JoaoJunior/formatted-java-preprocessed-code-APR

public DBCSPanel() { setLayout(new BorderLayout()); dbDriverField = new JComboBox(getDriverClasses()); dbDriverField.insertItemAt("", 0); dbNameField = new JTextField(); JComponent[] fields = new JComponent[] {dbNameField, dbDriverField, dbUrlField = new JTextField(), dbUserField ...

public DBCSPanel() { setLayout(new BorderLayout()); dbDriverField = new JComboBox(getDriverClasses()); dbDriverField.insertItemAt("", 0); dbNameField = new JTextField(); JComponent[] fields = new JComponent[] {historyBox, dbNameField, dbDriverField, dbUrlField = new JTextField(), ...

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public DBCSPanel() { setLayout(new BorderLayout()); dbDriverField = new JComboBox(getDriverClasses()); dbDriverField.insertItemAt("", 0); dbNameField = new JTextField(); JComponent[] fields = new JComponent[] {dbNameField, dbDriverField, dbUrlField = new JTextField(), dbUserField ...

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public DBCSPanel() { setLayout(new BorderLayout()); dbDriverField = new JComboBox(getDriverClasses()); dbDriverField.insertItemAt("", 0); dbNameField = new JTextField(); JComponent[] fields = new JComponent[] {dbNameField, dbDriverField, dbUrlField = new JTextField(), dbUserField ...

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public void full_em_breakup( byte[][] input_haplos, int max_missing, int[] num_haplos_present, Vector haplos_present, Vector haplo_freq, int[] block_size, int dump_phased_haplos) throws HaploViewException{ int i, j, k, num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_lo...

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public void full_em_breakup( byte[][] input_haplos, int max_missing, int[] num_haplos_present, Vector haplos_present, Vector haplo_freq, int[] block_size, int dump_phased_haplos) throws HaploViewException{ int i, j, k, num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_lo...

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Vector doSFS(){ float cutHighCI = 0.98f; float cutLowCI = 0.70f; float recHighCI = 0.90f; int numStrong = 0; int numRec = 0; int numInGroup = 0; Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first make a list of marker pairs in "strong LD", sorted by distance apart for (int x = 0; x < dPrime....

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Vector doSFS(){ float cutHighCI = 0.98f; float cutLowCI = 0.70f; float recHighCI = 0.90f; int numStrong = 0; int numRec = 0; int numInGroup = 0; Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first make a list of marker pairs in "strong LD", sorted by distance apart for (int x = 0; x < dPrime....

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Vector doSFS(){ float cutHighCI = 0.98f; float cutLowCI = 0.70f; float recHighCI = 0.90f; int numStrong = 0; int numRec = 0; int numInGroup = 0; Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first make a list of marker pairs in "strong LD", sorted by distance apart for (int x = 0; x < dPrime....

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Vector doMJD(){ // find blocks by searching for stretches between two markers A,B where // D prime is > 0.8 for all informative combinations of A, (A+1...B) int baddies; int verticalExtent=0; int horizontalExtent=0; Vector blocks = new Vector(); for (int i = 0; i < dPrime.length; i++){ baddies=0; //find ho...

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Vector doMJD(){ // find blocks by searching for stretches between two markers A,B where // D prime is > 0.8 for all informative combinations of A, (A+1...B) int baddies; int verticalExtent=0; int horizontalExtent=0; Vector blocks = new Vector(); for (int i = 0; i < dPrime.length; i++){ baddies=0; //find ho...

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Vector doMJD(){ // find blocks by searching for stretches between two markers A,B where // D prime is > 0.8 for all informative combinations of A, (A+1...B) int baddies; int verticalExtent=0; int horizontalExtent=0; Vector blocks = new Vector(); for (int i = 0; i < dPrime.length; i++){ baddies=0; //find ho...

