rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k |
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dPrimeDisplay = new DPrimeDisplay(theData.dPrimeTable, infoKnown, theData.markerInfo); | dPrimeDisplay = new DPrimeDisplay(theData.dPrimeTable, infoKnown); | void drawPicture(HaploData theData){ Container contents = getContentPane(); contents.removeAll(); //remember which tab we're in if they've already been set up int currentTabIndex = 0; if (!(tabs == null)){ currentTabIndex = tabs.getSelectedIndex(); } tabs ... |
window = new HaploView(); window.argHandler(args); | public static void main(String[] args) {//throws IOException{ boolean nogui = false; HaploView window; for(int i = 0;i<args.length;i++) { if(args[i].equals("-nogui") || args[i].equals("-n") ) { nogui = true; } } if(nogui) { window = ... | |
window = new HaploView(); window.argHandler(args); | public static void main(String[] args) {//throws IOException{ boolean nogui = false; HaploView window; for(int i = 0;i<args.length;i++) { if(args[i].equals("-nogui") || args[i].equals("-n") ) { nogui = true; } } if(nogui) { window = ... | |
dPrimeDisplay.loadMarkers(theData.markerInfo); | dPrimeDisplay.loadMarkers(); | void readMarkers(File inputFile){ try { int good = theData.prepareMarkerInput(inputFile); if (good == -1){ JOptionPane.showMessageDialog(this, "Number of markers in info file does not match number of markers in dataset.", "Err... |
new TextMethods().saveDprimeToText(theData.dPrimeTable, fc.getSelectedFile(), infoKnown, theData.markerInfo); | new TextMethods().saveDprimeToText(theData.dPrimeTable, fc.getSelectedFile(), infoKnown, new Vector()); | void saveDprimeToText(){ fc.setSelectedFile(null); try{ fc.setSelectedFile(null); int returnVal = fc.showSaveDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { new TextMethods().saveDprimeToText(theData.dPrimeTable, fc.getSelectedFile(), infoK... |
String databaseIdentifierQuoteString = null; | private void doColumnProfile(List<SQLColumn> columns, Connection conn) throws SQLException { Statement stmt = null; ResultSet rs = null; String lastSQL = null; try { if ( columns.size() == 0 ) return; SQLColumn col1 = columns.get(0); ... | |
sql.append(",\n AVG(\""); sql.append(col.getName()); sql.append("\") AS AVGVALUE_"+i); | sql.append(",\n "); sql.append(ddlg.getAverageSQLFunctionName("\""+col.getName()+"\"")); sql.append(" AS AVGVALUE_"+i); | private void doColumnProfile(List<SQLColumn> columns, Connection conn) throws SQLException { Statement stmt = null; ResultSet rs = null; String lastSQL = null; try { if ( columns.size() == 0 ) return; SQLColumn col1 = columns.get(0); ... |
sql.append(",\n MIN(LENGTH(\""); sql.append(col.getName()); sql.append("\")) AS MINLENGTH_"+i); | sql.append(",\n MIN("); sql.append(ddlg.getStringLengthSQLFunctionName("\""+col.getName()+"\"")); sql.append(") AS MINLENGTH_"+i); | private void doColumnProfile(List<SQLColumn> columns, Connection conn) throws SQLException { Statement stmt = null; ResultSet rs = null; String lastSQL = null; try { if ( columns.size() == 0 ) return; SQLColumn col1 = columns.get(0); ... |
sql.append(",\n MAX(LENGTH(\""); sql.append(col.getName()); sql.append("\")) AS MAXLENGTH_"+i); | sql.append(",\n MAX("); sql.append(ddlg.getStringLengthSQLFunctionName("\""+col.getName()+"\"")); sql.append(") AS MAXLENGTH_"+i); | private void doColumnProfile(List<SQLColumn> columns, Connection conn) throws SQLException { Statement stmt = null; ResultSet rs = null; String lastSQL = null; try { if ( columns.size() == 0 ) return; SQLColumn col1 = columns.get(0); ... |
sql.append(",\n AVG(LENGTH(\""); sql.append(col.getName()); sql.append("\")) AS AVGLENGTH_"+i); | sql.append(",\n AVG("); sql.append(ddlg.getStringLengthSQLFunctionName("\""+col.getName()+"\"")); sql.append(") AS AVGLENGTH_"+i); | private void doColumnProfile(List<SQLColumn> columns, Connection conn) throws SQLException { Statement stmt = null; ResultSet rs = null; String lastSQL = null; try { if ( columns.size() == 0 ) return; SQLColumn col1 = columns.get(0); ... |
sql.append("\n FROM ").append(DDLUtils.toQualifiedName(table.getCatalogName(),table.getSchemaName(),table.getName())); | sql.append("\n FROM "); sql.append(DDLUtils.toQualifiedName(table.getCatalogName(), table.getSchemaName(), table.getName(), databaseIdentifierQuoteString, databaseIdentifierQuoteString)); | private void doColumnProfile(List<SQLColumn> columns, Connection conn) throws SQLException { Statement stmt = null; ResultSet rs = null; String lastSQL = null; try { if ( columns.size() == 0 ) return; SQLColumn col1 = columns.get(0); ... |
sql.append(DDLUtils.toQualifiedName(table.getCatalogName(),table.getSchemaName(),table.getName())); | sql.append(DDLUtils.toQualifiedName(table.getCatalogName(), table.getSchemaName(), table.getName(), databaseIdentifierQuoteString, databaseIdentifierQuoteString)); | private void doColumnProfile(List<SQLColumn> columns, Connection conn) throws SQLException { Statement stmt = null; ResultSet rs = null; String lastSQL = null; try { if ( columns.size() == 0 ) return; SQLColumn col1 = columns.get(0); ... |
