JoaoJunior/formatted-java-preprocessed-code-APR

public void handleEvent(Event event) { ApplicationDowntimeHistory downtimeHistory = getDowntimeHistory(event.getApplicationConfig()); assert downtimeHistory != null; if(event instanceof ApplicationUpEvent){ // application must have went down earlier downtimeHistory.applica...

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private void argHandler(String[] args){ argHandlerMessages = new Vector(); int maxDistance = -1; //this means that user didn't specify any output type if it doesn't get changed below blockOutputType = -1; double hapThresh = -1; double minimumMAF=-1; double spacingThr...

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private void processTextOnly(){ String fileName; int fileType; if(hapsFileName != null) { fileName = hapsFileName; fileType = HAPS_FILE; } else if (pedFileName != null){ fileName = pedFileName; fileType = PED_FILE; } else i...

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public void doTag(XMLOutput output) throws Exception { // run the body first to configure any nested DataType instances getBody().run(context, output); AntTagSupport parentTag = (AntTagSupport) findAncestorWithClass( AntTagSupport.class); if ( parentTag == null ) { // ignore, ...

public void doTag(XMLOutput output) throws Exception { // run the body first to configure any nested DataType instances invokeBody(output); AntTagSupport parentTag = (AntTagSupport) findAncestorWithClass( AntTagSupport.class); if ( parentTag == null ) { // ignore, as all it ca...

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private User buildUser(ActionForm form){ UserForm userForm = (UserForm)form; User user = UserManager.getInstance().getUser(userForm.getUsername()); assert user != null; List<Role> roles = new ArrayList<Role>(1); roles.add(new Role(userForm.getRole())); user.setRoles(roles);...

private User buildUser(ActionForm form){ UserForm userForm = (UserForm)form; User user = UserManager.getInstance().getUser(userForm.getUsername()); assert user != null; List<Role> roles = new ArrayList<Role>(1); String[] rolesString = userForm.getRole(); for(int ctr=0; ctr < roles...

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public Vector linkageToChrom(File infile, int type) throws IllegalArgumentException, HaploViewException, PedFileException, IOException{ Vector pedFileStrings = new Vector(); Vector hapsDataStrings = new Vector(); BufferedReader reader = new BufferedReader(new FileReader(infile)); ...

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public void dbChildrenInserted(SQLObjectEvent e) { logger.debug("dbchildrenadd. source="+e.getSource()); if (!SwingUtilities.isEventDispatchThread()) return; if (logger.isDebugEnabled()) { if (e.getSQLSource() instanceof SQLRelationship) { SQLRelationship r = (SQLRelationship) e.getSQLSource(); logger.debug...

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public void dbChildrenRemoved(SQLObjectEvent e) { logger.debug("dbchildrenremove. source="+e.getSource()); if (!SwingUtilities.isEventDispatchThread()) return; if (logger.isDebugEnabled()) logger.debug("dbChildrenRemoved SQLObjectEvent: "+e); try { SQLObject[] oldEventSources = e.getChildren(); for (int i = 0;...

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public void dbObjectChanged(SQLObjectEvent e) { logger.debug("dbObjectChanged. source="+e.getSource()); if (!SwingUtilities.isEventDispatchThread()) return; if (logger.isDebugEnabled()) logger.debug("dbObjectChanged SQLObjectEvent: "+e); if (e.getPropertyName().equals("name") && !e.getNewValue().equals(e.getSQ...

public void dbObjectChanged(SQLObjectEvent e) { logger.debug("dbObjectChanged. source="+e.getSource()); if ((!SwingUtilities.isEventDispatchThread()) && (!testMode)) { logger.debug("Not refiring because this is not the EDT."); return; } if (logger.isDebugEnabled()) logger.debug("dbObjectChanged SQLObjectEvent: "+e)...

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public void dbStructureChanged(SQLObjectEvent e) { logger.debug("dbStructureChanged. source="+e.getSource()); if (!SwingUtilities.isEventDispatchThread()) return; try { ArchitectUtils.listenToHierarchy(this, e.getSQLSource()); TreeModelEvent tme = new TreeModelEvent(this, getPathToNode(e.getSQLSource())); ...

public void dbStructureChanged(SQLObjectEvent e) { logger.debug("dbStructureChanged. source="+e.getSource()); try { ArchitectUtils.listenToHierarchy(this, e.getSQLSource()); TreeModelEvent tme = new TreeModelEvent(this, getPathToNode(e.getSQLSource())); fireTreeStructureChanged(tme); } catch (ArchitectEx...

