JoaoJunior/formatted-java-preprocessed-code-APR

public PlayPenComponent getComponent(int i) { return children.get(i); }

public PlayPenComponent getComponent(int i) { if (i < children.size()){ return children.get(i); } else { return relations.get(i-children.size()); } }

1,112,121

public int getComponentCount() { return children.size(); }

public int getComponentCount() { return children.size()+relations.size(); }

1,112,123

public void remove(int j) { PlayPenComponent c = children.get(j); Rectangle r = c.getBounds(); c.removePlayPenComponentListener(playPenComponentEventPassthrough); c.removeSelectionListener(getOwner()); children.remove(j); getOwner().repaint(r); }

public void remove(int j) { PlayPenComponent c; if (j < children.size()) { c= children.get(j); } else { c = relations.get(j-children.size()); } Rectangle r = c.getBounds(); c.removePlayPenComponentListener(playPenComponentEventPassthrough); c.removeSelectionListener(getOwner()); children.remove(j); getOwner().re...

1,112,124

public void remove(int j) { PlayPenComponent c = children.get(j); Rectangle r = c.getBounds(); c.removePlayPenComponentListener(playPenComponentEventPassthrough); c.removeSelectionListener(getOwner()); children.remove(j); getOwner().repaint(r); }

public void remove(int j) { PlayPenComponent c = children.get(j); Rectangle r = c.getBounds(); c.removePlayPenComponentListener(playPenComponentEventPassthrough); c.removeSelectionListener(getOwner()); if (j < children.size()) { children.remove(j); } else { relations.remove(j-children.size()); } getOwner().repai...

1,112,125

public CheckDataPanel(HaploView hv){ this(hv.theData); this.hv = hv; setLayout(new BoxLayout(this,BoxLayout.Y_AXIS)); JPanel missingPanel = new JPanel(); JLabel countsLabel; countsLabel = new JLabel("Using " + theData.numSingletons + " singletons and " + theD...

1,112,128

public void saveDprimeToText(File dumpDprimeFile) throws IOException{ FileWriter saveDprimeWriter = new FileWriter(dumpDprimeFile); if (infoKnown){ saveDprimeWriter.write("L1\tL2\tD'\tLOD\tr^2\tCIlow\tCIhi\tDist\n"); long dist; for (int i = 0; i < filteredDPrimeTable.l...

1,112,130

public void saveHapsToText(Haplotype[][] finishedHaplos, double[] multidprime, File saveHapsFile) throws IOException{ if (finishedHaplos == null) return; NumberFormat nf = NumberFormat.getInstance(Locale.US); nf.setMinimumFractionDigits(3); nf.setMaximumFrac...

1,112,131

private void addUser(RemoteManagerClient remoteManagerClient, String username, String internalPassword) { remoteManagerClient.executeCommand("adduser " + username + " " + internalPassword); List answers = remoteManagerClient.readAnswer(); log.info("user created: " + username); }

private void addUser(RemoteManagerClient remoteManagerClient, String username, String internalPassword) { remoteManagerClient.executeCommand("adduser " + username + " " + internalPassword); remoteManagerClient.readAnswer(); log.info("user created: " + username); }

1,112,133

private void setupForwardedMailInterceptor() throws StartupException { SMTPMailSink smtpMailSink = new SMTPMailSink(); smtpMailSink.setSmtpListenerPort(m_postageConfiguration.getTestserverPortSMTPForwarding()); smtpMailSink.setResults(m_results); try { smtpMailSink.initialize(...

1,112,134

private void setupInternalUserAccounts() throws StartupException { try { String host = m_postageConfiguration.getTestserverHost(); int remoteManagerPort = m_postageConfiguration.getTestserverRemoteManagerPort(); String remoteManagerUsername = m_postageConfiguration.getTestser...

1,112,135

private void setupInternalUserAccounts() throws StartupException { try { String host = m_postageConfiguration.getTestserverHost(); int remoteManagerPort = m_postageConfiguration.getTestserverRemoteManagerPort(); String remoteManagerUsername = m_postageConfiguration.getTestser...

