bugged stringlengths 6 599k | fixed stringlengths 10 599k | __index_level_0__ int64 0 1.13M |
|---|---|---|
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... | 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... | 1,108,955 |
public void run(JellyContext context, XMLOutput output) throws Exception { try { tag.setContext(context); DynaTag dynaTag = (DynaTag) tag; // ### probably compiling this to 2 arrays might be quicker and smaller for (Iterator iter = attributes.entryS... | public void run(JellyContext context, XMLOutput output) throws Exception { try { tag.setContext(context); // ### probably compiling this to 2 arrays might be quicker and smaller for (Iterator iter = attributes.entrySet().iterator(); iter.hasNext();... | 1,108,956 |
public void run(JellyContext context, XMLOutput output) throws Exception { try { tag.setContext(context); DynaTag dynaTag = (DynaTag) tag; // ### probably compiling this to 2 arrays might be quicker and smaller for (Iterator iter = attributes.entryS... | public void run(JellyContext context, XMLOutput output) throws Exception { try { tag.setContext(context); DynaTag dynaTag = (DynaTag) tag; // ### probably compiling this to 2 arrays might be quicker and smaller for (Iterator iter = attributes.entryS... | 1,108,957 |
private MarkerResult checkMarker(int loc, String name)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, parenthet=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable(); Hashtable numindivs=n... | private MarkerResult checkMarker(int loc, String name)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, parenthet=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable(); Hashtable numindivs=n... | 1,108,958 |
private MarkerResult checkMarker(int loc, String name)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, parenthet=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable(); Hashtable numindivs=n... | private MarkerResult checkMarker(int loc, String name)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, parenthet=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable(); Hashtable numindivs=n... | 1,108,959 |
private MarkerResult checkMarker(int loc, String name)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, parenthet=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable(); Hashtable numindivs=n... | private MarkerResult checkMarker(int loc, String name)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, parenthet=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable(); Hashtable numindivs=n... | 1,108,960 |
private int getRating(double genopct, double pval, double obsHet, int menderr){ int rating = 0; if (obsHet < 0.01){ rating -= 1; } if (genopct < failedGenoCut){ rating -= 2; } if (pval < hwCut){ rating -= 4; } if (menderr > numMendErrCut){ rating -= 8; } if (rating == 0){ ra... | private int getRating(double genopct, double pval, double obsHet, int menderr, double maf){ int rating = 0; if (obsHet < 0.01){ rating -= 1; } if (genopct < failedGenoCut){ rating -= 2; } if (pval < hwCut){ rating -= 4; } if (menderr > numMendErrCut){ rating -= 8; } if (rating... | 1,108,962 |
public String getMessage(){ // TODO: look in the message catalog and get an error string return "To be implemented:errorCode:" + errorCode; } | public String getMessage(){ // TODO: look in the message catalog and get an error string return ErrorCatalog.getMessage(errorCode, values); } | 1,108,963 |
public static SwingWorker showUpdatePanel(){ final SwingWorker worker; worker = new SwingWorker(){ UpdateChecker uc; public Object construct() { uc = new UpdateChecker(); try { uc.checkForUpdate(); } catch(IOExceptio... | public static SwingWorker showUpdatePanel(){ final SwingWorker worker; worker = new SwingWorker(){ UpdateChecker uc; public Object construct() { uc = new UpdateChecker(); try { uc.checkForUpdate(); } catch(IOExceptio... | 1,108,965 |