databaseIdentifierQuoteString = conn.getMetaData().getIdentifierQuoteString(); | private void doTableProfile(SQLTable table) throws SQLException, ArchitectException { SQLDatabase db = table.getParentDatabase(); Connection conn = null; Statement stmt = null; ResultSet rs = null; String lastSQL = null; TableProfileResult tableResult = new TablePro... | |
sql.append("SELECT COUNT(*) AS ROWCOUNT"); sql.append("\nFROM ").append(DDLUtils.toQualifiedName(table.getCatalogName(),table.getSchemaName(),table.getName())); | sql.append("SELECT COUNT(*) AS ROW__COUNT"); sql.append("\nFROM "); sql.append(DDLUtils.toQualifiedName(table.getCatalogName(), table.getSchemaName(), table.getName(), databaseIdentifierQuoteString, databaseIdentifierQuoteString)); | private void doTableProfile(SQLTable table) throws SQLException, ArchitectException { SQLDatabase db = table.getParentDatabase(); Connection conn = null; Statement stmt = null; ResultSet rs = null; String lastSQL = null; TableProfileResult tableResult = new TablePro... |
tableResult.setRowCount(rs.getInt("ROWCOUNT")); | tableResult.setRowCount(rs.getInt("ROW__COUNT")); | private void doTableProfile(SQLTable table) throws SQLException, ArchitectException { SQLDatabase db = table.getParentDatabase(); Connection conn = null; Statement stmt = null; ResultSet rs = null; String lastSQL = null; TableProfileResult tableResult = new TablePro... |
return columnProfile.getNullCount() == 0 ? null : columnProfile.getNullCount() * 100D / rowCount ; | return rowCount == 0 ? null : (double)columnProfile.getNullCount() / rowCount ; | public Object getValueAt(int rowIndex, int columnIndex) { ColumnProfileResult columnProfile = resultList.get(rowIndex); SQLColumn col = columnProfile.getProfiledObject(); int rowCount = ((TableProfileResult) profileManager.getResult(col.getParentTable())).getRowCount(); if (columnIndex =... |
return columnProfile.getDistinctValueCount() == 0 ? null : columnProfile.getDistinctValueCount() * 100D / rowCount; | return rowCount == 0 ? null : (double)columnProfile.getDistinctValueCount() / rowCount; | public Object getValueAt(int rowIndex, int columnIndex) { ColumnProfileResult columnProfile = resultList.get(rowIndex); SQLColumn col = columnProfile.getProfiledObject(); int rowCount = ((TableProfileResult) profileManager.getResult(col.getParentTable())).getRowCount(); if (columnIndex =... |
for (int i = 0; i < getComponentCount(); i++) { Component c = getComponent(i); | for (int i = 0; i < contentPane.getComponentCount(); i++) { Component c = contentPane.getComponent(i); | public TablePane findTablePane(SQLTable t) { for (int i = 0; i < getComponentCount(); i++) { Component c = getComponent(i); if (c instanceof TablePane && ((TablePane) c).getModel() == t) { return (TablePane) c; } } return null; } |
JLabel renderer = (JLabel) getCellRenderer(row, col).getTableCellRendererComponent(this, getModel().getValueAt(row, col), false, false, row, col); | JLabel renderer = (JLabel) getCellRenderer(row, col).getTableCellRendererComponent(this, getModel().getValueAt(row, getColumnModel().getColumn(col).getModelIndex()), false, false, row, col); | public String getTextForCell(int row, int col) { // note: this will only work because we know all the renderers are jlabels JLabel renderer = (JLabel) getCellRenderer(row, col).getTableCellRendererComponent(this, getModel().getValueAt(row, col), false, false, row, col); return renderer.getText(... |
Object value = expression.evaluate(context); | Class type = dynaTag.getAttributeType(name); Object value = null; if (type != null && type.isAssignableFrom(Expression.class) && !type.isAssignableFrom(Object.class)) { value = expression; } else { value = expression.evaluate(context); } | public void run(JellyContext context, XMLOutput output) throws Exception { if ( ! context.isCacheTags() ) { clearTag(); } try { Tag tag = getTag(); if ( tag == null ) { return; } tag.setContext(context); if ( t... |
if (!(momAllele1 == 0 || momAllele2 == 0 || dadAllele1 == 0 || dadAllele2 ==0)){ if(momAllele1 == momAllele2){ if (dadAllele1 == dadAllele2){ if (momAllele1 == dadAllele1){ if (allele1 != momAllele1 || allele2 != momAllele1) { mendErrNum ++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID... | if(Chromosome.getDataChrom().equalsIgnoreCase("chrx")){ if(currentInd.getGender() == 1) { if (!(momAllele1 == 0 || momAllele2 == 0 || dadAllele1 == 0)){ if(allele1 != momAllele1 && allele1 != momAllele2) { mendErrNum ++; | private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable... |
}else{ if (dadAllele1 == dadAllele2){ if(allele1 != dadAllele1 && allele2 != dadAllele1){ mendErrNum++; | }else { if(momAllele1 == momAllele2) { if(dadAllele1 == momAllele1) { if(allele1 != momAllele1 || allele2 != momAllele2){ mendErrNum ++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } }else { if(a... | private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable... |