1,112,136

private void setupInternalUserAccounts() throws StartupException { try { String host = m_postageConfiguration.getTestserverHost(); int remoteManagerPort = m_postageConfiguration.getTestserverRemoteManagerPort(); String remoteManagerUsername = m_postageConfiguration.getTestser...

1,112,137

public void delete() { getODMGImplementation(); getODMGDatabase(); Transaction tx = odmg.newTransaction(); tx.begin(); // First make sure that this object is deleted from its parent's subfolders list (if it has a parent) setParentFolder( null ); try { db.deletePersistent( this ); tx.commit(); } catch ( Exce...

1,112,139

public void delete() { getODMGImplementation(); getODMGDatabase(); Transaction tx = odmg.newTransaction(); tx.begin(); // First make sure that this object is deleted from its parent's subfolders list (if it has a parent) setParentFolder( null ); try { db.deletePersistent( this ); tx.commit(); } catch ( Exce...

1,112,140

public void delete() { getODMGImplementation(); getODMGDatabase(); Transaction tx = odmg.newTransaction(); tx.begin(); // First make sure that this object is deleted from its parent's subfolders list (if it has a parent) setParentFolder( null ); try { db.deletePersistent( this ); tx.commit(); } catch ( Exce...

1,112,141

public static PhotoFolder getRoot() { getODMGImplementation(); getODMGDatabase(); DList folders = null; Transaction tx = odmg.newTransaction(); tx.begin(); try { OQLQuery query = odmg.newOQLQuery(); query.create( "select folders from " + PhotoFolder.class.getName() + " where folderId = 1" ); folders = (...

1,112,142

public static void main( String[] args ) { org.apache.log4j.BasicConfigurator.configure(); log.setLevel( org.apache.log4j.Level.DEBUG ); Implementation odmg = getODMGImplementation(); Database db = getODMGDatabase(); Transaction tx = odmg.newTransaction(); tx.begin(); DList folders = null; try { OQLQuery query ...

1,112,144

public void stateChanged(ChangeEvent e) { int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ exportMenuItems[0].setEnabled(true); exportMenuItems[1].setEnabled(true); }else if (tabNum == VIEW_TDT_NUM || tabNum...

1,112,147

void browse(int browseType){ String name; String markerInfoName = ""; HaploView h = (HaploView) this.getParent(); h.fc.setSelectedFile(null); int returned = h.fc.showOpenDialog(this); if (returned != JFileChooser.APPROVE_OPTION) return; File file = h.fc.getSelectedFi...

void browse(int browseType){ String name; String markerInfoName = ""; HaploView h = (HaploView) this.getParent(); h.fc.setSelectedFile(new File("")); int returned = h.fc.showOpenDialog(this); if (returned != JFileChooser.APPROVE_OPTION) return; File file = h.fc.getSe...

1,112,151

public Expression createExpression( ExpressionFactory factory, String tagName, 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")) ...

1,112,152

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

1,112,153

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

1,112,154

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

1,112,155

private static void hapsTextOnly(String hapsFile,int outputType){ try { HaploData theData; File OutputFile; File inputFile = new File(hapsFile); if(!inputFile.exists()){ System.out.println("haps input file " + hapsFile + " does not exist"); ...

private static void hapsTextOnly(String hapsFile,int outputType, int maxDistance){ try { HaploData theData; File OutputFile; File inputFile = new File(hapsFile); if(!inputFile.exists()){ System.out.println("haps input file " + hapsFile + " does not e...

1,112,156

private static void hapsTextOnly(String hapsFile,int outputType){ try { HaploData theData; File OutputFile; File inputFile = new File(hapsFile); if(!inputFile.exists()){ System.out.println("haps input file " + hapsFile + " does not exist"); ...

1,112,158

public static void main(String[] args) {//throws IOException{ try { UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); } catch (Exception e) { } //setup view object HaploView window = new HaploView(); window.setTitle("HaploView beta"); window.se...

1,112,159

public static void main(String[] args) {//throws IOException{ try { UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); } catch (Exception e) { } //setup view object HaploView window = new HaploView(); window.setTitle("HaploView beta"); window.se...