public static SwingWorker showUpdatePanel(){ final SwingWorker worker; worker = new SwingWorker(){ UpdateChecker uc; public Object construct() { uc = new UpdateChecker(); try { uc.checkForUpdate(); } catch(IOExceptio... | public static SwingWorker showUpdatePanel(){ final SwingWorker worker; worker = new SwingWorker(){ UpdateChecker uc; public Object construct() { uc = new UpdateChecker(); try { uc.checkForUpdate(); } catch(IOExceptio... | 1,108,966 |
public static SwingWorker showUpdatePanel(){ final SwingWorker worker; worker = new SwingWorker(){ UpdateChecker uc; public Object construct() { uc = new UpdateChecker(); try { uc.checkForUpdate(); } catch(IOExceptio... | public static SwingWorker showUpdatePanel(){ final SwingWorker worker; worker = new SwingWorker(){ UpdateChecker uc; public Object construct() { uc = new UpdateChecker(); try { uc.checkForUpdate(); } catch(IOExceptio... | 1,108,967 |
public void finished() { if(uc != null) { if(uc.isNewVersionAvailable()) { //theres an update available so lets pop some crap up final JLayeredPane jlp = window.getLayeredPane(); final JPanel udp = new JPa... | public void finished() { if(uc != null && Constants.BETA_VERSION == 0) { if(uc.isNewVersionAvailable()) { //theres an update available so lets pop some crap up final JLayeredPane jlp = window.getLayeredPane(); ... | 1,108,968 |
public void finished() { if(uc != null) { if(uc.isNewVersionAvailable()) { //theres an update available so lets pop some crap up final JLayeredPane jlp = window.getLayeredPane(); final JPanel udp = new JPa... | public void finished() { if(uc != null) { if(uc.isNewVersionAvailable()) { //theres an update available so lets pop some crap up final JLayeredPane jlp = window.getLayeredPane(); final JPanel udp = new JPa... | 1,108,969 |
public void finished() { if(uc != null) { if(uc.isNewVersionAvailable()) { //theres an update available so lets pop some crap up final JLayeredPane jlp = window.getLayeredPane(); final JPanel udp = new JPa... | public void finished() { if(uc != null) { if(uc.isNewVersionAvailable()) { //theres an update available so lets pop some crap up final JLayeredPane jlp = window.getLayeredPane(); final JPanel udp = new JPa... | 1,108,970 |
private void init() throws ArchitectException { int accelMask = Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(); prefs = PrefsUtils.getUserPrefsNode(architectSession); CoreUserSettings us; // must be done right away, because a static // initializer in this class effects BeanUtils // behaviour wh... | private void init() throws ArchitectException { int accelMask = Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(); prefs = PrefsUtils.getUserPrefsNode(architectSession); CoreUserSettings us; // must be done right away, because a static // initializer in this class effects BeanUtils // behaviour wh... | 1,108,971 |
private void init() throws ArchitectException { int accelMask = Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(); prefs = PrefsUtils.getUserPrefsNode(architectSession); CoreUserSettings us; // must be done right away, because a static // initializer in this class effects BeanUtils // behaviour wh... | private void init() throws ArchitectException { int accelMask = Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(); prefs = PrefsUtils.getUserPrefsNode(architectSession); CoreUserSettings us; // must be done right away, because a static // initializer in this class effects BeanUtils // behaviour wh... | 1,108,972 |
public void actionPerformed(ActionEvent e) { try { ExportCSV export = new ExportCSV(getProject().getPlayPen().getDatabase().getTables()); File file = null; JFileChooser fileDialog = new JFileChooser(); fileDialog.setS... | public void actionPerformed(ActionEvent e) { try { final MappingReport mr ; final List<SQLTable> selectedTables; if (playpen.getSelectedTables().size() == 0) { selectedTables = new ArrayList(playpen.getTables()); } else { if (JOptionPane.YES_OPTION == JOptionPane.showConfir... | 1,108,973 |