} }else{ if (!(momAllele1 == 0 || momAllele2 == 0 || dadAllele1 == 0 || dadAllele2 ==0)){ if(momAllele1 == momAllele2){ if (dadAllele1 == dadAllele2){ if (momAllele1 == dadAllele1){ if (allele1 != momAllele1 || allele2 != momAllele1) { mendErrNum ++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentI... | private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable... | |
this.path = path; | this.path = (path != null ) ? path.clone() : null; | public PhotoFolderEvent( PhotoFolder source, PhotoFolder subfolder, PhotoFolder[] path ) { super( source ); this.subfolder = subfolder; this.path = path; } |
} | } finally { event.getSQLSource().setMagicEnabled(true); } | public void redo() throws CannotRedoException { try { modifyProperty(event.getNewValue()); } catch (IllegalAccessException e) { logger.error("Couldn't access setter for "+ event.getPropertyName(), e); throw new CannotRedoException(); } catch (InvocationTargetException e) { logger.error("Setter for "+... |
} | } finally { event.getSQLSource().setMagicEnabled(true); } | public void undo() throws CannotUndoException { try { modifyProperty(event.getOldValue()); } catch (IllegalAccessException e) { logger.error("Couldn't access setter for "+ event.getPropertyName(), e); throw new CannotUndoException(); } catch (InvocationTargetException e) { logger.error("Setter for "+... |
fit(); | SwingUtilities.invokeLater( new java.lang.Runnable() { public void run() { fit(); } } ); | public void componentResized( ComponentEvent e) { if ( isFit ) { fit(); } } |
public SwingUIProject(String name) { | public SwingUIProject(String name) throws ArchitectException { | public SwingUIProject(String name) { this.name = name; this.sourceDatabases = new ArrayList(); this.targetDatabase = new SQLDatabase(); } |
this.sourceDatabases = new ArrayList(); this.targetDatabase = new SQLDatabase(); | this.playPen = new PlayPen(new SQLDatabase()); List initialDBList = new ArrayList(); initialDBList.add(playPen.getDatabase()); this.sourceDatabases = new DBTree(initialDBList); | public SwingUIProject(String name) { this.name = name; this.sourceDatabases = new ArrayList(); this.targetDatabase = new SQLDatabase(); } |
public List getSourceDatabases() { | public DBTree getSourceDatabases() { | public List getSourceDatabases() { return this.sourceDatabases; } |
return this.targetDatabase; | return playPen.getDatabase(); | public SQLDatabase getTargetDatabase() { return this.targetDatabase; } |
public void setSourceDatabases(List argSourceDatabases) { | public void setSourceDatabases(DBTree argSourceDatabases) { | public void setSourceDatabases(List argSourceDatabases) { this.sourceDatabases = argSourceDatabases; } |
if (!location.canRead()) { throw new IllegalArgumentException("pl.ini file cannot be read: " + location.getAbsolutePath()); } lastFileRead = location; ArchitectDataSource currentDS = null; Section currentSection = new Section(null); fileSections.add(currentSection); fileTime = location.lastModified(); BufferedInput... | try { dontAutoSave = true; if (!location.canRead()) { throw new IllegalArgumentException("pl.ini file cannot be read: " + location.getAbsolutePath()); } lastFileAccessed = location; ArchitectDataSource currentDS = null; Section currentSection = new Section(null); fileSections.add(currentSection); fileTime = location.... | public void read(File location) throws IOException { final int MODE_READ_DS = 0; // reading a data source section final int MODE_READ_GENERIC = 1; // reading a generic named section int mode = MODE_READ_GENERIC; if (!location.canRead()) { throw new IllegalArgumentException("pl.ini file... |
OutputStream out = new BufferedOutputStream(new FileOutputStream(location)); write(out); out.close(); fileTime = location.lastModified(); | try { dontAutoSave = true; OutputStream out = new BufferedOutputStream(new FileOutputStream(location)); write(out); out.close(); lastFileAccessed = location; fileTime = location.lastModified(); } finally { dontAutoSave = false; } | public void write(File location) throws IOException { OutputStream out = new BufferedOutputStream(new FileOutputStream(location)); write(out); out.close(); fileTime = location.lastModified(); } |
public void writeSection(OutputStream out, String name, Map properties) throws IOException { | private void writeSection(OutputStream out, String name, Map properties) throws IOException { | public void writeSection(OutputStream out, String name, Map properties) throws IOException { if (name != null) { String sectionHeading = "["+name+"]" + DOS_CR_LF; out.write(sectionHeading.getBytes()); } // output LOGICAL first (if it exists) String s = null; if ((s = (String) proper... |
public String put(String key, String value) { String oldValue = get(key); properties.put(key,value); getPcs().firePropertyChange(key,oldValue,value); return oldValue; | public String put(String key, String value) { return putImpl(key, value, key); | public String put(String key, String value) { String oldValue = get(key); properties.put(key,value); getPcs().firePropertyChange(key,oldValue,value); return oldValue; } |