1,112,160

public static void main(String[] args) {//throws IOException{ try { UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); } catch (Exception e) { } //setup view object HaploView window = new HaploView(); window.setTitle("HaploView beta"); window.se...

1,112,161

public synchronized String addTicket(String personalId) { HttpSession session = IWContext.getInstance().getSession(); String sessionId = session.getId(); if (!this.sessionIdSession.containsKey(sessionId)) { this.sessionIdSession.put(sessionId, session); } return getTicket(personalId, sessionId); }

1,112,162

public synchronized String addTicket(String personalId) { HttpSession session = IWContext.getInstance().getSession(); String sessionId = session.getId(); if (!this.sessionIdSession.containsKey(sessionId)) { this.sessionIdSession.put(sessionId, session); } return getTicket(personalId, sessionId); }

public synchronized String addTicket(String personalId) { HttpSession session = IWContext.getInstance().getSession(); String sessionId = session.getId(); if (!this.sessionIdSession.containsKey(sessionId)) { this.sessionIdSession.put(sessionId, session); } return getTicket(sessionId); }

1,112,163

private String getTicket(String personalId, String sessionId) { int length = personalId.length(); StringBuffer token = new StringBuffer(); token.append(length); token.append(SEPARATOR); token.append(personalId); token.append(sessionId); return token.toString(); }

1,112,164

public boolean isValid(String ticket) { return (validate(ticket) != null); }

1,112,165

public String validate(String ticket) { int index = ticket.indexOf(SEPARATOR); if (index < 1) { return null; } String personalId = null; String sessionId = null; try { int lengthOfPersonalId = Integer.parseInt(ticket.substring(0, index)); if (lengthOfPersonalId < 1) { return null; } int startIndexS...

1,112,166

public Object execute(String serviceMethod, Vector parameters) throws Exception { try { int index = serviceMethod.indexOf(ServiceProxy.CLASS_METHOD_DELIMITER); final String className = serviceMethod.substring(0, index); final String methodName = serviceMethod.subst...

1,112,167

private static Object[] toObjectArray(Vector parameters, Class[] parameterTypes){ Object[] args = new Object[parameterTypes.length]; for(int i=0; i<parameterTypes.length; i++){ if(i == 0){ /* first argument must always be ServiceContex...

1,112,168

protected String evaluteScriptAsText(String fileName) throws Exception { JellyContext context = new JellyContext(); // allow scripts to refer to any resource inside this project // using an absolute URI like /src/test/org/apache/foo.xml context.setRootURL(new File(".").toURL()); /...

1,112,170

public void testDoctype() throws Exception { String text = evaluteScriptAsText(testBaseDir + "/testDoctype.jelly"); assertEquals("Produces the correct output", "<!DOCTYPE foo PUBLIC \"publicID\" \"foo.dtd\">\n<foo></foo>", text); }

public void testDoctype() throws Exception { String text = evaluteScriptAsText(testBaseDir + "/testDoctype.jelly"); assertEquals("Should produce the correct output", "<!DOCTYPE foo PUBLIC \"publicID\" \"foo.dtd\">\n<foo></foo>", text); }

1,112,171

public void testParse() throws Exception { InputStream in = new FileInputStream(testBaseDir + "/example.jelly"); XMLParser parser = new XMLParser(); Script script = parser.parse(in); script = script.compile(); log.debug("Found: " + script); assertTrue("Parsed a Script", scr...

1,112,172

public void testTransform() throws Exception { String text = evaluteScriptAsText(testBaseDir + "/transformExample.jelly"); assertEquals("Produces the correct output", "It works!", text); }

public void testTransform() throws Exception { String text = evaluteScriptAsText(testBaseDir + "/transformExample.jelly"); assertEquals("Should produce the correct output", "It works!", text); }

1,112,173

public void testTransformAllInLine() throws Exception { String text = evaluteScriptAsText(testBaseDir + "/transformExampleAllInLine.jelly"); assertEquals("Produces the correct output", "It works!", text); }

public void testTransformAllInLine() throws Exception { String text = evaluteScriptAsText(testBaseDir + "/transformExampleAllInLine.jelly"); assertEquals("Should produce the correct output", "It works!", text); }