public void actionPerformed(ActionEvent e) { try { ExportCSV export = new ExportCSV(getProject().getPlayPen().getDatabase().getTables()); File file = null; JFileChooser fileDialog = new JFileChooser(); fileDialog.setS... | public void actionPerformed(ActionEvent e) { try { ExportCSV export = new ExportCSV(getProject().getPlayPen().getDatabase().getTables()); final JFrame f = new JFrame("Mapping Report"); JFileChooser fileDialog = new JFileChooser(); ... | 1,108,974 |
public void actionPerformed(ActionEvent e) { try { ExportCSV export = new ExportCSV(getProject().getPlayPen().getDatabase().getTables()); File file = null; JFileChooser fileDialog = new JFileChooser(); fileDialog.setS... | public void actionPerformed(ActionEvent e) { try { ExportCSV export = new ExportCSV(getProject().getPlayPen().getDatabase().getTables()); File file = null; JFileChooser fileDialog = new JFileChooser(); fileDialog.setS... | 1,108,975 |
public void actionPerformed(ActionEvent e) { try { ExportCSV export = new ExportCSV(getProject().getPlayPen().getDatabase().getTables()); File file = null; JFileChooser fileDialog = new JFileChooser(); fileDialog.setS... | public void actionPerformed(ActionEvent e) { try { ExportCSV export = new ExportCSV(getProject().getPlayPen().getDatabase().getTables()); File file = null; JFileChooser fileDialog = new JFileChooser(); fileDialog.setS... | 1,108,976 |
public void actionPerformed(ActionEvent e) { try { ExportCSV export = new ExportCSV(getProject().getPlayPen().getDatabase().getTables()); File file = null; JFileChooser fileDialog = new JFileChooser(); fileDialog.setS... | public void actionPerformed(ActionEvent e) { try { ExportCSV export = new ExportCSV(getProject().getPlayPen().getDatabase().getTables()); File file = null; JFileChooser fileDialog = new JFileChooser(); fileDialog.setS... | 1,108,977 |
public void actionPerformed(ActionEvent e) { try { ExportCSV export = new ExportCSV(selectedTables); File file = null; JFileChooser fileDialog = new JFileChooser(); ... | public void actionPerformed(ActionEvent e) { try { ExportCSV export = new ExportCSV(selectedTables); File file = null; JFileChooser fileDialog = new JFileChooser(); ... | 1,108,978 |
public void actionPerformed(ActionEvent e) { recent.clear(); } | public void actionPerformed(ActionEvent e) { recent.clear(); } | 1,108,979 |
public void actionPerformed(ActionEvent e) { saveOrSaveAs(false, true); } | public void actionPerformed(ActionEvent e) { saveOrSaveAs(true, true); } | 1,108,980 |
public void actionPerformed(ActionEvent e) { saveOrSaveAs(true, true); } | public void actionPerformed(ActionEvent e) { playpen.setZoom(1.0); } | 1,108,981 |
public void actionPerformed(ActionEvent e) { playpen.setZoom(1.0); } | public void actionPerformed(ActionEvent e) { Rectangle rect = null; if ( playpen != null ) { for (int i = 0; i < playpen.getContentPane().getComponentCount(); i++) { PlayPenComponent ppc = playpen.getContentPane().getComponent(i); if ( rect == null ) { rect = new Rectangle(ppc.getLocation(),ppc.getSize()); } ... | 1,108,982 |
public void actionPerformed(ActionEvent e) { Rectangle rect = null; if ( playpen != null ) { for (int i = 0; i < playpen.getContentPane().getComponentCount(); i++) { PlayPenComponent ppc = playpen.getContentPane().getComponent(i); if ( rect == null ) { rect = new Rectangle(ppc.getLoc... | public void actionPerformed(ActionEvent e) { Rectangle rect = null; if ( playpen != null ) { for (int i = 0; i < playpen.getContentPane().getComponentCount(); i++) { PlayPenComponent ppc = playpen.getContentPane().getComponent(i); if ( rect == null ) { rect = new Rectangle(ppc.getLoc... | 1,108,984 |