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Chromosome(String p, String i, byte[] g, boolean isTransmitted){ ped = p; individual = i; genotypes = g; origin = "unknown"; trueSize = genotypes.length; transmitted = isTransmitted; }

Chromosome(String p, String i, byte[] g, boolean a, String o){ ped = p; individual = i; genotypes = g; origin = "unknown"; trueSize = genotypes.length; transmitted = isTransmitted; }

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Chromosome(String p, String i, byte[] g, boolean isTransmitted){ ped = p; individual = i; genotypes = g; origin = "unknown"; trueSize = genotypes.length; transmitted = isTransmitted; }

Chromosome(String p, String i, byte[] g, boolean isTransmitted){ ped = p; individual = i; genotypes = g; affected = a; origin = o; trueSize = genotypes.length; transmitted = isTransmitted; }

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Chromosome(String p, String i, byte[] g, boolean isTransmitted){ ped = p; individual = i; genotypes = g; origin = "unknown"; trueSize = genotypes.length; transmitted = isTransmitted; }

Chromosome(String p, String i, byte[] g, boolean isTransmitted){ ped = p; individual = i; genotypes = g; origin = "unknown"; trueSize = genotypes.length; }

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public void mouseReleased(MouseEvent evt) { maybeShowPopup(evt); // table/column selection if ((evt.getModifiers() & MouseEvent.BUTTON1_MASK) != 0) { TablePane tp = (TablePane) evt.getComponent(); PlayPen pp = (PlayPen) tp.getParent(); try { pp.selectNone(); tp.setSelected(true); tp.selectN...

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public void actionPerformed(ActionEvent evt) { List selection = pp.getSelectedItems(); if (selection.size() < 1) { JOptionPane.showMessageDialog(pp, "Select a table (by clicking on it) and try again."); } else if (selection.size() > 1) { JOptionPane.showMessageDialog(pp, "You have selected multiple items, but y...

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public void actionPerformed(ActionEvent evt) { List selection = pp.getSelectedItems(); if (selection.size() < 1) { JOptionPane.showMessageDialog(pp, "Select a table (by clicking on it) and try again."); } else if (selection.size() > 1) { JOptionPane.showMessageDialog(pp, "You have selected multiple items, but y...

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public void actionPerformed(ActionEvent evt) { List selection = pp.getSelectedItems(); if (selection.size() < 1) { JOptionPane.showMessageDialog(pp, "Select a table (by clicking on it) and try again."); } else if (selection.size() > 1) { JOptionPane.showMessageDialog(pp, "You have selected multiple items, but y...

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public void actionPerformed(ActionEvent evt) { List selection = pp.getSelectedItems(); if (selection.size() < 1) { JOptionPane.showMessageDialog(pp, "Select a table (by clicking on it) and try again."); } else if (selection.size() > 1) { JOptionPane.showMessageDialog(pp, "You have selected multiple items, but y...

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public void actionPerformed(ActionEvent evt) { List selection = pp.getSelectedItems(); if (selection.size() < 1) { JOptionPane.showMessageDialog(pp, "Select a table (by clicking on it) and try again."); } else if (selection.size() > 1) { JOptionPane.showMessageDialog(pp, "You have selected multiple items, but y...

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public void actionPerformed(ActionEvent evt) { List selection = pp.getSelectedItems(); if (selection.size() < 1) { JOptionPane.showMessageDialog(pp, "Select a column (by clicking on it) and try again."); } else if (selection.size() > 1) { JOptionPane.showMessageDialog(pp, "You have selected multiple items, but ...

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public void actionPerformed(ActionEvent evt) { List selection = pp.getSelectedItems(); if (selection.size() < 1) { JOptionPane.showMessageDialog(pp, "Select a column (by clicking on it) and try again."); } else if (selection.size() > 1) { JOptionPane.showMessageDialog(pp, "You have selected multiple items, but ...

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public void actionPerformed(ActionEvent evt) { List selection = pp.getSelectedItems(); if (selection.size() < 1) { JOptionPane.showMessageDialog(pp, "Select a column (by clicking on it) and try again."); } else if (selection.size() > 1) { JOptionPane.showMessageDialog(pp, "You have selected multiple items, but ...

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public void inherit(int pos, SQLTable source) throws ArchitectException { SQLColumn c; boolean addToPK; int pkSize = pkSize(); int sourceSize = source.columnsFolder.children.size(); int originalSize = columnsFolder.children.size(); if (originalSize == 0 || pos < pkSize) { addToPK = true; normalizePrimaryKey(...

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public void removeColumn(SQLColumn col) throws LockedColumnException {// List keys = keysOfColumn(col);// if (keys.isEmpty()) {// columnsFolder.removeChild(col);// normalizePrimaryKey();// } else {// throw new LockedColumnException("This column can't be removed because it belongs to the "+keys.get(0)+" ...