1,112,174

public void testTransformParams() throws Exception { String text = evaluteScriptAsText(testBaseDir + "/transformParamExample.jelly"); assertEquals("Produces the correct output", "It works!", text); }

public void testTransformParams() throws Exception { String text = evaluteScriptAsText(testBaseDir + "/transformParamExample.jelly"); assertEquals("Should produce the correct output", "It works!", text); }

1,112,175

public void testTransformParamsInLine() throws Exception { String text = evaluteScriptAsText(testBaseDir + "/transformParamExample2.jelly"); assertEquals("Produces the correct output", "It works!", text); }

public void testTransformParamsInLine() throws Exception { String text = evaluteScriptAsText(testBaseDir + "/transformParamExample2.jelly"); assertEquals("Should produce the correct output", "It works!", text); }

1,112,176

public void testTransformSAXOutput() throws Exception { String text = evaluteScriptAsText(testBaseDir + "/transformExampleSAXOutput.jelly"); assertEquals("Produces the correct output", "It works!", text); }

public void testTransformSAXOutput() throws Exception { String text = evaluteScriptAsText(testBaseDir + "/transformExampleSAXOutput.jelly"); assertEquals("Should produce the correct output", "It works!", text); }

1,112,177

public void testTransformSAXOutputNestedTransforms() throws Exception { String text = evaluteScriptAsText(testBaseDir + "/transformExampleSAXOutputNestedTransforms.jelly"); assertEquals("Produces the correct output", "It works!", text); }

public void testTransformSAXOutputNestedTransforms() throws Exception { String text = evaluteScriptAsText(testBaseDir + "/transformExampleSAXOutputNestedTransforms.jelly"); assertEquals("Should produce the correct output", "It works!", text); }

1,112,178

public void testTransformSchematron() throws Exception { String text = evaluteScriptAsText(testBaseDir + "/schematron/transformSchematronExample.jelly"); assertEquals("Produces the correct output", "Report count=1:assert count=2", text); }

public void testTransformSchematron() throws Exception { String text = evaluteScriptAsText(testBaseDir + "/schematron/transformSchematronExample.jelly"); assertEquals("Should produce the correct output", "Report count=1:assert count=2", text); }

1,112,179

public void testTransformXmlVar() throws Exception { String text = evaluteScriptAsText(testBaseDir + "/transformExampleXmlVar.jelly"); assertEquals("Produces the correct output", "It works!", text); }

public void testTransformXmlVar() throws Exception { String text = evaluteScriptAsText(testBaseDir + "/transformExampleXmlVar.jelly"); assertEquals("Should produce the correct output", "It works!", text); }

1,112,180

public void testSourceDropDownsWithOnlyCatalog() { ArchitectDataSource ds = new ArchitectDataSource(); ds.setDisplayName("Schemaless Database"); ds.setDriverClass("regress.ca.sqlpower.architect.MockJDBCDriver"); ds.setUser("fake"); ds.setPass("fake"); //this creates a mock jdbc database with only catalogs ds.se...

1,112,181

public void testSourceDropDownsWithSchemaAndCatalog() { ArchitectDataSource ds = new ArchitectDataSource(); ds.setDisplayName("Schemaless Database"); ds.setDriverClass("regress.ca.sqlpower.architect.MockJDBCDriver"); ds.setUser("fake"); ds.setPass("fake"); //this creates a mock jdbc database with catalogs and sc...

1,112,182

public Context newContext(Map newVariables) { // XXXX: should allow this new context to // XXXX: inherit parent contexts? // XXXX: Or at least publish the parent scope // XXXX: as a Map in this new variable scope? newVariables.put( "parentScope", variables ); Context answe...

1,112,184

public void stateChanged(ChangeEvent e) { int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ exportMenuItems[0].setEnabled(true); exportMenuItems[1].setEnabled(true); }else if (tabNum == VIEW_TDT_NUM || tabNum...