public void actionPerformed(ActionEvent e) { Rectangle rect = null; if ( playpen != null ) { for (int i = 0; i < playpen.getContentPane().getComponentCount(); i++) { PlayPenComponent ppc = playpen.getContentPane().getComponent(i); if ( rect == null ) { rect = new Rectangle(ppc.getLoc... | public void actionPerformed(ActionEvent e) { Rectangle rect = null; if ( playpen != null ) { for (int i = 0; i < playpen.getContentPane().getComponentCount(); i++) { PlayPenComponent ppc = playpen.getContentPane().getComponent(i); if ( rect == null ) { rect = new Rectangle(ppc.getLoc... | 1,108,985 |
public void actionPerformed(ActionEvent e) { Rectangle rect = null; if ( playpen != null ) { for (int i = 0; i < playpen.getContentPane().getComponentCount(); i++) { PlayPenComponent ppc = playpen.getContentPane().getComponent(i); if ( rect == null ) { rect = new Rectangle(ppc.getLoc... | public void actionPerformed(ActionEvent e) { Rectangle rect = null; if ( playpen != null ) { for (int i = 0; i < playpen.getContentPane().getComponentCount(); i++) { PlayPenComponent ppc = playpen.getContentPane().getComponent(i); if ( rect == null ) { rect = new Rectangle(ppc.getLoc... | 1,108,986 |
public void actionPerformed(ActionEvent e) { Rectangle rect = null; if ( playpen != null ) { for (int i = 0; i < playpen.getContentPane().getComponentCount(); i++) { PlayPenComponent ppc = playpen.getContentPane().getComponent(i); if ( rect == null ) { rect = new Rectangle(ppc.getLoc... | public void actionPerformed(ActionEvent e) { Rectangle rect = null; if ( playpen != null ) { for (int i = 0; i < playpen.getContentPane().getComponentCount(); i++) { PlayPenComponent ppc = playpen.getContentPane().getComponent(i); if ( rect == null ) { rect = new Rectangle(ppc.getLoc... | 1,108,987 |
public void run() { Thread.setDefaultUncaughtExceptionHandler(new ExceptionHandler()); // this doesn't appear to have any effect on the motion threshold // in the Playpen, but it does seem to work on the DBTree... logger.debug("current motion threshold is: " + System.getPropert... | public void run() { Thread.setDefaultUncaughtExceptionHandler(new ExceptionHandler()); // this doesn't appear to have any effect on the motion threshold // in the Playpen, but it does seem to work on the DBTree... logger.debug("current motion threshold is: " + System.getPropert... | 1,108,988 |
public Dimension getPreferredSize() { Rectangle cbounds = null; //int minx = Integer.MAX_VALUE, miny = Integer.MAX_VALUE, maxx = 0, maxy = 0; int minx = 0, miny = 0, maxx = 0, maxy = 0; for (int i = 0; i < contentPane.getComponentCount(); i++) { Component c = contentPane.getComponent(i); if (c.isVisible()) { ... | public Dimension getPreferredSize() { Rectangle cbounds = null; //int minx = Integer.MAX_VALUE, miny = Integer.MAX_VALUE, maxx = 0, maxy = 0; int minx = 0, miny = 0, maxx = 0, maxy = 0; for (int i = 0; i < contentPane.getComponentCount(); i++) { Component c = contentPane.getComponent(i); if (c.isVisible()) { ... | 1,108,989 |
public Dimension getPreferredSize() { Rectangle cbounds = null; //int minx = Integer.MAX_VALUE, miny = Integer.MAX_VALUE, maxx = 0, maxy = 0; int minx = 0, miny = 0, maxx = 0, maxy = 0; for (int i = 0; i < contentPane.getComponentCount(); i++) { Component c = contentPane.getComponent(i); if (c.isVisible()) { ... | public Dimension getPreferredSize() { Rectangle cbounds = null; //int minx = Integer.MAX_VALUE, miny = Integer.MAX_VALUE, maxx = 0, maxy = 0; int minx = 0, miny = 0, maxx = 0, maxy = 0; for (int i = 0; i < contentPane.getComponentCount(); i++) { Component c = contentPane.getComponent(i); if (c.isVisible()) { ... | 1,108,990 |
public Dimension getPreferredSize() { Rectangle cbounds = null; //int minx = Integer.MAX_VALUE, miny = Integer.MAX_VALUE, maxx = 0, maxy = 0; int minx = 0, miny = 0, maxx = 0, maxy = 0; for (int i = 0; i < contentPane.getComponentCount(); i++) { Component c = contentPane.getComponent(i); if (c.isVisible()) { ... | public Dimension getPreferredSize() { Rectangle cbounds = null; //int minx = Integer.MAX_VALUE, miny = Integer.MAX_VALUE, maxx = 0, maxy = 0; int minx = 0, miny = 0, maxx = 0, maxy = 0; for (int i = 0; i < contentPane.getComponentCount(); i++) { Component c = contentPane.getComponent(i); if (c.isVisible()) { ... | 1,108,991 |
