssertTag.class); registerTag("assertEquals", AssertEqualsTag.class); registerTag("fail", FailTag.class); registerTag("run", RunTestTag.class ); registerTag("case", TestCaseTag.class ); registerTag("suite", TestSuiteTag.class...

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private void generateClass() throws SupportException { // Declare some types. final TypeDesc storableType = TypeDesc.forClass(Storable.class); final TypeDesc triggerSupportType = TypeDesc.forClass(TriggerSupport.class); final TypeDesc masterSupportType = TypeDesc.forClass(MasterSupport.c...

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public void layoutContainer(Container parent) { LeftRightHeight lrh = calcSizes(parent); Dimension size = parent.getSize(); Insets ins = parent.getInsets(); int lColWidth = Math.min(size.width, lrh.left); int rColWidth = size.width - lColWidth - ins.left - ins.right; int height = Math.min(size.height, lrh.heig...

public void layoutContainer(Container parent) { LeftRightHeight lrh = calcSizes(parent); Dimension size = parent.getSize(); Insets ins = parent.getInsets(); int lColWidth = Math.min(size.width, lrh.left); int rColWidth = size.width - ins.left - lColWidth - hgap - ins.right; int height = Math.min(size.height, l...

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public void layoutContainer(Container parent) { LeftRightHeight lrh = calcSizes(parent); Dimension size = parent.getSize(); Insets ins = parent.getInsets(); int lColWidth = Math.min(size.width, lrh.left); int rColWidth = size.width - lColWidth - ins.left - ins.right; int height = Math.min(size.height, lrh.heig...

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public void windowClosing(WindowEvent e) { frame.dispose(); }

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public void showSelectionPropsDialog() { PhotoInfo photo = getSelected(); if ( photo != null ) { // TODO: Change PhotoInfoEditor to a dialog!!! final JFrame frame = new JFrame( "Photo properties" ); PhotoInfoController ctrl = new PhotoInfoController(); PhotoInfoEditor editor = new PhotoInfoEditor( c...

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public Dimension getPreferredSize() { int wide = BORDER*2; int high = BORDER*2; if (filteredHaplos == null) {return new Dimension(wide, high);} // height for the marker digits int markerDigits = (int) (0.0000001 + Math.log(theData.markerInfo.size()) / Math.log(10)) ...

public Dimension getPreferredSize() { int wide = BORDER*2; int high = BORDER*2; if (filteredHaplos == null) {return new Dimension(wide, high);} // height for the marker digits int markerDigits = (int) (0.0000001 + Math.log(Chromosome.size()) / Math.log(10)) + 1; ...

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public void paintComponent(Graphics graphics) { if (filteredHaplos == null){ super.paintComponent(graphics); return; } Graphics2D g = (Graphics2D) graphics; g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); ...

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public void normalizePrimaryKey() { try { if (getColumns().isEmpty()) return; boolean donePk = false; int i = 0; Iterator it = getColumns().iterator(); while (it.hasNext()) { SQLColumn col = (SQLColumn) it.next(); if (col.getPrimaryKeySeq() == null) donePk = true; if (!donePk) { col.primaryKe...

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public void normalizePrimaryKey() { try { if (getColumns().isEmpty()) return; boolean donePk = false; int i = 0; Iterator it = getColumns().iterator(); while (it.hasNext()) { SQLColumn col = (SQLColumn) it.next(); if (col.getPrimaryKeySeq() == null) donePk = true; if (!donePk) { col.primaryKe...

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public void doTag(XMLOutput output) throws Exception { if (select == null) { throw new MissingAttributeException( "select" ); } Object xpathContext = getXPathContext(); if ( select.booleanValueOf(xpathContext) ) { getBody().run( context, output ); } ...

public void doTag(XMLOutput output) throws Exception { if (select == null) { throw new MissingAttributeException( "select" ); } Object xpathContext = getXPathContext(); if ( select.booleanValueOf(xpathContext) ) { invokeBody(output); } }

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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 doTag(XMLOutput output) throws Exception { if (endpoint == null) { throw new MissingAttributeException("endpoint"); } if (namespace == null) { throw new MissingAttributeException("namespace"); } if (method == null) { throw new MissingAt...

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public void doTag(XMLOutput output) throws Exception { if (endpoint == null) { throw new MissingAttributeException("endpoint"); } if (namespace == null) { throw new MissingAttributeException("namespace"); } if (method == null) { throw new MissingAt...