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public void dbStructureChanged(SQLObjectEvent e) { logger.debug("dbStructureChanged. source="+e.getSource()); if (!SwingUtilities.isEventDispatchThread()) return; try { ArchitectUtils.listenToHierarchy(this, e.getSQLSource()); TreeModelEvent tme = new TreeModelEvent(this, getPathToNode(e.getSQLSource())); ...

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public SQLObject[] getFkPathToRelationship(SQLRelationship rel) { SQLObject[] pathToFkTable = getPathToNode(rel.getFkTable()); SQLObject[] path = new SQLObject[pathToFkTable.length + 1]; System.arraycopy(pathToFkTable, 0, path, 0, pathToFkTable.length); path[path.length - 1] = rel; return path; }

public SQLObject[] getFkPathToRelationship(SQLRelationship rel) { SQLObject[] pathToFkTable = getPathToNode(rel.getFkTable()); SQLObject[] path = new SQLObject[pathToFkTable.length + 2]; System.arraycopy(pathToFkTable, 0, path, 0, pathToFkTable.length); path[path.length - 1] = rel; return path; }

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public SQLObject[] getPkPathToRelationship(SQLRelationship rel) { SQLObject[] pathToPkTable = getPathToNode(rel.getPkTable()); SQLObject[] path = new SQLObject[pathToPkTable.length + 1]; System.arraycopy(pathToPkTable, 0, path, 0, pathToPkTable.length); path[path.length - 1] = rel; return path; }

public SQLObject[] getPkPathToRelationship(SQLRelationship rel) { SQLObject[] pathToPkTable = getPathToNode(rel.getPkTable()); SQLObject[] path = new SQLObject[pathToPkTable.length + 2]; System.arraycopy(pathToPkTable, 0, path, 0, pathToPkTable.length); path[path.length - 1] = rel; return path; }

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public SQLObject[] getPkPathToRelationship(SQLRelationship rel) { SQLObject[] pathToPkTable = getPathToNode(rel.getPkTable()); SQLObject[] path = new SQLObject[pathToPkTable.length + 1]; System.arraycopy(pathToPkTable, 0, path, 0, pathToPkTable.length); path[path.length - 1] = rel; return path; }

public SQLObject[] getPkPathToRelationship(SQLRelationship rel) { SQLObject[] pathToPkTable = getPathToNode(rel.getPkTable()); SQLObject[] path = new SQLObject[pathToPkTable.length + 1]; System.arraycopy(pathToPkTable, 0, path, 0, pathToPkTable.length); path[path.length - 2] = rel.getPkTable().getExportedKeysFolde...

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public Dimension getPreferredSize(JComponent jc) { TablePane c = (TablePane) jc; SQLTable table = c.getModel(); if (table == null) return null; int height = 0; int width = 0; try { Insets insets = c.getInsets(); java.util.List columnList = table.getColumns(); int cols = columnList.size(); Font font = c.g...

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public Dimension getPreferredSize(JComponent jc) { TablePane c = (TablePane) jc; SQLTable table = c.getModel(); if (table == null) return null; int height = 0; int width = 0; try { Insets insets = c.getInsets(); java.util.List columnList = table.getColumns(); int cols = columnList.size(); Font font = c.g...

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public String draw(DashboardContext context) { StringBuffer output = new StringBuffer(); // wrap wih div tag output.append("<div id=\"" + getId() + "\">"); output.append(component.draw(context)); output.append("</div>"); // append script String appId = context.getWeb...

public String draw(DashboardContext context) { StringBuffer output = new StringBuffer(); // wrap wih div tag output.append(component.draw(context)); output.append("</div>"); // append script String appId = context.getWebContext().getApplicationConfig().getApplicatio...

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public String draw(DashboardContext context) { StringBuffer output = new StringBuffer(); // wrap wih div tag output.append("<div id=\"" + getId() + "\">"); output.append(component.draw(context)); output.append("</div>"); // append script String appId = context.getWeb...

public String draw(DashboardContext context) { StringBuffer output = new StringBuffer(); // wrap wih div tag output.append("<div id=\"" + getId() + "\">"); output.append(component.draw(context)); // append script String appId = context.getWebContext().getApplication...