public Dimension getPreferredSize() { Rectangle cbounds = null; //int minx = Integer.MAX_VALUE, miny = Integer.MAX_VALUE, maxx = 0, maxy = 0; int minx = 0, miny = 0, maxx = 0, maxy = 0; for (int i = 0; i < contentPane.getComponentCount(); i++) { Component c = contentPane.getComponent(i); if (c.isVisible()) { ... | public Dimension getPreferredSize() { Rectangle cbounds = null; //int minx = Integer.MAX_VALUE, miny = Integer.MAX_VALUE, maxx = 0, maxy = 0; int minx = 0, miny = 0, maxx = 0, maxy = 0; for (int i = 0; i < contentPane.getComponentCount(); i++) { Component c = contentPane.getComponent(i); if (c.isVisible()) { ... | 1,108,992 |
public Dimension getPreferredSize() { Rectangle cbounds = null; //int minx = Integer.MAX_VALUE, miny = Integer.MAX_VALUE, maxx = 0, maxy = 0; int minx = 0, miny = 0, maxx = 0, maxy = 0; for (int i = 0; i < contentPane.getComponentCount(); i++) { Component c = contentPane.getComponent(i); if (c.isVisible()) { ... | public Dimension getPreferredSize() { Rectangle cbounds = null; //int minx = Integer.MAX_VALUE, miny = Integer.MAX_VALUE, maxx = 0, maxy = 0; int minx = 0, miny = 0, maxx = 0, maxy = 0; for (int i = 0; i < contentPane.getComponentCount(); i++) { Component c = contentPane.getComponent(i); if (c.isVisible()) { ... | 1,108,993 |
public Dimension getPreferredSize() { Rectangle cbounds = null; //int minx = Integer.MAX_VALUE, miny = Integer.MAX_VALUE, maxx = 0, maxy = 0; int minx = 0, miny = 0, maxx = 0, maxy = 0; for (int i = 0; i < contentPane.getComponentCount(); i++) { Component c = contentPane.getComponent(i); if (c.isVisible()) { ... | public Dimension getPreferredSize() { Rectangle cbounds = null; //int minx = Integer.MAX_VALUE, miny = Integer.MAX_VALUE, maxx = 0, maxy = 0; int minx = 0, miny = 0, maxx = 0, maxy = 0; for (int i = 0; i < contentPane.getComponentCount(); i++) { Component c = contentPane.getComponent(i); if (c.isVisible()) { ... | 1,108,994 |
public void doTag(final XMLOutput output) throws Exception { if ( verifier == null ) { throw new MissingAttributeException("verifier"); } boolean valid = false; // evaluate the body using the current Verifier if ( errorHandler != null ) { // we a... | public void doTag(final XMLOutput output) throws Exception { if ( verifier == null ) { throw new MissingAttributeException("verifier"); } boolean valid = false; // evaluate the body using the current Verifier if ( errorHandler != null ) { // we a... | 1,108,996 |
public void changeColumnIndex(int oldIdx, int newIdx) throws ArchitectException { // remove and add the column directly, then manually fire the event. // This is necessary because the relationships prevent deletion of locked keys. SQLColumn col = (SQLColumn) columnsFolder.children.remove(oldIdx); columnsFolde... | public void changeColumnIndex(int oldIdx, int newIdx) throws ArchitectException { // remove and add the column directly, then manually fire the event. // This is necessary because the relationships prevent deletion of locked keys. SQLColumn col = (SQLColumn) columnsFolder.children.remove(oldIdx); columnsFolde... | 1,108,998 |
public void changeColumnIndex(int oldIdx, int newIdx) throws ArchitectException { // remove and add the column directly, then manually fire the event. // This is necessary because the relationships prevent deletion of locked keys. SQLColumn col = (SQLColumn) columnsFolder.children.remove(oldIdx); columnsFolde... | public void changeColumnIndex(int oldIdx, int newIdx) throws ArchitectException { // remove and add the column directly, then manually fire the event. // This is necessary because the relationships prevent deletion of locked keys. SQLColumn col = (SQLColumn) columnsFolder.children.remove(oldIdx); columnsFolde... | 1,108,999 |