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public void doTag(XMLOutput output) throws Exception { if (endpoint == null) { throw new MissingAttributeException("endpoint"); } if (namespace == null) { throw new MissingAttributeException("namespace"); } if (method == null) { throw new MissingAt...

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public Object evaluate(JellyContext context) { try { JellyInterpreter interpreter = BeanShellExpressionFactory.getInterpreter(context); if ( log.isDebugEnabled() ) { log.debug( "Evaluating EL: " + text ); } return interpreter....

public Object evaluate(JellyContext context) { try { JellyInterpreter interpreter = new JellyInterpreter(); interpreter.setJellyContext(context); if ( log.isDebugEnabled() ) { log.debug( "Evaluating EL: " + text ); } return in...

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public Object evaluate(JellyContext context) { try { JellyInterpreter interpreter = BeanShellExpressionFactory.getInterpreter(context); if ( log.isDebugEnabled() ) { log.debug( "Evaluating EL: " + text ); } return interpreter....

public Object evaluate(JellyContext context) { try { JellyInterpreter interpreter = BeanShellExpressionFactory.getInterpreter(context); if ( log.isDebugEnabled() ) { log.debug( "Evaluating beanshell: " + text ); } return inter...

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public JellyContext getJellyContext() throws MalformedURLException { if (context == null) { // take off the name off the URL String text = getUrl().toString(); int idx = text.lastIndexOf('/'); text = text.substring(0, idx + 1); JellyContext parentContext...

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

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public void doTag(XMLOutput output) throws Exception { if (!maxRowsSpecified) { Object obj = context.getVariable("org.apache.commons.jelly.sql.maxRows"); if (obj != null) { if (obj instanceof Integer) { maxRows = ((Integer) obj).intValue(); ...

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public void doTag(XMLOutput output) throws Exception { if (!maxRowsSpecified) { Object obj = context.getVariable("org.apache.commons.jelly.sql.maxRows"); if (obj != null) { if (obj instanceof Integer) { maxRows = ((Integer) obj).intValue(); ...

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public void start() { // TODO: threads for new applications are not getting started for (ApplicationConfig appConfig : ApplicationConfigManager .getAllApplications()) { ApplicationDowntimeTrackingThread thread = new ApplicationDowntimeTrackingThread(appConfig)...

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public void start() { // TODO: threads for new applications are not getting started for (ApplicationConfig appConfig : ApplicationConfigManager .getAllApplications()) { ApplicationDowntimeTrackingThread thread = new ApplicationDowntimeTrackingThread(appConfig)...

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public void stop() { for(ApplicationDowntimeTrackingThread thread: threads){ thread.end(); } threads.clear(); eventListeners.clear(); }

public void stop() { for(ApplicationHeartBeatThread thread: threads){ thread.end(); } threads.clear(); eventListeners.clear(); }

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public void stop() { for(ApplicationDowntimeTrackingThread thread: threads){ thread.end(); } threads.clear(); eventListeners.clear(); }

public void stop() { for(ApplicationDowntimeTrackingThread thread: threads){ thread.end(); } threads.clear(); }

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

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public void testRetrieve() { DList folders = null; Transaction tx = odmg.newTransaction(); tx.begin(); try { OQLQuery query = odmg.newOQLQuery(); query.create( "select folders from " + PhotoFolder.class.getName() ); folders = (DList) query.execute(); tx.commit(); } catch ( Exception e ) { tx.abo...

public void testRetrieve() { DList folders = null; Transaction tx = odmg.newTransaction(); tx.begin(); try { OQLQuery query = odmg.newOQLQuery(); query.create( "select folders from " + PhotoFolder.class.getName() + " where name = \"Top\"" ); folders = (DList) query.execute(); tx.commit(); } catch ( ...

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public SQLObject[] getPathToNode(SQLObject node) { LinkedList path = new LinkedList(); if (! (node instanceof DBTreeRoot)) { while (node != null) { path.add(0, node); node = node.getParent(); } } path.add(0, root); return (SQLObject[]) path.toArray(new SQLObject[path.size()]); }

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public LockedColumnException(String message) { super(message); }

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public JUnitTagLibrary() { registerTag("assert", AssertTag.class); registerTag("assertEquals", AssertEqualsTag.class); registerTag("assertThrown", AssertThrownTag.class); registerTag("fail", FailTag.class); registerTag("run", RunTag.class ); registerTag("case", CaseTag.class )...

public JUnitTagLibrary() { registerTag("assert", AssertTag.class); registerTag("assertEquals", AssertEqualsTag.class); registerTag("assertThrows", AssertThrowsTag.class); registerTag("fail", FailTag.class); registerTag("run", RunTag.class ); registerTag("case", CaseTag.class )...