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private void sqlScriptGenerator(Map<DiffType, AttributeSet> styles, List<DiffChunk<SQLObject>> diff, DDLGenerator gen) throws ArchitectDiffException, SQLException, ArchitectException, BadLocationException, InstantiationException, IllegalAccessException { for (DiffChunk<SQLObject> chunk : diff) ...

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private void sqlScriptGenerator(Map<DiffType, AttributeSet> styles, List<DiffChunk<SQLObject>> diff, DDLGenerator gen) throws ArchitectDiffException, SQLException, ArchitectException, BadLocationException, InstantiationException, IllegalAccessException { for (DiffChunk<SQLObject> chunk : diff) ...

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private void sqlScriptGenerator(Map<DiffType, AttributeSet> styles, List<DiffChunk<SQLObject>> diff, DDLGenerator gen) throws ArchitectDiffException, SQLException, ArchitectException, BadLocationException, InstantiationException, IllegalAccessException { for (DiffChunk<SQLObject> chunk : diff) ...

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private void sqlScriptGenerator(Map<DiffType, AttributeSet> styles, List<DiffChunk<SQLObject>> diff, DDLGenerator gen) throws ArchitectDiffException, SQLException, ArchitectException, BadLocationException, InstantiationException, IllegalAccessException { for (DiffChunk<SQLObject> chunk : diff) ...

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public void actionPerformed(ActionEvent evt) { // update the progress bar logger.debug("updating progress bar..."); try { Integer jobSize = monitorable.getJobSize(); if (bar != null) { if (monitorable.hasStarted()) { if (jobSize == null) { bar.setIndeterminate(true); } else { bar.setIndeter...

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public Vector calcTDT(Vector chromosomes) { int numChroms; Chromosome chromT, chromU,chromTemp; String ped,ind; Vector temp; numChroms = chromosomes.size(); temp = (Vector)chromosomes.clone(); chromosomes = temp; int numMarkers = Chromosome.getSize(); f...

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public SQLCatalog(SQLDatabase parent, String name) { this.parent = parent; this.catalogName = name; this.children = new LinkedList(); }

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public Test_ThumbnailView() { testRefImageDir = new File( "/home/harri/projects/photovault/tests/images/photovault/swingui/TestThumbnailView/" ); testRefImageDir.mkdirs(); }

public Test_ThumbnailView() { super(); testRefImageDir = new File( "tests/images/photovault/swingui/TestThumbnailView/" ); testRefImageDir.mkdirs(); }

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protected void setUp() { // Create a frame with the test instance name as the title frame = new JFrame(getName()); pane = (JPanel)frame.getContentPane(); pane.setLayout(new FlowLayout()); pane.setBorder(new EmptyBorder(50, 50, 50, 50)); tester = ComponentTester.getT...

public void setUp() { super.setUp(); // Create a frame with the test instance name as the title frame = new JFrame(getName()); pane = (JPanel)frame.getContentPane(); pane.setLayout(new FlowLayout()); pane.setBorder(new EmptyBorder(50, 50, 50, 50)); tester = Componen...

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public void doTag(XMLOutput output) throws Exception { output.write("output - ignored body"); }

public void doTag(XMLOutput output) throws JellyTagException { output.write("output - ignored body"); }

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public void doTag(XMLOutput output) throws Exception { output.write("output - ignored body"); }

public void doTag(XMLOutput output) throws Exception { try { output.write("output - ignored body"); } catch (SAXException e) { throw new JellyTagException(e); } }

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public void testComplexUnionPlan3() throws Exception { UnionQueryAnalyzer uqa = new UnionQueryAnalyzer(StorableTestBasic.class, TestIndexedQueryAnalyzer.RepoAccess.INSTANCE); Filter<StorableTestBasic> filter = Filter.filterFor (StorableTestBasic....

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public void testComplexUnionPlan3() throws Exception { UnionQueryAnalyzer uqa = new UnionQueryAnalyzer(StorableTestBasic.class, TestIndexedQueryAnalyzer.RepoAccess.INSTANCE); Filter<StorableTestBasic> filter = Filter.filterFor (StorableTestBasic....

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public void save(ProgressMonitor pm) throws IOException, ArchitectException { // write to temp file and then rename (this preserves old project file // when there's problems) if (file.exists() && !file.canWrite()) { // write problems with architect file will muck up the save process throw new ArchitectExceptio...

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public void exportPhoto( File file, int width, int height ) { 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++ ) { ImageInstance instance = (ImageInstance)...