public int getColumnIndex(SQLColumn col) { logger.debug("Looking for column index of: " + col); Iterator it = columnsFolder.children.iterator(); int colIdx = 0; while (it.hasNext()) { if (it.next() == col) { return colIdx; } colIdx++; } logger.debug("NOT FOUND"); return -1; } | public int getColumnIndex(SQLColumn col) { logger.debug("Looking for column index of: " + col); Iterator it = columnsFolder.children.iterator(); int colIdx = 0; while (it.hasNext()) { if (it.next() == col) { return colIdx; } colIdx++; } logger.debug("NOT FOUND"); return -1; } | 1,109,000 |
public int getColumnIndex(SQLColumn col) { logger.debug("Looking for column index of: " + col); Iterator it = columnsFolder.children.iterator(); int colIdx = 0; while (it.hasNext()) { if (it.next() == col) { return colIdx; } colIdx++; } logger.debug("NOT FOUND"); return -1; } | public int getColumnIndex(SQLColumn col) { logger.debug("Looking for column index of: " + col); Iterator it = columnsFolder.children.iterator(); int colIdx = 0; while (it.hasNext()) { if (it.next() == col) { return colIdx; } } catch (ArchitectException e) { logger.warn("Unexpected ArchitectException in ge... | 1,109,001 |
public List keysOfColumn(SQLColumn col) { LinkedList keys = new LinkedList(); Iterator it = exportedKeysFolder.children.iterator(); while (it.hasNext()) { SQLRelationship r = (SQLRelationship) it.next(); if (r.containsPkColumn(col)) { keys.add(r); } } it = importedKeysFolder.children.iterator(); while (... | public List keysOfColumn(SQLColumn col) throws ArchitectException { LinkedList keys = new LinkedList(); Iterator it = exportedKeysFolder.children.iterator(); while (it.hasNext()) { SQLRelationship r = (SQLRelationship) it.next(); if (r.containsPkColumn(col)) { keys.add(r); } } it = importedKeysFolder.chi... | 1,109,002 |
public List keysOfColumn(SQLColumn col) { LinkedList keys = new LinkedList(); Iterator it = exportedKeysFolder.children.iterator(); while (it.hasNext()) { SQLRelationship r = (SQLRelationship) it.next(); if (r.containsPkColumn(col)) { keys.add(r); } } it = importedKeysFolder.children.iterator(); while (... | public List keysOfColumn(SQLColumn col) { LinkedList keys = new LinkedList(); Iterator it = getExportedKeys().iterator(); while (it.hasNext()) { SQLRelationship r = (SQLRelationship) it.next(); if (r.containsPkColumn(col)) { keys.add(r); } } it = importedKeysFolder.children.iterator(); while (it.hasNext... | 1,109,003 |
public List keysOfColumn(SQLColumn col) { LinkedList keys = new LinkedList(); Iterator it = exportedKeysFolder.children.iterator(); while (it.hasNext()) { SQLRelationship r = (SQLRelationship) it.next(); if (r.containsPkColumn(col)) { keys.add(r); } } it = importedKeysFolder.children.iterator(); while (... | public List keysOfColumn(SQLColumn col) { LinkedList keys = new LinkedList(); Iterator it = exportedKeysFolder.children.iterator(); while (it.hasNext()) { SQLRelationship r = (SQLRelationship) it.next(); if (r.containsPkColumn(col)) { keys.add(r); } } it = getExportedKeys().iterator(); while (it.hasNext... | 1,109,004 |
public void normalizePrimaryKey() { if (columnsFolder.children.isEmpty()) return; boolean donePk = false; int i = 0; Iterator it = columnsFolder.children.iterator(); while (it.hasNext()) { SQLColumn col = (SQLColumn) it.next(); if (col.getPrimaryKeySeq() == null) donePk = true; if (!donePk) { col.primary... | public void normalizePrimaryKey() { if (columnsFolder.children.isEmpty()) return; boolean donePk = false; int i = 0; Iterator it = columnsFolder.children.iterator(); while (it.hasNext()) { SQLColumn col = (SQLColumn) it.next(); if (col.getPrimaryKeySeq() == null) donePk = true; if (!donePk) { col.primary... | 1,109,005 |