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public static PhotoInfo create() { PhotoInfo photo = new PhotoInfo(); ODMGXAWrapper txw = new ODMGXAWrapper(); Database db = ODMG.getODMGDatabase(); // db.makePersistent( photo ); txw.lock( photo, Transaction.WRITE ); txw.commit(); return photo; }

public static PhotoInfo create() { PhotoInfo photo = new PhotoInfo(); ODMGXAWrapper txw = new ODMGXAWrapper(); // db.makePersistent( photo ); txw.lock( photo, Transaction.WRITE ); txw.commit(); return photo; }

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public void delete() { Implementation odmg = ODMG.getODMGImplementation(); Database db = ODMG.getODMGDatabase(); ODMGXAWrapper txw = new ODMGXAWrapper(); // First delete all instances for ( int i = 0; i < instances.size(); i++ ) { ImageInstance f = (ImageInstanc...

public void delete() { ODMGXAWrapper txw = new ODMGXAWrapper(); Database db = ODMG.getODMGDatabase(); ODMGXAWrapper txw = new ODMGXAWrapper(); // First delete all instances for ( int i = 0; i < instances.size(); i++ ) { ImageInstance f = (ImageInstance) instance...

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public void delete() { Implementation odmg = ODMG.getODMGImplementation(); Database db = ODMG.getODMGDatabase(); ODMGXAWrapper txw = new ODMGXAWrapper(); // First delete all instances for ( int i = 0; i < instances.size(); i++ ) { ImageInstance f = (ImageInstanc...

public void delete() { Implementation odmg = ODMG.getODMGImplementation(); Database db = ODMG.getODMGDatabase(); // First delete all instances for ( int i = 0; i < instances.size(); i++ ) { ImageInstance f = (ImageInstance) instances.get( i ); f.dele...

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public boolean equals( Object obj ) { if ( obj.getClass() != this.getClass() ) { return false; } PhotoInfo p = (PhotoInfo)obj; ODMGXAWrapper txw = new ODMGXAWrapper(); txw.lock( this, Transaction.READ ); txw.lock( p, Transaction.READ ); txw.commit(); ...

public boolean equals( Object obj ) { if ( obj == null || obj.getClass() != this.getClass() ) { return false; } PhotoInfo p = (PhotoInfo)obj; ODMGXAWrapper txw = new ODMGXAWrapper(); txw.lock( this, Transaction.READ ); txw.lock( p, Transaction.READ ); txw....

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public final java.util.Date getLastModified() { return lastModified; }

public final java.util.Date getLastModified() { return lastModified != null ? (java.util.Date) lastModified.clone() : null; }

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public java.util.Date getShootTime() { ODMGXAWrapper txw = new ODMGXAWrapper(); txw.lock( this, Transaction.READ ); txw.commit(); return shootTime; }

public java.util.Date getShootTime() { ODMGXAWrapper txw = new ODMGXAWrapper(); txw.lock( this, Transaction.READ ); txw.commit(); return shootTime != null ? (java.util.Date) shootTime.clone() : null; }

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public void setLastModified(final java.util.Date newDate) { ODMGXAWrapper txw = new ODMGXAWrapper(); txw.lock( this, Transaction.WRITE ); this.lastModified = newDate; modified(); txw.commit(); }

public void setLastModified(final java.util.Date newDate) { ODMGXAWrapper txw = new ODMGXAWrapper(); txw.lock( this, Transaction.WRITE ); this.lastModified = (newDate != null) ? (java.util.Date) newDate.clone() : null; modified(); txw.commit(); }

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public void setShootTime(java.util.Date v) { ODMGXAWrapper txw = new ODMGXAWrapper(); txw.lock( this, Transaction.WRITE ); this.shootTime = v; modified(); txw.commit(); }

public void setShootTime(java.util.Date v) { ODMGXAWrapper txw = new ODMGXAWrapper(); txw.lock( this, Transaction.WRITE ); this.shootTime = (v != null) ? (java.util.Date) v.clone() : null; modified(); txw.commit(); }

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public static ImageInstance create( VolumeBase volume, File imageFile, PhotoInfo photo ) { log.debug( "Creating instance, volume = " + volume.getName() + " photo = " + photo.getUid() + " image file = " + imageFile.getName() ); // Initialize transaction context ODMGXAWrapper txw = new ODMGXAWrapper(); ImageInst...