1,112,185

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

1,112,186

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

1,112,187

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

1,112,188

public static void main(String[] args) { boolean nogui = false; //HaploView window; for(int i = 0;i<args.length;i++) { if(args[i].equals("-n") || args[i].equals("-h")) { nogui = true; } } if(nogui) { HaploText textOnly = new HaploTex...

1,112,190

void processData(final String[][] hminfo) { if (inputOptions[2].equals("")){ inputOptions[2] = "0"; } maxCompDist = Long.parseLong(inputOptions[2])*1000; this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); final SwingWorker worker = new SwingWorker(){ ...

1,112,191

public Object construct(){ dPrimeDisplay=null; theData.infoKnown = false; if (!(inputOptions[1].equals(""))){ readMarkers(new File(inputOptions[1]), null); } if (hminfo != null){ readMarkers(null...

1,112,192

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

1,112,193

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

1,112,194

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

1,112,195

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

1,112,196

public static void main( String args[] ) { JFrame frame = new JFrame( "PhotoInfoEditorTest" ); PhotoView view = new PhotoView(); frame.getContentPane().add( view, BorderLayout.CENTER ); frame.addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent e) { System.exit(0); } } ); File f ...

1,112,197

public static void main( String args[] ) { JFrame frame = new JFrame( "PhotoInfoEditorTest" ); PhotoView view = new PhotoView(); frame.getContentPane().add( view, BorderLayout.CENTER ); frame.addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent e) { System.exit(0); } } ); File f ...

1,112,198

public Tag createTag() throws Exception;

public Tag createTag(String name, Attributes attributes) throws Exception;

1,112,199

public Vector readBlocks(File infile) throws HaploViewException, IOException{ if (!infile.exists()){ throw new HaploViewException("File " + infile.getName() + " doesn't exist!"); } Vector cust = new Vector(); BufferedReader in = new BufferedReader(new FileReader(infile)); ...

1,112,200

public Vector readBlocks(File infile) throws HaploViewException, IOException{ if (!infile.exists()){ throw new HaploViewException("File " + infile.getName() + " doesn't exist!"); } Vector cust = new Vector(); BufferedReader in = new BufferedReader(new FileReader(infile)); ...

1,112,201

public Vector readBlocks(File infile) throws HaploViewException, IOException{ if (!infile.exists()){ throw new HaploViewException("File " + infile.getName() + " doesn't exist!"); } Vector cust = new Vector(); BufferedReader in = new BufferedReader(new FileReader(infile)); ...

1,112,202

public void testReadFromDB() throws Exception { Connection con = db.getConnection(); Statement stmt = null; String lastSQL = null; try { stmt = con.createStatement(); try { stmt.executeUpdate("DROP TABLE relationship_test_child"); } catch (SQLException ex) { System.out.println("Ignoring SQL Exception; ...

1,112,203

public void testReadFromDB() throws Exception { Connection con = db.getConnection(); Statement stmt = null; String lastSQL = null; try { stmt = con.createStatement(); try { stmt.executeUpdate("DROP TABLE relationship_test_child"); } catch (SQLException ex) { System.out.println("Ignoring SQL Exception; ...

1,112,204

public Expression createExpression(final String text) throws Exception { final Expression jexlExpression = new JexlExpression( org.apache.commons.jexl.ExpressionFactory.createExpression(text) ); if ( isSupportAntVariables() && isValidAntVariableName(text) ) { Expre...

1,112,205

public Expression createExpression(final String text) throws Exception { final Expression jexlExpression = new JexlExpression( org.apache.commons.jexl.ExpressionFactory.createExpression(text) ); if ( isSupportAntVariables() && isValidAntVariableName(text) ) { Expre...

1,112,206

public Object evaluate(JellyContext context) { Object answer = jexlExpression.evaluate(context); if ( answer == null ) { answer = context.getScopedVariable(text); } return answer; }

1,112,207

public Object evaluate(JellyContext context) { Object answer = jexlExpression.evaluate(context); if ( answer == null ) { answer = context.getScopedVariable(text); } return answer; }

1,112,208

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( (Strin...

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

1,112,209

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 ) { ...