public void normalizePrimaryKey() { if (columnsFolder.children.isEmpty()) return; boolean donePk = false; int i = 0; Iterator it = columnsFolder.children.iterator(); while (it.hasNext()) { SQLColumn col = (SQLColumn) it.next(); if (col.getPrimaryKeySeq() == null) donePk = true; if (!donePk) { col.primary... | public void normalizePrimaryKey() { if (columnsFolder.children.isEmpty()) return; boolean donePk = false; int i = 0; Iterator it = columnsFolder.children.iterator(); while (it.hasNext()) { SQLColumn col = (SQLColumn) it.next(); if (col.getPrimaryKeySeq() == null) donePk = true; if (!donePk) { col.primary... | 1,109,006 |
protected synchronized void populateColumns() throws ArchitectException { if (columnsFolder.isPopulated()) return; if (columnsFolder.children.size() > 0) throw new IllegalStateException("Can't populate table because it already contains columns"); try { SQLColumn.addColumnsToTable(this, getCatalogName(), ... | private synchronized void populateColumns() throws ArchitectException { if (columnsFolder.isPopulated()) return; if (columnsFolder.children.size() > 0) throw new IllegalStateException("Can't populate table because it already contains columns"); try { SQLColumn.addColumnsToTable(this, getCatalogName(), ... | 1,109,007 |
public synchronized void populateRelationships() throws ArchitectException { if (!columnsFolder.isPopulated()) throw new IllegalStateException("Table must be populated before relationships are added"); if (importedKeysFolder.isPopulated()) return; int oldSize = importedKeysFolder.children.size(); /* this must come... | private synchronized void populateRelationships() throws ArchitectException { if (!columnsFolder.isPopulated()) throw new IllegalStateException("Table must be populated before relationships are added"); if (importedKeysFolder.isPopulated()) return; int oldSize = importedKeysFolder.children.size(); /* this must com... | 1,109,008 |
public void actionPerformed(ActionEvent e) { final SQLDatabase souDB =playpen.getDatabase(); final PLExport plexp = new PLExport(); final JDialog d = new JDialog(ArchitectFrame.getMainInstance(), "PL Repository"); JPanel plp = new JPanel(new BorderLayout(12,12)); plp.setBorder(BorderFactory.createEmpt... | public void actionPerformed(ActionEvent e) { final SQLDatabase souDB =playpen.getDatabase(); final PLExport plexp = new PLExport(); final JDialog d = new JDialog(ArchitectFrame.getMainInstance(), "PL Repository"); JPanel plp = new JPanel(new BorderLayout(12,12)); plp.setBorder(BorderFactory.createEmpt... | 1,109,009 |
public void actionPerformed(ActionEvent e) { final SQLDatabase souDB =playpen.getDatabase(); final PLExport plexp = new PLExport(); final JDialog d = new JDialog(ArchitectFrame.getMainInstance(), "PL Repository"); JPanel plp = new JPanel(new BorderLayout(12,12)); plp.setBorder(BorderFactory.createEmpt... | public void actionPerformed(ActionEvent e) { final SQLDatabase souDB =playpen.getDatabase(); final PLExport plexp = new PLExport(); final JDialog d = new JDialog(ArchitectFrame.getMainInstance(), "PL Repository"); JPanel plp = new JPanel(new BorderLayout(12,12)); plp.setBorder(BorderFactory.createEmpt... | 1,109,010 |
public void actionPerformed(ActionEvent e) { final SQLDatabase souDB =playpen.getDatabase(); final PLExport plexp = new PLExport(); final JDialog d = new JDialog(ArchitectFrame.getMainInstance(), "PL Repository"); JPanel plp = new JPanel(new BorderLayout(12,12)); plp.setBorder(BorderFactory.createEmpt... | public void actionPerformed(ActionEvent e) { final SQLDatabase souDB =playpen.getDatabase(); final PLExport plexp = new PLExport(); final JDialog d = new JDialog(ArchitectFrame.getMainInstance(), "PL Repository"); JPanel plp = new JPanel(new BorderLayout(12,12)); plp.setBorder(BorderFactory.createEmpt... | 1,109,011 |