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public static ImageInstance create( VolumeBase volume, File imageFile, PhotoInfo photo ) { log.debug( "Creating instance, volume = " + volume.getName() + " photo = " + photo.getUid() + " image file = " + imageFile.getName() ); // Initialize transaction context ODMGXAWrapper txw = new ODMGXAWrapper(); ImageInst...

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public static ImageInstance create( VolumeBase volume, File imageFile, PhotoInfo photo ) { log.debug( "Creating instance, volume = " + volume.getName() + " photo = " + photo.getUid() + " image file = " + imageFile.getName() ); // Initialize transaction context ODMGXAWrapper txw = new ODMGXAWrapper(); ImageInst...

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public static ImageInstance create( VolumeBase volume, File imageFile, PhotoInfo photo ) { log.debug( "Creating instance, volume = " + volume.getName() + " photo = " + photo.getUid() + " image file = " + imageFile.getName() ); // Initialize transaction context ODMGXAWrapper txw = new ODMGXAWrapper(); ImageInst...

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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") || args[i].equals("-help")) { nogui = true; } } if(nogui) { HaploT...

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

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public Cell(GridBagConstraints constraints, Component component) { this.constraints = constraints; this.component = component; }

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public void setTask(Task task) { this.task = task; setDynaBean( new WrapDynaBean(task) ); }

public void setTask(Task task) { this.task = task; setDynaBean( new ConvertingWrapDynaBean(task) ); }

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public Iterator evaluateAsIterator(Context context);

public Iterator evaluateAsIterator(JellyContext context);

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public BSFExpression(String text, BSFEngine engine, BSFManager manager, ContextRegistry registry) { this.text = text; this.engine = engine; this.manager = manager; this.registry = registry; }

public BSFExpression(String text, BSFEngine engine, BSFManager manager, JellyContextRegistry registry) { this.text = text; this.engine = engine; this.manager = manager; this.registry = registry; }

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public void createToolTip() { if (e.getChildren() != null) { if (e.getChildren()[0] instanceof SQLTable) { toolTip = "Add table"; } if (e.getChildren()[0] instanceof SQLColumn) { toolTip = "Add column"; } if (e.getChildren()[0] instanceof SQLRelationship) { toolTip = "Add relation"; } if...

public void createToolTip() { if (e.getChildren().length > 0) { if (e.getChildren()[0] instanceof SQLTable) { toolTip = "Add table"; } if (e.getChildren()[0] instanceof SQLColumn) { toolTip = "Add column"; } if (e.getChildren()[0] instanceof SQLRelationship) { toolTip = "Add relation"; } ...

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public JVMResourceSampler(String host, int port, PostageRunnerResult results) { Class workerClass; Constructor constructor; try { // the class is only present, when the package _was compiled_ with at least Java 5 (see build script) workerClass = Class.forName("org.apache.j...

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public JVMResourceSampler(String host, int port, PostageRunnerResult results) { Class workerClass; Constructor constructor; try { // the class is only present, when the package _was compiled_ with at least Java 5 (see build script) workerClass = Class.forName("org.apache.j...

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public JVMResourceSampler(String host, int port, PostageRunnerResult results) { Class workerClass; Constructor constructor; try { // the class is only present, when the package _was compiled_ with at least Java 5 (see build script) workerClass = Class.forName("org.apache.j...

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public void connectRemoteJamesJMXServer() throws SamplingException { if(jvmResourceSampleWorker == null) throw new SamplingException("JSE specific features not present. (compile the project with JSE 5)"); try { m_connectMethod.invoke(jvmResourceSampleWorker, (Class)null); } catch (Ex...

public void connectRemoteJamesJMXServer() throws SamplingException { if(jvmResourceSampleWorker == null) throw new SamplingException("JSE specific features not present. (compile the project with JSE 5)"); try { m_connectMethod.invoke(jvmResourceSampleWorker, VOID_ARGUMENT_LIST); } ca...