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public void parseHapMap(Vector rawLines) throws PedFileException { int colNum = -1; int numLines = rawLines.size(); Individual ind; this.order = new Vector(); //sort first Vector lines = new Vector(); Hashtable sortHelp = new Hashtable(numLines-1,1.0f); long[]...

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public void mouseClicked(MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON1_MASK) == InputEvent.BUTTON1_MASK) { int clickX = e.getX(); int clickY = e.getY(); if (showWM && wmInteriorRect.contains(clickX,clickY)){ //convert a click on the ...

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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 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]); // later we m...

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

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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]); // later we m...

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protected void setUp() throws Exception { super.setUp(); SQLDatabase mydb = new SQLDatabase(db.getDataSource()); Connection con = mydb.getConnection(); /* * Setting up a clean db for each of the tests */ Statement stmt = con.createStatement(); try { stmt.executeUpdate("DROP TABLE REGRESSION_TEST1"); ...

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protected QueryExecutor<UserAddress> addressExecutor() throws Exception { Storage<UserAddress> addressStorage = mRepository.storageFor(UserAddress.class); QueryExecutor<UserAddress> addressExecutor = new ScanQueryExecutor<UserAddress>(addressStorage.query()); addressExecutor = new Fi...

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public void testJoin() throws Exception { QueryExecutor<UserAddress> addressExecutor = addressExecutor(); QueryExecutor<UserInfo> userExecutor = new JoinedQueryExecutor<UserAddress, UserInfo> (mRepository, UserInfo.class, "address", addressExecutor); assertEquals("address.state = ?",...

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public void testJoin() throws Exception { QueryExecutor<UserAddress> addressExecutor = addressExecutor(); QueryExecutor<UserInfo> userExecutor = new JoinedQueryExecutor<UserAddress, UserInfo> (mRepository, UserInfo.class, "address", addressExecutor); assertEquals("address.state = ?",...

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public void run(Context context, XMLOutput output) throws Exception { if ( value != null ) { String text = value.evaluateAsString( context ); if ( text != null ) { output.write( text ); } } }

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public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if(command.equals("Show CC counts")) { HaplotypeAssociationModel ham = (HaplotypeAssociationModel)jtt.getTree().getModel(); ham.setCountsOrRatios(SHOW_COUNTS); jtt.repaint(); } ...

public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if(command.equals("Show CC counts")) { HaplotypeAssociationModel ham = (HaplotypeAssociationModel)jtt.getTree().getModel(); ham.setCountsOrRatios(SHOW_HAP_COUNTS); jtt.repaint(); ...

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public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if(command.equals("Show CC counts")) { HaplotypeAssociationModel ham = (HaplotypeAssociationModel)jtt.getTree().getModel(); ham.setCountsOrRatios(SHOW_COUNTS); jtt.repaint(); } ...

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public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if(command.equals("Show CC counts")) { HaplotypeAssociationModel ham = (HaplotypeAssociationModel)jtt.getTree().getModel(); ham.setCountsOrRatios(SHOW_COUNTS); jtt.repaint(); } ...

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public void saveDprimeToText(String[][] dPrimeTable, File dumpDprimeFile, boolean info, Vector markerinfo) throws IOException{ FileWriter saveDprimeWriter = new FileWriter(dumpDprimeFile); if (info){ saveDprimeWriter.write("L1\tL2\tD'\tLOD\tr^2\tCIlow\tCIhi\tDist\n"); long dist; for (int i = 0; i ...

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public void saveDprimeToText(String[][] dPrimeTable, File dumpDprimeFile, boolean info, Vector markerinfo) throws IOException{ FileWriter saveDprimeWriter = new FileWriter(dumpDprimeFile); if (info){ saveDprimeWriter.write("L1\tL2\tD'\tLOD\tr^2\tCIlow\tCIhi\tDist\n"); long dist; for (int i = 0; i ...

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public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command.equals("Filter")){ doFilters(); }else if (command.equals("top filter")){ numResults = Integer.parseInt(topField.getText()); doTopFilter(); }else if (command.eq...

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public void doTag(XMLOutput output) throws Exception { connection = MessengerManager.get( name ); if ( var != null ) { context.setVariable( var, connection ); } getBody().run(context, output); }

public void doTag(XMLOutput output) throws Exception { connection = MessengerManager.get( name ); if ( var != null ) { context.setVariable( var, connection ); } invokeBody(output); }

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private void argHandler(String[] args){ //TODO: -specify values from HaplotypeDisplayController (min hap percentage etc) // -want to be able to output haps file from pedfile boolean nogui = false; String batchMode = ""; String hapsFileName = ""; String pedFileName = ""...