db.addVolume( v ); | try { db.addVolume( v ); } catch (PhotovaultException ex) { fail( ex.getMessage() ); } | public void testVolumeAddition() { PVDatabase db = new PVDatabase(); db.setDbHost( "" ); db.setDbName( "test" ); Volume v = new Volume( "test", "c:/temp" ); db.addVolume( v ); List volumes = db.getVolumes(); assertTrue( volumes.get( 0 ) == v ); assertT... |
db.addVolume( v ); | public void testXMLOutput() { PVDatabase db = new PVDatabase(); db.setDbHost( "" ); db.setDbName( "test" ); Volume v = new Volume( "test", "c:/temp/voltest" ); db.addVolume( v ); ExternalVolume ev = new ExternalVolume( "test_extvol", "c./tem/extvoltest" ); db... | |
db.addVolume( ev ); | try { db.addVolume( v ); db.addVolume( ev ); } catch (PhotovaultException ex) { fail( ex.getMessage() ); } | public void testXMLOutput() { PVDatabase db = new PVDatabase(); db.setDbHost( "" ); db.setDbName( "test" ); Volume v = new Volume( "test", "c:/temp/voltest" ); db.addVolume( v ); ExternalVolume ev = new ExternalVolume( "test_extvol", "c./tem/extvoltest" ); db... |
if (isExportLibraries() && parent != null) { parent.registerTagLibrary( namespaceURI, taglib ); } | public void registerTagLibrary(String namespaceURI, TagLibrary taglib) { if (log.isDebugEnabled()) { log.debug("Registering tag library to: " + namespaceURI + " taglib: " + taglib); } taglibs.put(namespaceURI, taglib); } | |
public void run(Context context, XMLOutput output) throws Exception { | public void run(JellyContext context, XMLOutput output) throws Exception { | public void run(Context context, XMLOutput output) throws Exception { if ( uri == null ) { throw new JellyException( "<j:include> must have a 'uri' attribute defined" ); } // we need to create a new Context of the URI // take off the script name from the URL ... |
out.println("GO"); | println("GO"); | public void writeDDLTransactionEnd() { out.println("GO"); } |
out.println("-- Created by SQLPower SQLServer 2000 DDL Generator "+GENERATOR_VERSION+" --"); | println("-- Created by SQLPower SQLServer 2000 DDL Generator "+GENERATOR_VERSION+" --"); | public void writeHeader() { out.println("-- Created by SQLPower SQLServer 2000 DDL Generator "+GENERATOR_VERSION+" --"); } |
line.append(theTag.getName()).append("\t"); line.append(getPairwiseCompRsq(snp,theTag.getSequence())).append("\t"); | if(theTag != null) { line.append(theTag.getName()).append("\t"); line.append(getPairwiseCompRsq(snp,theTag.getSequence())).append("\t"); } | public void saveResultToFile(File outFile) throws IOException { BufferedWriter bw = new BufferedWriter(new FileWriter(outFile)); bw.write("#tagging with r^2 cutoff: " + minRSquared); bw.newLine(); bw.write("Marker\tBest Tag\tr^2 w/tag"); bw.newLine(); for (int i = 0; i < sn... |
log.info("valid matches: " + m_results.getValidMails()); | private void logElapsedData() { log.info("unmatched messages: " + m_results.getUnmatchedMails()); log.info("matched messages: " + m_results.getMatchedMails()); log.info("recorded errors: " + m_results.getErrorCount()); } | |
setLayout(new BorderLayout()); setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10)); | protected void createUI() { tabPane = new JTabbedPane(); add( tabPane ); // General pane JPanel generalPane = new JPanel(); tabPane.addTab( "General", generalPane ); // Create the fields & their labels // Photographer field JLabel photographerLabel = new JLabel( "Photographer" ); photographerField = new JTextField... | |
add( tabPane ); | add( tabPane, BorderLayout.CENTER ); | protected void createUI() { tabPane = new JTabbedPane(); add( tabPane ); // General pane JPanel generalPane = new JPanel(); tabPane.addTab( "General", generalPane ); // Create the fields & their labels // Photographer field JLabel photographerLabel = new JLabel( "Photographer" ); photographerField = new JTextField... |
c.fill = GridBagConstraints.NONE; | c.fill = GridBagConstraints.BOTH; | protected void createUI() { tabPane = new JTabbedPane(); add( tabPane ); // General pane JPanel generalPane = new JPanel(); tabPane.addTab( "General", generalPane ); // Create the fields & their labels // Photographer field JLabel photographerLabel = new JLabel( "Photographer" ); photographerField = new JTextField... |
generalPane.add( saveBtn ); layout.setConstraints( saveBtn, c ); | protected void createUI() { tabPane = new JTabbedPane(); add( tabPane ); // General pane JPanel generalPane = new JPanel(); tabPane.addTab( "General", generalPane ); // Create the fields & their labels // Photographer field JLabel photographerLabel = new JLabel( "Photographer" ); photographerField = new JTextField... | |
generalPane.add( discardBtn ); layout.setConstraints( discardBtn, c ); | protected void createUI() { tabPane = new JTabbedPane(); add( tabPane ); // General pane JPanel generalPane = new JPanel(); tabPane.addTab( "General", generalPane ); // Create the fields & their labels // Photographer field JLabel photographerLabel = new JLabel( "Photographer" ); photographerField = new JTextField... | |