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

1,112,210

public String evaluateAsString(JellyContext context) { Object value = evaluate(context); if ( value != null ) { return value.toString(); } return null; }

public String evaluateAsString(JellyContext context) { Object value = evaluateAsValue(context); if ( value != null ) { return value.toString(); } return null; }

1,112,211

public HaplotypeDisplayController(HaplotypeDisplay parent) { this.parent = parent; setLayout(new BoxLayout(this, BoxLayout.Y_AXIS)); JPanel hapPercentPanel = new JPanel(); hapPercentPanel.add(new JLabel("Examine haplotypes above ")); hapPercentPanel.add(minDisplayField = new NumberTextField(String.va...

1,112,215

public HaplotypeDisplayController(HaplotypeDisplay parent) { this.parent = parent; setLayout(new BoxLayout(this, BoxLayout.Y_AXIS)); JPanel hapPercentPanel = new JPanel(); hapPercentPanel.add(new JLabel("Examine haplotypes above ")); hapPercentPanel.add(minDisplayField = new NumberTextField(String.va...

1,112,216

public HaplotypeDisplayController(HaplotypeDisplay parent) { this.parent = parent; setLayout(new BoxLayout(this, BoxLayout.Y_AXIS)); JPanel hapPercentPanel = new JPanel(); hapPercentPanel.add(new JLabel("Examine haplotypes above ")); hapPercentPanel.add(minDisplayField = new NumberTextField(String.va...

1,112,217

public HaplotypeDisplayController(HaplotypeDisplay parent) { this.parent = parent; setLayout(new BoxLayout(this, BoxLayout.Y_AXIS)); JPanel hapPercentPanel = new JPanel(); hapPercentPanel.add(new JLabel("Examine haplotypes above ")); hapPercentPanel.add(minDisplayField = new NumberTextField(String.va...

1,112,218

public void actionPerformed(ActionEvent evt) { SQLTable t = new SQLTable(); try { t.initFolders(true); } catch (ArchitectException e) { logger.error("Couldn't add folder to table \""+t.getName()+"\"", e); JOptionPane.showMessageDialog(null, "Failed to add folder to table:\n"+e.getMessage()); } t.setName("Ne...

1,112,221

public String draw(DashboardContext context) { ApplicationConfig appConfig = context.getWebContext().getApplicationConfig(); assert appConfig != null: "No application context present"; try{ StringBuffer graphComponent = new StringBuffer().append( "<applet code=\"org/jmanag...

1,112,222

EM(Vector chromosomes, int numTrios){ //we need to add extra copies of haploid chromosomes so we add a second copy this.chromosomes = new Vector(); for(int i=0;i<chromosomes.size();i++) { this.chromosomes.add(chromosomes.elementAt(i)); if(((Chromosome)this.chromosomes.last...

EM(Vector chromosomes, int numTrios, Vector extraInds){ //we need to add extra copies of haploid chromosomes so we add a second copy this.chromosomes = new Vector(); for(int i=0;i<chromosomes.size();i++) { this.chromosomes.add(chromosomes.elementAt(i)); if(((Chromosome)thi...

1,112,223

EM(Vector chromosomes, int numTrios){ //we need to add extra copies of haploid chromosomes so we add a second copy this.chromosomes = new Vector(); for(int i=0;i<chromosomes.size();i++) { this.chromosomes.add(chromosomes.elementAt(i)); if(((Chromosome)this.chromosomes.last...

1,112,224

public void doEM(int[] theBlock) throws HaploViewException{ //break up large blocks if needed int[] block_size; if (theBlock.length < 9){ block_size = new int[1]; block_size[0] = theBlock.length; } else { //some base-8 arithmetic int ones = the...

1,112,226

public void doEM(int[] theBlock) throws HaploViewException{ //break up large blocks if needed int[] block_size; if (theBlock.length < 9){ block_size = new int[1]; block_size[0] = theBlock.length; } else { //some base-8 arithmetic int ones = the...

1,112,227

private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus, Vector kidAffStatus) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_blocks = block_size.len...

1,112,228

private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus, Vector kidAffStatus) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_blocks = block_size.len...