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public void doSample() throws SamplingException { if(jvmResourceSampleWorker == null) throw new SamplingException("JSE specific features not present. (compile the project with JSE 5)"); try { m_doSampleMethod.invoke(jvmResourceSampleWorker, (Class)null); } catch (Exception e) { ...

public void doSample() throws SamplingException { if(jvmResourceSampleWorker == null) throw new SamplingException("JSE specific features not present. (compile the project with JSE 5)"); try { m_doSampleMethod.invoke(jvmResourceSampleWorker, VOID_ARGUMENT_LIST); } catch (Exception e) ...

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public void setModel(SQLTable newModel) { if (model != null) { model.removeSQLObjectListener(tableListModel); } model = newModel; tableListModel = new SQLTableListModel(model); model.addSQLObjectListener(tableListModel); try { for (int i = 0; i < model.getChildCount(); i++) { model.getChild(i).addSQLObjec...

public void setModel(SQLTable newModel) { if (model != null) { model.getColumnsFolder().removeSQLObjectListener(tableListModel); } model = newModel; tableListModel = new SQLTableListModel(model); model.addSQLObjectListener(tableListModel); try { for (int i = 0; i < model.getChildCount(); i++) { model.getC...

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public void setModel(SQLTable newModel) { if (model != null) { model.removeSQLObjectListener(tableListModel); } model = newModel; tableListModel = new SQLTableListModel(model); model.addSQLObjectListener(tableListModel); try { for (int i = 0; i < model.getChildCount(); i++) { model.getChild(i).addSQLObjec...

public void setModel(SQLTable newModel) { if (model != null) { model.removeSQLObjectListener(tableListModel); } model = newModel; tableListModel = new SQLTableListModel(model); model.getColumnsFolder().addSQLObjectListener(tableListModel); try { for (int i = 0; i < model.getChildCount(); i++) { model.getC...

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public void setModel(SQLTable newModel) { if (model != null) { model.removeSQLObjectListener(tableListModel); } model = newModel; tableListModel = new SQLTableListModel(model); model.addSQLObjectListener(tableListModel); try { for (int i = 0; i < model.getChildCount(); i++) { model.getChild(i).addSQLObjec...

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protected URL resolveURL(String name) throws MalformedURLException { File file = new File(name); if (file.exists()) { return file.toURL(); } return new URL(name); }

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protected URL resolveURL(String name) throws MalformedURLException { File file = new File(name); if (file.exists()) { return file.toURL(); } return new URL(name); }

protected URL resolveURL(String name) throws MalformedURLException { File file = new File(name); if (file.exists()) { return file.toURL(); } else { File file = new File(name); if (file.exists()) { return file.toURL(); } return new URL(name); } }

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public void invokeCommandLineJelly(String[] args) throws JellyException { CommandLine cmdLine = null; try { cmdLine = parseCommandLineOptions(args); } catch (ParseException e) { throw new JellyException(e); } // get the -script option. If there isn't one then...

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

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public void doTag(XMLOutput output) throws Exception { if ( var == null ) { var = "org.apache.commons.jelly.ojb.Broker"; } if ( broker != null ) { context.setVariable(var, broker); invokeBody(output); } else { ...

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public void doTag(XMLOutput output) throws Exception { if ( var == null ) { var = "org.apache.commons.jelly.ojb.Broker"; } if ( broker != null ) { context.setVariable(var, broker); invokeBody(output); } else { ...

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public void actionPerformed( ActionEvent e ) { System.exit( 0 ); }

public void actionPerformed( ActionEvent e ) { exportSelected(); }

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public void testSaveCoversAllDatabaseProperties() throws Exception { testLoad(); DBTree dbTree = project.getSourceDatabases(); DBTreeModel dbTreeModel = (DBTreeModel) dbTree.getModel(); ArchitectDataSource fakeDataSource = new ArchitectDataSource(); SQLDatabase db = new SQLDatabase() { @Override public Conn...