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protected TagScript createStaticTag( final String namespaceURI, final String localName, final String qName, Attributes list) throws SAXException { try { StaticTag tag = new StaticTag( namespaceURI, localName, qName ); StaticTagScript script = new Stati...

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private static void saveConfig(){ ConfigWriter writer = ConfigWriter.getInstance(); writer.write(new Config(applicationConfigs, dashboardConfigs)); }

private static void saveConfig(){ ConfigWriter writer = ConfigWriter.getInstance(); writer.write(new Config(applicationConfigs)); }

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public void run(JellyContext context, XMLOutput output) throws Exception { DynaTag dynaTag = (DynaTag) tag; // ### probably compiling this to 2 arrays might be quicker and smaller for (Iterator iter = attributes.entrySet().iterator(); iter.hasNext();) { Map.Entry entry = (Map...

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public static JDialog createArchitectPanelDialog( final ArchitectPanel arch, final Window dialogParent, final String dialogTitle, final String actionButtonTitle, final Action okAction, final Action cancelAction) { final JDialog d; if (dialogParent instanceof Frame) { d = new JDialog((Frame) dial...

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public static JDialog createArchitectPanelDialog( final ArchitectPanel arch, final Window dialogParent, final String dialogTitle, final String actionButtonTitle, final Action okAction, final Action cancelAction) { final JDialog d; if (dialogParent instanceof Frame) { d = new JDialog((Frame) dial...

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public void actionPerformed(ActionEvent evt) { SQLTable t = new SQLTable(); t.initFolders(true); t.setTableName("New_Table"); TablePane tp = new TablePane(t); pp.addFloating(tp); }

public void actionPerformed(ActionEvent evt) { SQLTable t = new SQLTable(); t.initFolders(true); t.setTableName("New_Table"); TablePane tp = new TablePane(t, pp.getFontRenderContext()); pp.addFloating(tp); }

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protected void runScript(String name) throws Exception { InputStream in = getClass().getResourceAsStream( name ); Script script = parser.parse( in ); script = script.compile(); log.info( "Evaluating: " + script ); script.run( parser.getContext(), output ); ...

protected void runScript(String name) throws Exception { InputStream in = getClass().getResourceAsStream( name ); Script script = parser.parse( in ); script = script.compile(); log.info( "Evaluating: " + script ); script.run( parser.getJellyContext(), outpu...

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public Expression createExpression( ExpressionFactory factory, TagScript tagScript, String attributeName, String attributeValue) throws Exception { // #### may need to include some namespace URI information in the XPath instance? if (attributeName.equals("select")) { ...

public Expression createExpression( ExpressionFactory factory, TagScript tagScript, String attributeName, String attributeValue) throws Exception { // #### may need to include some namespace URI information in the XPath instance? if (attributeName.equals("select") || attrib...

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public Object getValueAt(Object node, int column) { HaplotypeAssociationNode n = (HaplotypeAssociationNode) node; switch (column){ case 0: return n.getName(); case 1: return n.getFreq(); case 2: i...

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public Object getValueAt(Object node, int column) { HaplotypeAssociationNode n = (HaplotypeAssociationNode) node; switch (column){ case 0: return n.getName(); case 1: return n.getFreq(); case 2: i...

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public Map runNamedScript( String name, Map params ) throws Exception { return runNamedScript(name, params, createXMLOutput()); }

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public Map runScript( String url, Map params, XMLOutput output ) throws Exception { URL actualUrl = null; try { actualUrl = new URL( url ); } catch( MalformedURLException x ) { throw new JellyException( "Could not find script at URL [" + url + "]: " + ...

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public void login(ServiceContext context, String username, String password) throws ServiceException{ LoginCallbackHandler callbackHandler = new LoginCallbackHandler(); callbackHandler.setUsername(username); callbackHandler.setPassword(password); ...

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public void populate() throws ArchitectException { if (populated) return; logger.debug("SQLCatalog: populate starting"); int oldSize = children.size(); synchronized (parent) { Connection con = null; ResultSet rs = null; try { con = ((SQLDatabase) parent).getConnection(); DatabaseMetaData dbmd = ...

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public synchronized TablePane importTableCopy(SQLTable source, Point preferredLocation) throws ArchitectException { SQLTable newTable = SQLTable.getDerivedInstance(source, db); // adds newTable to db String key = source.getTableName().toLowerCase(); // ensure tablename is unique if (logger.isDebugEnabled()) logg...