JPanel buttonPane = new JPanel(); buttonPane.setLayout(new BoxLayout(buttonPane, BoxLayout.X_AXIS)); buttonPane.setBorder(BorderFactory.createEmptyBorder(10, 0, 0, 0)); buttonPane.add(Box.createHorizontalGlue()); buttonPane.add(discardBtn); buttonPane.add(Box.createRigidArea(new Dimension(10, 0))); buttonPane.add(saveB... | protected void createUI() { tabPane = new JTabbedPane(); add( tabPane ); // General pane JPanel generalPane = new JPanel(); tabPane.addTab( "General", generalPane ); // Create the fields & their labels // Photographer field JLabel photographerLabel = new JLabel( "Photographer" ); photographerField = new JTextField... | |
if ( project.getTaskDefinitions().containsKey( tagName ) ) { if(tagName.equals(ANT_MANIFEST_TAG)) { TaskSource ancestor = (TaskSource) findAncestorWithClass( TaskSource.class ); if ( ancestor != null ) { Object nested = null; Object parentObject = null; | TaskSource ancestor = (TaskSource) findAncestorWithClass( TaskSource.class ); if ( ancestor != null ) { parentObject = ancestor.getTaskObject(); } | public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); if ( project.getTaskDefinitions().containsKey( tagName ) ) { // check if manifest is contained within a jar // special handling for Ant 1.5 manif... |
parentObject = ancestor.getTaskObject(); nested = createNestedObject( parentObject, tagName ); String body = getBodyText(); setBeanProperties(); if ( parentObject != null) { IntrospectionHelper ih = IntrospectionHelper.getHelper( parentObject.getClass() ); try { ih.storeElement( project, parentObject, nested, tag... | if ( ! ( parentObject instanceof Task ) && project.getTaskDefinitions().containsKey( tagName ) ) { if ( log.isDebugEnabled() ) { log.debug( "Creating an ant Task for name: " + tagName ); | public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); if ( project.getTaskDefinitions().containsKey( tagName ) ) { // check if manifest is contained within a jar // special handling for Ant 1.5 manif... |
else { Object nested = null; Object parentObject = null; | else { | public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); if ( project.getTaskDefinitions().containsKey( tagName ) ) { // check if manifest is contained within a jar // special handling for Ant 1.5 manif... |
TaskSource ancestor = (TaskSource) findAncestorWithClass( TaskSource.class ); if ( ancestor != null ) { parentObject = ancestor.getTaskObject(); nested = createNestedObject( parentObject, tagName ); | if ( log.isDebugEnabled() ) { log.debug( "Creating a nested object name: " + tagName ); | public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); if ( project.getTaskDefinitions().containsKey( tagName ) ) { // check if manifest is contained within a jar // special handling for Ant 1.5 manif... |
Object nested = createNestedObject( parentObject, tagName ); | public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); if ( project.getTaskDefinitions().containsKey( tagName ) ) { // check if manifest is contained within a jar // special handling for Ant 1.5 manif... | |
assertEquals("fully qualified attributes not passed", "<html xmlns=\"http: data); | public void testSimpleFileTag() throws Exception { setUpScript("testFileTag.jelly"); Script script = getJelly().compileScript(); script.run(getJellyContext(), getXMLOutput()); String data = (String)getJellyContext().getVariable("testFileTag"); //FIXME This doesn't take into acc... | |
setTag(tag); | public void run(JellyContext context, XMLOutput output) throws Exception { startNamespacePrefixes(output); Tag tag = getTag(); // lets see if we have a dynamic tag tag = findDynamicTag(context, (StaticTag) tag); try { ... | |
Options.setMissingThreshold(0.4); | Options.setMissingThreshold(1.0); | public HaploView(){ Options.setMissingThreshold(0.4); try{ fc = new JFileChooser(System.getProperty("user.dir")); }catch(NullPointerException n){ try{ UIManager.setLookAndFeel(UIManager.getCrossPlatformLookAndFeelClassName()); fc = new JFileCh... |
theData = new HaploData(assocTest); | theData = new HaploData(); | 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... |
tdtPanel = new TDTPanel(theData.chromosomes, assocTest); | tdtPanel = new TDTPanel(theData.getPedFile(), assocTest); | 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... |
tdtPanel = new TDTPanel(theData.chromosomes, assocTest); | tdtPanel = new TDTPanel(theData.getPedFile(), assocTest); | public Object construct(){ dPrimeDisplay=null; changeKey(1); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ... |
if(usedParents.contains(mom) || usedParents.contains(dad)) { continue; } | private void buildParenTDTTrioSet(PedFile pf, Vector permuteInd, TreeSet snpsToBeTested) throws PedFileException{ Vector results = new Vector(); Vector indList = pf.getAllIndividuals(); if(permuteInd == null || permuteInd.size() != indList.size()) { permuteInd = new Vector(); ... | |
if(usedParents.contains(mom) || usedParents.contains(dad)) { continue; } | private void buildParenTDTTrioSet(PedFile pf, Vector permuteInd, TreeSet snpsToBeTested) throws PedFileException{ Vector results = new Vector(); Vector indList = pf.getAllIndividuals(); if(permuteInd == null || permuteInd.size() != indList.size()) { permuteInd = new Vector(); ... | |