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

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

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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 run(Context context, XMLOutput output) throws Exception { if ( trim && ! hasTrimmed ) { trimBody(); hasTrimmed = true; } if ( log.isDebugEnabled() ) { log.debug( "Running body: " + getBody() ); } getBody().run( context, output ); }

public void run(JellyContext context, XMLOutput output) throws Exception { if ( trim && ! hasTrimmed ) { trimBody(); hasTrimmed = true; } if ( log.isDebugEnabled() ) { log.debug( "Running body: " + getBody() ); } getBody().run( context, output ); ...

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public static boolean initODMG( String user, String passwd, String dbName ) { getODMGImplementation(); db = odmg.newDatabase(); boolean success = false; try { log.debug( "Opening database" ); db.open( dbName + "#" + user + "#" + passwd, Database.OPEN_READ_WRITE ); log.debug( "Success!!!" ); } catch ( Ex...

public static boolean initODMG( String user, String passwd, String dbName ) { getODMGImplementation(); db = odmg.newDatabase(); boolean success = false; log.error( t.getMessage() ); t.printStackTrace(); try { log.debug( "Opening database" ); db.open( dbName + "#" + user + "#" + passwd, Database.OPEN_READ_WR...

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public Vector linkageToChrom(File infile, int type) throws IllegalArgumentException, HaploViewException, PedFileException, IOException{ //okay, for now we're going to assume the ped file has no header Vector pedFileStrings = new Vector(); BufferedReader reader = new BufferedReader(ne...

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public Vector linkageToChrom(File infile, int type) throws IllegalArgumentException, HaploViewException, PedFileException, IOException{ //okay, for now we're going to assume the ped file has no header Vector pedFileStrings = new Vector(); BufferedReader reader = new BufferedReader(ne...

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public void doTag(final XMLOutput output) throws Exception { getGoal(getName()).addPreActionCallback( new PreActionCallback() { public void firePreAction(Goal goal) throws Exception { // lets run the body log.debug( "Running pre action: ...

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public void firePreAction(Goal goal) throws Exception { // lets run the body log.debug( "Running pre action: " + getName() ); getBody().run( context, output); }

public void firePreAction(Goal goal) throws Exception { // lets run the body log.debug( "Running pre action: " + getName() ); invokeBody( output); }

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private void argHandler(String[] args){ //TODO: -specify values from HaplotypeDisplayController (min hap percentage etc) // -want to be able to output haps file from pedfile boolean nogui = false; String batchMode = ""; String hapsFileName = ""; String pedFileName = ""...

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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")); ...

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void export(int tabNum, int format, int start, int stop){ fc.setSelectedFile(new File("")); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION){ File outfile = fc.getSelectedFile(); if (format == PNG_MODE){ BufferedImage image; if (tabNum == ...

void export(int tabNum, int format, int start, int stop){ fc.setSelectedFile(new File("")); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION){ File outfile = fc.getSelectedFile(); if (format == PNG_MODE || format == COMPRESSED_PNG_MODE){ BufferedImage ima...

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void export(int tabNum, int format, int start, int stop){ fc.setSelectedFile(new File("")); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION){ File outfile = fc.getSelectedFile(); if (format == PNG_MODE){ BufferedImage image; if (tabNum == ...

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public byte elementAt(int i){ return genotypes[i]; }

public byte elementAt(int i){ return genotypes[realIndex[i]]; }

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public int size(){ return genotypes.length; }

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private void deleteReplica(S replica) throws PersistException { // Disable replication to prevent trigger from being invoked by // deleting replica. setReplicationDisabled(true); try { replica.tryDelete(); } finally { setReplicationDisabled(false); } ...

void deleteReplica(Storable replica) throws PersistException { // Disable replication to prevent trigger from being invoked by // deleting replica. setReplicationDisabled(true); try { replica.tryDelete(); } finally { setReplicationDisabled(false); } ...