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public static void main(String[] args) { //set defaults Options.setMissingThreshold(0.5); Options.setSpacingThreshold(0.0); Options.setAssocTest(ASSOC_NONE); Options.setHaplotypeDisplayThreshold(1); Options.setMaxDistance(500); Options.setLDColorScheme(STD_SCHEME); ...

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public void register(AlertHandler handler, String alertId, String alertName){ assert this.handler == null; assert connection == null; this.handler = handler; /* start looking for this notification */ connection = ServerConnector.getS...

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public void register(AlertHandler handler, String alertId, String alertName){ assert this.handler == null; assert connection == null; this.handler = handler; /* start looking for this notification */ connection = ServerConnector.getS...

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public void unregister() { assert connection != null; assert monitorObjName != null; try { /* remove notification listener */ connection.removeNotificationListener(monitorObjName, listener, filter, null); } catch (Exception e) { logger.l...

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private PresentationObject getMailInputTable(IWContext iwc){ Table T = new Table(); T.setCellpaddingAndCellspacing(0); T.setColor(_bgColor); TextInput email = new TextInput("nl_email"); email.setStyleAttribute(_inputStyle); email.setLength(_inputLength); email.setContent(iwrb.getLocal...

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private PresentationObject getMailInputTable(IWContext iwc){ Table T = new Table(); T.setCellpaddingAndCellspacing(0); T.setColor(_bgColor); TextInput email = new TextInput("nl_email"); email.setStyleAttribute(_inputStyle); email.setLength(_inputLength); email.setContent(iwrb.getLocal...

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private PresentationObject getMailInputTable(IWContext iwc){ Table T = new Table(); T.setCellpaddingAndCellspacing(0); T.setColor(_bgColor); TextInput email = new TextInput("nl_email"); email.setStyleAttribute(_inputStyle); email.setLength(_inputLength); email.setContent(iwrb.getLocal...

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private PresentationObject getMailInputTable(IWContext iwc){ Table T = new Table(); T.setCellpaddingAndCellspacing(0); T.setColor(_bgColor); TextInput email = new TextInput("nl_email"); email.setStyleAttribute(_inputStyle); email.setLength(_inputLength); email.setContent(iwrb.getLocal...

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public void dragGestureRecognized(DragGestureEvent dge) { Point p = ((MouseEvent) dge.getTriggerEvent()).getPoint(); PlayPenComponent c = contentPane.getComponentAt(p); if ( c instanceof TablePane ) { TablePane tp = (TablePane) c; int colIndex = TablePane.COLUMN_INDEX_NONE; Point dragOrigi...

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public void waitForProcessCompletion() { try { iss.join(); ess.join(); } catch (InterruptedException ex) { System.out.println("Interrupted while waiting for engine"); } output.append("Execution halted"); }

public void waitForProcessCompletion() { try { iss.join(); ess.join(); } catch (InterruptedException ex) { logger.error("Interrupted while waiting for engine", ex); } output.append("Execution halted"); }

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public Vector findTags() { tags = new Vector(); untagged = new Vector(); taggedSoFar = 0; //potentialTagsHash stores the PotentialTag objects keyed on the corresponding sequences Hashtable potentialTagByVarSeq = new Hashtable(); PotentialTagComparator ptcomp = new Potential...

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public ExportDialog(HaploView h){ super(h, "Export Data"); hv = h; JPanel contents = new JPanel(); contents.setLayout(new BoxLayout(contents, BoxLayout.Y_AXIS)); JPanel tabPanel = new JPanel(); int currTab = hv.tabs.getSelectedIndex(); tabPanel.setBorder(new TitledBo...

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public LocusCorrelation getCorrelation(VariantSequence v1, VariantSequence v2) { if(v1 == v2) { return new LocusCorrelation(null,1); } if (v1 instanceof SNP && v2 instanceof SNP){ //we are comparing two snps int v1Index = ((Integer)indicesByVarSeq.get(v1)).intVa...

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public LocusCorrelation getCorrelation(VariantSequence v1, VariantSequence v2) { if(v1 == v2) { return new LocusCorrelation(null,1); } if (v1 instanceof SNP && v2 instanceof SNP){ //we are comparing two snps int v1Index = ((Integer)indicesByVarSeq.get(v1)).intVa...

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public Component getTableCellRendererComponent (JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) { Component cell = super.getTableCellRendererComponent (table, value, isSelected, hasFocus, row, column); ...

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