Haplotype h = (Haplotype) alleles.get(i); | Haplotype h = (Haplotype) filteredAlleles.get(i); | public String getCountString(int i){ nf.setMinimumFractionDigits(1); nf.setMaximumFractionDigits(1); Haplotype h = (Haplotype) alleles.get(i); StringBuffer countSB = new StringBuffer(); if(Options.getAssocTest() == ASSOC_TRIO) { countSB.append(nf.format(h.getTransCount(... |
public String getPValue(int i) { | public Double getPValue(int i) { | public String getPValue(int i) { if (pValues == null || i >= pValues.size()){ return ""; } return Util.formatPValue(((Double)pValues.get(i)).doubleValue()); } |
return ""; | return new Double(0); | public String getPValue(int i) { if (pValues == null || i >= pValues.size()){ return ""; } return Util.formatPValue(((Double)pValues.get(i)).doubleValue()); } |
return Util.formatPValue(((Double)pValues.get(i)).doubleValue()); | return new Double(Util.formatPValue(((Double)pValues.get(i)).doubleValue())); | public String getPValue(int i) { if (pValues == null || i >= pValues.size()){ return ""; } return Util.formatPValue(((Double)pValues.get(i)).doubleValue()); } |
long mDistance = Long.parseLong(st.nextToken()); | double mDistance = Double.parseDouble(st.nextToken()); | public void parseWGA(String wga, String map, boolean embed) throws PlinkException { markers = new Vector(); results = new Vector(); columns = new Vector(); columns.add("Result"); columns.add("Chrom"); columns.add("Marker"); columns.add("Position"); final File ... |
long morganDistance = 0; | double morganDistance = 0; | public void parseWGA(String wga, String map, boolean embed) throws PlinkException { markers = new Vector(); results = new Vector(); columns = new Vector(); columns.add("Result"); columns.add("Chrom"); columns.add("Marker"); columns.add("Position"); final File ... |
morganDistance = (new Long(new String(tokenizer.nextToken()))).longValue(); | morganDistance = (new Double(new String(tokenizer.nextToken()))).doubleValue(); | public void parseWGA(String wga, String map, boolean embed) throws PlinkException { markers = new Vector(); results = new Vector(); columns = new Vector(); columns.add("Result"); columns.add("Chrom"); columns.add("Marker"); columns.add("Position"); final File ... |
final DDLExportPanel ddlPanel = new DDLExportPanel(architectFrame.getProject()); Action okAction, cancelAction; okAction = new AbstractAction() { public void actionPerformed(ActionEvent evt) { try { if (ddlPanel.applyChanges()) { GenericDDLGenerator ddlg = architectFrame.getProject().getDDLGenerator(); ddlg.setTarget... | final DDLExportPanel ddlPanel = new DDLExportPanel(architectFrame.getProject()); Action okAction, cancelAction; okAction = new AbstractAction() { public void actionPerformed(ActionEvent evt) { try { if (ddlPanel.applyChanges()) { GenericDDLGenerator ddlg = architectFrame.getProject().getDDLGenerator(); ddlg.setTarget... | public void actionPerformed(ActionEvent e) { final DDLExportPanel ddlPanel = new DDLExportPanel(architectFrame.getProject()); Action okAction, cancelAction; okAction = new AbstractAction() { public void actionPerformed(ActionEvent evt) { try { if (ddlPanel.applyChanges()) { GenericDDLGene... |
try { if (ddlPanel.applyChanges()) { GenericDDLGenerator ddlg = architectFrame.getProject().getDDLGenerator(); ddlg.setTargetSchema(ddlPanel.getSchemaField().getText()); ddlg.generateDDL(architectFrame.getProject().getPlayPen().getDatabase()); List warnings = ddlg.getWarnings(); if (warnings.size() > 0) { TableSorte... | try { if (ddlPanel.applyChanges()) { GenericDDLGenerator ddlg = architectFrame.getProject().getDDLGenerator(); ddlg.setTargetSchema(ddlPanel.getSchemaField().getText()); for (;;) { ddlg.generateDDL(architectFrame.getProject().getPlayPen().getDatabase()); List warnings = ddlg.getWarnings(); if (warnings.size() == 0) ... | public void actionPerformed(ActionEvent evt) { try { if (ddlPanel.applyChanges()) { GenericDDLGenerator ddlg = architectFrame.getProject().getDDLGenerator(); ddlg.setTargetSchema(ddlPanel.getSchemaField().getText()); // XXX is it OK that is this generated but never used?? ... |
mi = new JMenuItem(af.deleteRelationshipAction); popup.add(mi); | protected void createPopup() { ArchitectFrame af = ArchitectFrame.getMainInstance(); popup = new JPopupMenu(); JMenuItem mi; mi = new JMenuItem(af.editRelationshipAction); popup.add(mi); addMouseListener(new PopupListener()); } | |
if (e.getPropertyName() != null && e.getPropertyName().equals("name")) { setToolTipText(model.getName()); | if (e.getPropertyName() != null) { if (e.getPropertyName().equals("name")) { setToolTipText(model.getName()); } else if (e.getPropertyName().equals("identifying") || e.getPropertyName().equals("pkCardinality") || e.getPropertyName().equals("fkCardinality")) { repaint(); } | public void dbObjectChanged(SQLObjectEvent e) { if (e.getPropertyName() != null && e.getPropertyName().equals("name")) { setToolTipText(model.getName()); } } |