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public void setDisplayName(String argDisplayName){ put(PL_LOGICAL, argDisplayName); }

public void setDisplayName(String argDisplayName){ putImpl(PL_LOGICAL, argDisplayName, "displayName"); }

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public void setDriverClass(String argDriverClass){ put(DBCS_DRIVER_CLASS, argDriverClass); }

public void setDriverClass(String argDriverClass){ putImpl(DBCS_DRIVER_CLASS, argDriverClass, "driverClass"); }

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public void setUser(String argUser){ put(PL_UID, argUser); }

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public void setPass(String argPass){ put(PL_PWD, argPass); }

public void setPass(String argPass){ putImpl(PL_PWD, argPass, "pass"); }

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public void setUrl(String argUrl) { put(DBCS_URL, argUrl); }

public void setUrl(String argUrl) { putImpl(DBCS_URL, argUrl, "url"); }

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public SQLCatalog(SQLDatabase parent, String name) { this.parent = parent; setName(name); this.children = new LinkedList(); this.nativeTerm = "catalog"; }

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public void save(PrintWriter out, String encoding) throws IOException, ArchitectException { objectIdMap = new HashMap(); dbcsIdMap = new HashMap(); indent = 0; try { println(out, "<?xml version=\"1.0\" encoding=\""+encoding+"\"?>"); println(out, "<architect-...

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public void save(PrintWriter out, String encoding) throws IOException, ArchitectException { objectIdMap = new HashMap(); dbcsIdMap = new HashMap(); indent = 0; try { println(out, "<?xml version=\"1.0\" encoding=\""+encoding+"\"?>"); println(out, "<architect-...

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public static XMLOutput createXMLOutput(Writer writer) { return createXMLOutput(writer, DEFAULT_ESCAPE_TEXT); }

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public Volume( String volName, String volBaseDir ) { super( volName, volBaseDir ); }

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public void changeColumnIndex(int oldIdx, int newIdx) throws ArchitectException { // this old way didn't cause any events// SQLColumn col = (SQLColumn) columnsFolder.children.remove(oldIdx);// columnsFolder.children.add(newIdx, col);// if (newIdx == 0// || ((SQLColumn) columnsFolder.children.get(newIdx-1)).p...

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public SQLSchema(SQLObject parent, String name) { this.parent = parent; this.schemaName = name; this.children = new LinkedList(); this.nativeTerm = "schema"; }

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static void addColumnsToTable(SQLTable addTo, String catalog, String schema, String tableName) throws SQLException, DuplicateColumnException, ArchitectException { Connection con = null; ResultSet rs = null; try { con = addTo.getParentDatabase().getConnection(); DatabaseMetaData d...

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static void addColumnsToTable(SQLTable addTo, String catalog, String schema, String tableName) throws SQLException, DuplicateColumnException, ArchitectException { Connection con = null; ResultSet rs = null; try { con = addTo.getParentDatabase().getConnection(); DatabaseMetaData d...

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public boolean removeChild(SQLObject child) { int childIdx = children.indexOf(child); if (childIdx >= 0) { children.remove(childIdx); fireDbChildRemoved(childIdx, child); } return childIdx >= 0; }

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public LockedColumnException(SQLRelationship lockingRelationship) { super("Locked column belongs to relationship "+lockingRelationship); this.lockingRelationship = lockingRelationship; }

public LockedColumnException(SQLRelationship lockingRelationship, SQLColumn col) { super("Locked column belongs to relationship "+lockingRelationship); this.lockingRelationship = lockingRelationship; }

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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("xpath")) { ...

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("xpath")) {...

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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("xpath")) { ...

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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("xpath")) { ...

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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){ try { HaploData textData; File OutputFile; File inputFile; AssociationTestSet customAssocSet; if(!quietMode && fileName != null){ System.out.println("Using data ...

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public int compare( Object o1, Object o2 ) { PhotoInfo p1 = (PhotoInfo) o1; PhotoInfo p2 = (PhotoInfo) o2; String place1 = p1.getShootingPlace(); String place2 = p2.getShootingPlace(); if ( place1 == null ) { place1 = ""; } if ( place2 == null ) { ...

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private void createDatabase() { File dbDir = null; try { dbDir = File.createTempFile("pv_junit_derby_instance", ""); } catch (IOException ex) { ex.printStackTrace(); } dbDir.delete(); PVDatabase pvd = new PVDatabase(); pvd.setInstanceType( PVDat...

private void createDatabase() { File dbDir = null; try { dbDir = File.createTempFile("pv_junit_derby_instance", ""); } catch (IOException ex) { ex.printStackTrace(); } PVDatabase pvd = new PVDatabase(); pvd.setInstanceType( PVDatabase.TYPE_EMBE...