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private void deleteReplica(S replica) throws PersistException { // Disable replication to prevent trigger from being invoked by // deleting replica. setReplicationDisabled(true); try { replica.tryDelete(); } finally { setReplicationDisabled(false); } ...

private void deleteReplica(S replica) throws PersistException { // Disable replication to prevent trigger from being invoked by // deleting replica. setReplicationDisabled(true); try { replica.delete(); } finally { setReplicationDisabled(false); } }

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public void run(Context context, XMLOutput output) throws Exception { if ( select != null ) { Iterator iter = select.selectNodes(null).iterator(); while ( iter.hasNext() ) { Object value = iter.next(); if (var != null) { context.setVaria...

public void run(JellyContext context, XMLOutput output) throws Exception { if ( select != null ) { Iterator iter = select.selectNodes(null).iterator(); while ( iter.hasNext() ) { Object value = iter.next(); if (var != null) { context.set...

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public void run(Context context, XMLOutput output) throws Exception { for ( int i = 0, size = whenTags.length; i < size; i++ ) { TagScript script = whenTags[i]; script.run( context, output ); WhenTag tag = (WhenTag) script.getTag(); if ( tag.getValue() ) { ...

public void run(JellyContext context, XMLOutput output) throws Exception { for ( int i = 0, size = whenTags.length; i < size; i++ ) { TagScript script = whenTags[i]; script.run( context, output ); WhenTag tag = (WhenTag) script.getTag(); if ( tag.getValue() ) { ...

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private String getAttributeType(ServerConnection connection, ObjectAttributeInfo[] objAttributes, String attribute, ObjectName objectName){ String itemName = null; int index = attribute.indexOf('.'...

private String getAttributeType(ServerConnection connection, ObjectAttributeInfo[] objAttributes, String attribute, ObjectName objectName){ String itemName = null; final int index = attribute.index...

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private String getAttributeType(ServerConnection connection, ObjectAttributeInfo[] objAttributes, String attribute, ObjectName objectName){ String itemName = null; int index = attribute.indexOf('.'...

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private String getAttributeType(ServerConnection connection, ObjectAttributeInfo[] objAttributes, String attribute, ObjectName objectName){ String itemName = null; int index = attribute.indexOf('.'...

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public ObjectAttribute getObjectAttribute(ServiceContext context, String attribute) throws ServiceException{ assert context.getObjectName() != null; assert context.getApplicationConfig() != null; canAccessThisMBean(context); AccessC...

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public ObjectAttribute getObjectAttribute(ServiceContext context, String attribute) throws ServiceException{ assert context.getObjectName() != null; assert context.getApplicationConfig() != null; canAccessThisMBean(context); AccessC...

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public ObjectAttribute getObjectAttribute(ServiceContext context, String attribute) throws ServiceException{ assert context.getObjectName() != null; assert context.getApplicationConfig() != null; canAccessThisMBean(context); AccessC...

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private void handleCompositeData(ServerConnection connection, ObjectName objectName, ObjectAttributeInfo attrInfo, String[] dataTypes, List attributesList){ Composit...

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public PresentationObject getLettersHeads() { Table T = new Table(); if (letters != null && letters.size() > 0) { Iterator iter = letters.iterator(); EmailLetter let; int row = 1; //T.add(getStyleText(iwrb.getLocalizedString("from","From"),SN_TITLE),1,row); //T.add(getStyleText(iwrb.getLocalizedString("sub...

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public PresentationObject getLettersHeads() { Table T = new Table(); if (letters != null && letters.size() > 0) { Iterator iter = letters.iterator(); EmailLetter let; int row = 1; //T.add(getStyleText(iwrb.getLocalizedString("from","From"),SN_TITLE),1,row); //T.add(getStyleText(iwrb.getLocalizedString("sub...

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private PresentationObject getTopics() { Table T = new Table(); //T.add(getStyleText(iwrb.getLocalizedString("topic","Topic"),SN_TITLE),1,1); //T.add(getStyleText(iwrb.getLocalizedString("issue","Issue"),SN_TITLE),2,1); if (topics != null && topics.size() > 0) { Iterator iter = topics.iterator(); EmailTopic tp...

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private PresentationObject getTopics() { Table T = new Table(); //T.add(getStyleText(iwrb.getLocalizedString("topic","Topic"),SN_TITLE),1,1); //T.add(getStyleText(iwrb.getLocalizedString("issue","Issue"),SN_TITLE),2,1); if (topics != null && topics.size() > 0) { Iterator iter = topics.iterator(); EmailTopic tp...