return tag.getProject(); | answer = tag.getProject(); | protected Project getProject() { ProjectTag tag = (ProjectTag) findAncestorWithClass(ProjectTag.class); if ( tag != null) { return tag.getProject(); } return (Project) context.findVariable( "org.apache.commons.jelly.werkz.Project" ); } |
return (Project) context.findVariable( "org.apache.commons.jelly.werkz.Project" ); | if (answer == null) { answer = (Project) context.findVariable( "org.apache.commons.jelly.werkz.Project" ); } return answer; | protected Project getProject() { ProjectTag tag = (ProjectTag) findAncestorWithClass(ProjectTag.class); if ( tag != null) { return tag.getProject(); } return (Project) context.findVariable( "org.apache.commons.jelly.werkz.Project" ); } |
if(((Integer)affStatus.elementAt(i)).intValue() != ((Integer)affStatus.elementAt(i+1)).intValue()) { | if(Options.getTdtType() == TDT_PAREN && ((Integer)affStatus.elementAt(i)) .intValue() != ((Integer)affStatus.elementAt(i+1)).intValue()) { | public void doAssociationTests(Vector affStatus, Vector permuteInd,Vector permuteDiscPar, Vector kidAffStatus) { if(fullProbMap == null || superdata == null || realAffectedStatus == null || realKidAffectedStatus == null) { return; } if(affStatus == null){ affStatus = realA... |
guessBlocks(method, new Vector()); | guessBlocks(method, blocks); | void guessBlocks(int method){ guessBlocks(method, new Vector()); } |
cust.add(thisBlock); | if (thisBlock.length > 1){ cust.add(thisBlock); } | 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)); ... |
protected void computeBounds() { | public void computeBounds() { | protected void computeBounds() { // XXX: should check for valid cached bounds before recomputing! TablePane pkTable = relationship.pkTable; TablePane fkTable = relationship.fkTable; if (!isOrientationLegal()) { // bestConnectionPoints also updates orientation as a side effect bestConnectionPoints(); } if (pk... |
((ProfileTableModel)viewTable.getModel()).refresh(); | TableModelSortDecorator t = (TableModelSortDecorator) viewTable.getModel(); ProfileTableModel t2 = (ProfileTableModel) t.getTableModel(); t2.refresh(); | public void actionPerformed(ActionEvent e) { if (dbTree == null) { logger.debug("dbtree was null when actionPerformed called"); return; } if ( dbTree.getSelectionPaths() == null ) { logger.debug("dbtree path selection was null when actionPerformed called"); ... |
((ProfileTableModel)viewTable.getModel()).refresh(); | TableModelSortDecorator t = (TableModelSortDecorator) viewTable.getModel(); ProfileTableModel t2 = (ProfileTableModel) t.getTableModel(); t2.refresh(); | public void run() { try { List<SQLTable> toBeProfiled = new ArrayList<SQLTable>(); for (SQLTable t: tables) { if (profileManager.getResult(t)== null) { toBeProfiled.add(t); ... |
((ProfileTableModel)viewTable.getModel()).refresh(); | TableModelSortDecorator t = (TableModelSortDecorator) viewTable.getModel(); ProfileTableModel t2 = (ProfileTableModel) t.getTableModel(); t2.refresh(); | public void actionPerformed(ActionEvent e) { Set<SQLTable> uniqueTables = new HashSet(); for (int i: viewTable.getSelectedRows()) { Object o = viewTable.getValueAt(i,3); ... |
model.removeColumn(idx); | public ColumnEditPanel(SQLTable table, int idx) throws ArchitectException { super(new BorderLayout(12,12)); JPanel westPanel = new JPanel(new BorderLayout()); columns = new JList(); columns.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); columns.addListSelectionListener(this); westPanel.add(new JScrollP... | |
if (size > 0) { columns.setSelectedIndex(Math.min(idx, size-1)); | if (idx == size - 1) { columns.setSelectedIndex(size-2); model.removeColumn(idx); } else { model.removeColumn(idx); columns.setSelectedIndex(idx); | public ColumnEditPanel(SQLTable table, int idx) throws ArchitectException { super(new BorderLayout(12,12)); JPanel westPanel = new JPanel(new BorderLayout()); columns = new JList(); columns.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); columns.addListSelectionListener(this); westPanel.add(new JScrollP... |
model.removeColumn(idx); | public void actionPerformed(ActionEvent e) { int idx = columns.getSelectedIndex(); if (idx < 0) { JOptionPane.showMessageDialog(ColumnEditPanel.this, "Please select a column, then click delete"); } else { try { model.removeColumn(idx); int size = model.getColumns().si... | |
if (size > 0) { columns.setSelectedIndex(Math.min(idx, size-1)); | if (idx == size - 1) { columns.setSelectedIndex(size-2); model.removeColumn(idx); } else { model.removeColumn(idx); columns.setSelectedIndex(idx); | public void actionPerformed(ActionEvent e) { int idx = columns.getSelectedIndex(); if (idx < 0) { JOptionPane.showMessageDialog(ColumnEditPanel.this, "Please select a column, then click delete"); } else { try { model.removeColumn(idx); int size = model.getColumns().si... |