1,112,229

private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus, Vector kidAffStatus) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_blocks = block_size.len...

1,112,230

private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus, Vector kidAffStatus) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_blocks = block_size.len...

1,112,231

public void saveHapsToText(Haplotype[][] finishedHaplos, File saveHapsFile) throws IOException{ NumberFormat nf = NumberFormat.getInstance(); nf.setMinimumFractionDigits(3); nf.setMaximumFractionDigits(3); //open file for saving haps text FileWriter saveHapsWriter = new FileWriter(saveHapsFile); int[][]lookupPos ...

1,112,232

public Object evaluate(JellyContext context) { try { JexlContext jexlContext = new JellyJexlContext( context ); if (log.isDebugEnabled()) { log.debug("Evaluating EL: " + expression); } Object value = expression.evaluate(jexlContext); ...

public Object evaluate(JellyContext context) { try { JexlContext jexlContext = new JellyJexlContext( context ); if (log.isDebugEnabled()) { log.debug("Evaluating EL: " + expression.getExpression()); } Object value = expression.evaluate(jex...

1,112,238

public PairwiseLinkage computeDPrime(int pos1, int pos2){ compsDone++; int doublehet = 0; int[][] twoMarkerHaplos = new int[3][3]; for (int i = 0; i < twoMarkerHaplos.length; i++){ for (int j = 0; j < twoMarkerHaplos[i].length; j++){ twoMarkerHaplos[i][j] = 0; ...

1,112,239

public PairwiseLinkage computeDPrime(int pos1, int pos2){ compsDone++; int doublehet = 0; int[][] twoMarkerHaplos = new int[3][3]; for (int i = 0; i < twoMarkerHaplos.length; i++){ for (int j = 0; j < twoMarkerHaplos[i].length; j++){ twoMarkerHaplos[i][j] = 0; ...

1,112,240

public Object evaluate(Context context) { return value; }

public Object evaluate(JellyContext context) { return value; }

1,112,241

public static Volume getVolume( String volName ) { Volume vol = null; if ( volumes != null ) { vol = (Volume) volumes.get( volName ); } return vol; }

1,112,242

public Tag getTag() throws Exception { Tag tag = (Tag) tagHolder.get(); if ( tag == null ) { tag = createTag(); if ( tag != null ) { configureTag(tag); tagHolder.set(tag); } } return tag; }

public Tag getTag() throws Exception { Tag tag = (Tag) tagHolder.get(); if ( tag == null ) { tag = createTag(); if ( tag != null ) { tagHolder.set(tag); } } return tag; }

1,112,244

public TableCellRenderer getCellRenderer(int row, int column) { ProfileColumn pc = ProfileColumn.values()[column]; switch(pc) { case DATABASE: case SCHEMA: case CATALOG: case TABLE: case COLUMN: return new SQLObjectRendererFactory(); case RUNDATE: return new DateRen...

public TableCellRenderer getCellRenderer(int row, int column) { int modelColumn = convertColumnIndexToModel(column); ProfileColumn pc = ProfileColumn.values()[modelColumn]; switch(pc) { case DATABASE: case SCHEMA: case CATALOG: case TABLE: case COLUMN: return new SQLObjectRendererFac...

1,112,246

void browse(int browseType){ String name; String markerInfoName = ""; HaploView h = (HaploView) this.getParent(); h.fc.setSelectedFile(new File("")); int returned = h.fc.showOpenDialog(this); if (returned != JFileChooser.APPROVE_OPTION) return; File file = h.fc.getSe...

1,112,247

public void run(Context context, XMLOutput output) throws Exception { // #### note this mechanism does not work properly for arbitrarily // #### nested dynamic tags. A better way is required. Tag tag = findAncestorWithClass(this, DynamicTag.class); if ( tag == null ) { ...

1,112,248

public void run(Context context, XMLOutput output) throws Exception { // #### note this mechanism does not work properly for arbitrarily // #### nested dynamic tags. A better way is required. Tag tag = findAncestorWithClass(this, DynamicTag.class); if ( tag == null ) { ...

1,112,249