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private PresentationObject getTopics() { Table T = new Table(); //T.add(getStyleText(iwrb.getLocalizedString("topic","Topic"),SN_TITLE),1,1); //T.add(getStyleText(iwrb.getLocalizedString("issue","Issue"),SN_TITLE),2,1); if (topics != null && topics.size() > 0) { Iterator iter = topics.iterator(); EmailTopic tp...

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private PresentationObject getTopics() { Table T = new Table(); //T.add(getStyleText(iwrb.getLocalizedString("topic","Topic"),SN_TITLE),1,1); //T.add(getStyleText(iwrb.getLocalizedString("issue","Issue"),SN_TITLE),2,1); if (topics != null && topics.size() > 0) { Iterator iter = topics.iterator(); EmailTopic tp...

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public void main(IWContext iwc) { iwb = getBundle(iwc); core = iwc.getApplication().getCoreBundle(); iwrb = getResourceBundle(iwc); Table T = new Table(); int row = 1; df = DateFormat.getDateInstance(DateFormat.LONG, iwc.getCurrentLocale()); if (iwc.isParameterSet(prmTopic)) { topic = Integer.parseInt(iwc.get...

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public void removeNotificationListener(ObjectName objectName, ObjectNotificationListener listener, ObjectNotificationFilter filter, Object handback){ throw new RuntimeException("Notif...

public void removeNotificationListener(ObjectName objectName, ObjectNotificationListener listener, ObjectNotificationFilter filter, Object handback){ NotificationListener notifListene...

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private static OperationResultData executeMBeanOperation( ServiceContext context, ApplicationConfig appConfig, ObjectName objectName, String operationName, String[] params, String[] signature){ OperationResultData resultData = n...

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public void doTag(XMLOutput output) throws Exception { suite = createSuite(); TestSuite parent = (TestSuite) context.getVariable("org.apache.commons.jelly.junit.suite"); if ( parent == null ) { context.setVariable("org.apache.commons.jelly.junit.suite", suite ); ...

public void doTag(XMLOutput output) throws JellyTagException { suite = createSuite(); TestSuite parent = (TestSuite) context.getVariable("org.apache.commons.jelly.junit.suite"); if ( parent == null ) { context.setVariable("org.apache.commons.jelly.junit.suite", suite ...

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public void doTag(final XMLOutput output) throws Exception { if ( name != null ) { Writer writer = new FileWriter(name); writeBody(writer); } else if (var != null) { StringWriter writer = new StringWriter(); writeBody(writer); context.setVa...

public void doTag(final XMLOutput output) throws Exception { if ( name != null ) { String encoding = (this.encoding != null) ? this.encoding : "UTF-8"; Writer writer = new OutputStreamWriter( new FileOutputStream( name ), encoding ); writeBody(writer); } else if (var != nu...

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void readGenotypes(String[] inputOptions, int type){ //input is a 3 element array with //inputOptions[0] = ped file //inputOptions[1] = info file ("" if none) //inputOptions[2] = max comparison distance (don't compute d' if markers are greater than this dist apart) //type is eithe...

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public void addColumn(SQLColumn c, SQLTable t) throws ArchitectDiffException { Map colNameMap = new HashMap(); print("\n ALTER TABLE "); printQualified(t.getPhysicalName()); print(" ADD COLUMN "); print(columnDefinition(c,colNameMap)); endStatement(DDLStatement.StatementType.CREATE, c); }

public void addColumn(SQLColumn c, SQLTable t) throws ArchitectDiffException { Map colNameMap = new HashMap(); print("\n ALTER TABLE "); print( DDLUtils.toQualifiedName(t.getCatalogName(),t.getSchemaName(),t.getPhysicalName()) ); print(" ADD COLUMN "); print(columnDefinition(c,colNameMap)); endStatement(DDLSta...

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public void addRelationship(SQLRelationship r) throws ArchitectDiffException { print("\n ALTER TABLE "); printQualified(r.getFkTable().getPhysicalName()); print(" ADD CONSTRAINT "); print(r.getName()); print(" FOREIGN KEY ( "); Map<String, SQLColumn> colNameMap = new HashMap<String, SQLColumn> (); boolean fi...

public void addRelationship(SQLRelationship r) throws ArchitectDiffException { print("\n ALTER TABLE "); print( DDLUtils.toQualifiedName(r.getFkTable().getCatalogName(),r.getFkTable().getSchemaName(),r.getFkTable().getPhysicalName()) ); print(" ADD CONSTRAINT "); print(r.getName()); print(" FOREIGN KEY ( "); M...