public void runScript(String uri, XMLOutput output) throws Exception { URL url = getResource(uri); if (url == null) { throw new JellyException("Could not find Jelly script: " + url); } Script script = compileScript(url); URL newJellyContextURL = getJellyContextURL(url); JellyContext newJellyContext = new JellyContext(... | public void runScript(File file, XMLOutput output) throws Exception { runScript(file.toURL(), output); | public void runScript(String uri, XMLOutput output) throws Exception { URL url = getResource(uri); if (url == null) { throw new JellyException("Could not find Jelly script: " + url); } Script script = compileScript(url); URL newJellyContextURL = getJellyContextU... |
db.setIgnoreReset(true); | db.setPlayPenDatabase(true); | private final void setDatabase(SQLDatabase newdb) { if (newdb == null) throw new NullPointerException("db must be non-null"); this.db = newdb; db.setIgnoreReset(true); if (db.getDataSource() == null) { ArchitectDataSource dbcs = new ArchitectDataSource(); dbcs.setName("Not Configured"); dbcs.setDisplayName("... |
ResultSet mdTables = null; | ResultSet rs = null; | protected static void addTablesToDatabase(SQLDatabase addTo) throws SQLException, ArchitectException { HashMap catalogs = new HashMap(); HashMap schemas = new HashMap(); synchronized (addTo) { Connection con = addTo.getConnection(); DatabaseMetaData dbmd = con.getMetaData(); ResultSet mdTables = null; try... |
mdTables = dbmd.getTables(null, null, "%", new String[] {"TABLE", "VIEW"}); while (mdTables.next()) { | rs = dbmd.getTables(null, null, "%", new String[] {"TABLE", "VIEW"}); while (rs.next()) { | protected static void addTablesToDatabase(SQLDatabase addTo) throws SQLException, ArchitectException { HashMap catalogs = new HashMap(); HashMap schemas = new HashMap(); synchronized (addTo) { Connection con = addTo.getConnection(); DatabaseMetaData dbmd = con.getMetaData(); ResultSet mdTables = null; try... |
String catName = mdTables.getString(1); | String catName = rs.getString(1); | protected static void addTablesToDatabase(SQLDatabase addTo) throws SQLException, ArchitectException { HashMap catalogs = new HashMap(); HashMap schemas = new HashMap(); synchronized (addTo) { Connection con = addTo.getConnection(); DatabaseMetaData dbmd = con.getMetaData(); ResultSet mdTables = null; try... |
String schName = mdTables.getString(2); | String schName = rs.getString(2); | protected static void addTablesToDatabase(SQLDatabase addTo) throws SQLException, ArchitectException { HashMap catalogs = new HashMap(); HashMap schemas = new HashMap(); synchronized (addTo) { Connection con = addTo.getConnection(); DatabaseMetaData dbmd = con.getMetaData(); ResultSet mdTables = null; try... |
mdTables.getString(3), mdTables.getString(5), mdTables.getString(4), | rs.getString(3), rs.getString(5), rs.getString(4), | protected static void addTablesToDatabase(SQLDatabase addTo) throws SQLException, ArchitectException { HashMap catalogs = new HashMap(); HashMap schemas = new HashMap(); synchronized (addTo) { Connection con = addTo.getConnection(); DatabaseMetaData dbmd = con.getMetaData(); ResultSet mdTables = null; try... |
if (mdTables != null) mdTables.close(); | if (rs != null) rs.close(); | protected static void addTablesToDatabase(SQLDatabase addTo) throws SQLException, ArchitectException { HashMap catalogs = new HashMap(); HashMap schemas = new HashMap(); synchronized (addTo) { Connection con = addTo.getConnection(); DatabaseMetaData dbmd = con.getMetaData(); ResultSet mdTables = null; try... |
logger.error("Selection list and children are out of sync: selection="+columnSelection+"; children="+model.getChildren()); | logger.error("Selection list and children are out of sync: selection="+columnSelection+"; children="+this.model.getColumns()); | public void dbChildrenRemoved(SQLObjectEvent e) { if (e.getSource() == this.model.getColumnsFolder()) { int ci[] = e.getChangedIndices(); for (int i = 0; i < ci.length; i++) { columnSelection.remove(ci[i]); } if (columnSelection.size() > 0) { selectNone(); columnSelection.set(Math.min(ci[0], columnSe... |
catch (Error e) { handleException(e); } | public void run(JellyContext context, XMLOutput output) throws Exception { if ( ! context.isCacheTags() ) { clearTag(); } try { Tag tag = getTag(); if ( tag == null ) { return; } tag.setContext(context); if ( t... | |
log.info("Deleting bogus entry: " + replicaEntry); | log.info("Deleting bogus replica entry: " + replicaEntry); | void resyncEntries(S replicaEntry, S masterEntry) throws FetchException, PersistException { if (replicaEntry == null && masterEntry == null) { return; } Log log = LogFactory.getLog(ReplicatedRepository.class); setReplicationDisabled(true); try { Transaction t... |
replicaEntry.tryDelete(); | try { replicaEntry.tryDelete(); } catch (PersistException e) { log.error("Unable to delete replica entry: " + replicaEntry, e); if (masterEntry != null) { S newReplicaEntry = mReplicaStorage.prepare(); transferToReplicaEntry(replicaEntry, masterEntry, newReplicaEntry); log.info("Replacing corrupt replica entry with: "... | void resyncEntries(S replicaEntry, S masterEntry) throws FetchException, PersistException { if (replicaEntry == null && masterEntry == null) { return; } Log log = LogFactory.getLog(ReplicatedRepository.class); setReplicationDisabled(true); try { Transaction t... |
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