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public static void initODMG( String user, String passwd, PVDatabase dbDesc ) throws PhotovaultException { getODMGImplementation(); // Find the connection repository info ConnectionRepository cr = MetadataManager.getInstance().connectionRepository(); PBKey connKey = cr.getStandardPBKeyFor...

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public void upgradeDatabase() { fireStatusChangeEvent( new SchemaUpdateEvent( PHASE_ALTERING_SCHEMA, 0 ) ); int oldVersion = db.getSchemaVersion(); // Find needed information fr DdlUtils ConnectionRepository cr = MetadataManager.getInstance().connectionRepository(); ...

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public void addDatabase(PVDatabase db) { databases.addDatabase( db ); }

public void addDatabase(PVDatabase db) throws PhotovaultException { databases.addDatabase( db ); }

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

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

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

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public static void main(String[] args) throws Exception { if ( args.length <= 0 ) { System.out.println( "Usage: Jelly scriptFile [outputFile]" ); return; } String input = args[0]; /* // later we might wanna add some command line arguments // checking ...

public static void main(String[] args) throws Exception { if ( args.length <= 0 ) { System.out.println( "Usage: Jelly scriptFile [outputFile]" ); return; } Jelly jelly = new Jelly(); jelly.setScript( args[0] ); /* // later we might wanna add some command line...

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public static void main(String[] args) throws Exception { if ( args.length <= 0 ) { System.out.println( "Usage: Jelly scriptFile [outputFile]" ); return; } String input = args[0]; /* // later we might wanna add some command line arguments // checking ...

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public void testRetrievalSuccess() { String photoId = "02120108000000001"; try { PhotoInfo photo = PhotoInfo.retrievePhotoInfo( photoId ); assertTrue(photo != null ); } catch (PhotoNotFoundException e) { fail( "Photo " + photoId + " not found" ); } // TODO: check some other properties of the object }

public void testRetrievalSuccess() { int photoId = 1; try { PhotoInfo photo = PhotoInfo.retrievePhotoInfo( photoId ); assertTrue(photo != null ); } catch (PhotoNotFoundException e) { fail( "Photo " + photoId + " not found" ); } // TODO: check some other properties of the object }

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public static void main(String[] args) throws Exception{ Runtime.getRuntime().addShutdownHook(new Thread(){ public void run(){ logger.info("jManage shutting down..."); DBUtils.shutdownDB(); } }); if (System.getSecurityManager() == null) { ...

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public void start() { for (ApplicationConfig appConfig : ApplicationConfigManager .getAllApplications()) { addApplication(appConfig); } // TODO: perfect dependency to be injected via Spring framework --rk EventSystem eventSystem = EventSystem.getInstance...

public void start() { for (ApplicationConfig appConfig : ApplicationConfigManager .getAllApplications()) { if(!appConfig.isCluster()) addApplication(appConfig); } // TODO: perfect dependency to be injected via Spring framework --rk EventSystem eventSyste...

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public PermutationTestPanel(PermutationTestSet pts) { if(pts == null) { throw new NullPointerException(); } testSet = pts; this.setLayout(new BoxLayout(this,BoxLayout.Y_AXIS)); JPanel permCountPanel = new JPanel(); JPanel selectionPanel = new JPanel(); sel...

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public PermutationTestPanel(PermutationTestSet pts) { if(pts == null) { throw new NullPointerException(); } testSet = pts; this.setLayout(new BoxLayout(this,BoxLayout.Y_AXIS)); JPanel permCountPanel = new JPanel(); JPanel selectionPanel = new JPanel(); sel...

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public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); Object parentObject = findBeanAncestor(); Object parentTask = findParentTaskObject(); // lets assume that Task instances are not nested inside other Task instances ...

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public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); Object parentObject = findBeanAncestor(); Object parentTask = findParentTaskObject(); // lets assume that Task instances are not nested inside other Task instances ...

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public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); Object parentObject = findBeanAncestor(); Object parentTask = findParentTaskObject(); // lets assume that Task instances are not nested inside other Task instances ...

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public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); Object parentObject = findBeanAncestor(); Object parentTask = findParentTaskObject(); // lets assume that Task instances are not nested inside other Task instances ...

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public Project getAntProject() { return AntTagLibrary.getProject(context); }

public Project getAntProject() { Project project = AntTagLibrary.getProject(context); if (project == null) { throw new NullPointerException("No Ant Project object is available"); } return project; }

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