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public void addRelationship(SQLRelationship r) throws ArchitectDiffException { print("\n ALTER TABLE "); printQualified(r.getFkTable().getPhysicalName()); print(" ADD CONSTRAINT "); print(r.getName()); print(" FOREIGN KEY ( "); Map<String, SQLColumn> colNameMap = new HashMap<String, SQLColumn> (); boolean fi...

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public void dropColumn(SQLColumn c, SQLTable t) throws ArchitectDiffException { Map colNameMap = new HashMap(); print("\n ALTER TABLE "); printQualified(t.getPhysicalName()); print(" DROP COLUMN "); print(getPhysicalName(colNameMap,c)); endStatement(DDLStatement.StatementType.DROP, c); }

public void dropColumn(SQLColumn c, SQLTable t) throws ArchitectDiffException { Map colNameMap = new HashMap(); print("\n ALTER TABLE "); print( DDLUtils.toQualifiedName(t.getCatalogName(),t.getSchemaName(),t.getPhysicalName()) ); print(" DROP COLUMN "); print(getPhysicalName(colNameMap,c)); endStatement(DDLSt...

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public void dropRelationship(SQLRelationship r) { print("\n ALTER TABLE "); printQualified(r.getFkTable().getPhysicalName()); print(" DROP CONSTRAINT "); print(r.getName()); endStatement(DDLStatement.StatementType.DROP, r); }

public void dropRelationship(SQLRelationship r) { print("\n ALTER TABLE "); print( DDLUtils.toQualifiedName(r.getFkTable().getCatalogName(),r.getFkTable().getSchemaName(),r.getFkTable().getPhysicalName()) ); print(" DROP CONSTRAINT "); print(r.getName()); endStatement(DDLStatement.StatementType.DROP, r); }

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protected void writeExportedRelationships(SQLTable t) throws ArchitectException { Iterator it = t.getExportedKeys().iterator(); while (it.hasNext()) { SQLRelationship rel = (SQLRelationship) it.next(); // geneate a physical name for this relationship getPhysicalName(topLevelNames,rel); // println(""); p...

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protected void writeExportedRelationships(SQLTable t) throws ArchitectException { Iterator it = t.getExportedKeys().iterator(); while (it.hasNext()) { SQLRelationship rel = (SQLRelationship) it.next(); // geneate a physical name for this relationship getPhysicalName(topLevelNames,rel); // println(""); p...

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protected void writePrimaryKey(SQLTable t) throws ArchitectException { boolean firstCol = true; Iterator it = t.getColumns().iterator(); while (it.hasNext()) { SQLColumn col = (SQLColumn) it.next(); if (col.getPrimaryKeySeq() == null) break; if (firstCol) { // generate a unique primary key name ...

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public void writeTable(SQLTable t) throws SQLException, ArchitectException { Map colNameMap = new HashMap(); // for detecting duplicate column names // generate a new physical name if necessary getPhysicalName(topLevelNames,t); // also adds generated physical name to the map print("\nCREATE TABLE "); printQualif...

public void writeTable(SQLTable t) throws SQLException, ArchitectException { Map colNameMap = new HashMap(); // for detecting duplicate column names // generate a new physical name if necessary getPhysicalName(topLevelNames,t); // also adds generated physical name to the map print("\nCREATE TABLE "); print( DDLU...

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public boolean evaluateAsBoolean(Context context) { Object value = evaluate(context); if ( value instanceof Boolean ) { Boolean b = (Boolean) value; return b.booleanValue(); } else if ( value instanceof String ) { return Boolean.getBoolean( (String) value...

public boolean evaluateAsBoolean(JellyContext context) { Object value = evaluate(context); if ( value instanceof Boolean ) { Boolean b = (Boolean) value; return b.booleanValue(); } else if ( value instanceof String ) { return Boolean.getBoolean( (String) ...

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public Iterator evaluateAsIterator(Context context) { Object value = evaluate(context); if ( value == null ) { return EMPTY_ITERATOR; } else if ( value instanceof Iterator ) { return (Iterator) value; } else if ( value instanceof List ) { ...

public Iterator evaluateAsIterator(JellyContext context) { Object value = evaluate(context); if ( value == null ) { return EMPTY_ITERATOR; } else if ( value instanceof Iterator ) { return (Iterator) value; } else if ( value instanceof List ) { ...

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