public void actionPerformed(ActionEvent evt) { if (plPanel.historyBox.getSelectedIndex() == 0) { JOptionPane.showMessageDialog(plPanel, "You have to select a target database from the list.", "Error", JOptionPane.ERROR_MESSAGE); return; } try { //plPanel.applyChanges(); plexp.setJobId... | public void actionPerformed(ActionEvent evt) { if (plPanel.getTargetDBCS() == null) { JOptionPane.showMessageDialog(plPanel, "You have to select a target database from the list.", "Error", JOptionPane.ERROR_MESSAGE); return; } try { //plPanel.applyChanges(); plexp.setJobId(plPanel.ge... | 1,109,012 |
public void actionPerformed(ActionEvent evt) { if (plPanel.historyBox.getSelectedIndex() == 0) { JOptionPane.showMessageDialog(plPanel, "You have to select a target database from the list.", "Error", JOptionPane.ERROR_MESSAGE); return; } try { //plPanel.applyChanges(); plexp.setJobId... | public void actionPerformed(ActionEvent evt) { if (plPanel.historyBox.getSelectedIndex() == 0) { JOptionPane.showMessageDialog(plPanel, "You have to select a target database from the list.", "Error", JOptionPane.ERROR_MESSAGE); return; } try { //plPanel.applyChanges(); plexp.setJobId... | 1,109,013 |
public void actionPerformed(ActionEvent evt) { if (plPanel.historyBox.getSelectedIndex() == 0) { JOptionPane.showMessageDialog(plPanel, "You have to select a target database from the list.", "Error", JOptionPane.ERROR_MESSAGE); return; } try { //plPanel.applyChanges(); plexp.setJobId... | public void actionPerformed(ActionEvent evt) { if (plPanel.historyBox.getSelectedIndex() == 0) { JOptionPane.showMessageDialog(plPanel, "You have to select a target database from the list.", "Error", JOptionPane.ERROR_MESSAGE); return; } try { //plPanel.applyChanges(); plexp.setJobId... | 1,109,014 |
public PlayPen(SQLDatabase db) { super(); if (db == null) throw new NullPointerException("db must be non-null"); this.db = db; relationships = new LinkedList(); db.addSQLObjectListener(this); setLayout(new PlayPenLayout(this)); setName("Play Pen"); setMinimumSize(new Dimension(200,200)); setBackground(java.aw... | public PlayPen(SQLDatabase db) { super(); if (db == null) throw new NullPointerException("db must be non-null"); this.db = db; relationships = new LinkedList(); try { ArchitectUtils.listenToHierarchy(this, db); } catch (ArchitectException ex) { logger.error("Couldn't listen to database", ex); } setLayout(new Pla... | 1,109,015 |
public void dbChildrenInserted(SQLObjectEvent e) { logger.debug("SQLObject children got inserted: "+e); SQLObject o = e.getSQLSource(); SQLObject[] c = e.getChildren(); for (int i = 0; i < c.length; i++) { if (c[i] instanceof SQLTable) { c[i].addSQLObjectListener(this); } } firePropertyChange("model.child... | public void dbChildrenInserted(SQLObjectEvent e) { logger.debug("SQLObject children got inserted: "+e); SQLObject o = e.getSQLSource(); SQLObject[] c = e.getChildren(); for (int i = 0; i < c.length; i++) { if (c[i] instanceof SQLTable) { c[i].addSQLObjectListener(this); } } firePropertyChange("model.child... | 1,109,016 |
public void dbChildrenInserted(SQLObjectEvent e) { logger.debug("SQLObject children got inserted: "+e); SQLObject o = e.getSQLSource(); SQLObject[] c = e.getChildren(); for (int i = 0; i < c.length; i++) { if (c[i] instanceof SQLTable) { c[i].addSQLObjectListener(this); } } firePropertyChange("model.child... | public void dbChildrenInserted(SQLObjectEvent e) { logger.debug("SQLObject children got inserted: "+e); SQLObject o = e.getSQLSource(); SQLObject[] c = e.getChildren(); for (int i = 0; i < c.length; i++) { if (c[i] instanceof SQLTable) { c[i].addSQLObjectListener(this); } } firePropertyChange("model.child... | 1,109,017 |
public void dbChildrenRemoved(SQLObjectEvent e) { logger.debug("SQLObject children got removed: "+e); SQLObject o = e.getSQLSource(); SQLObject[] c = e.getChildren(); for (int i = 0; i < c.length; i++) { if (c[i] instanceof SQLTable) { c[i].removeSQLObjectListener(this); for (int j = 0; j < getComponentCou... | public void dbChildrenRemoved(SQLObjectEvent e) { logger.debug("SQLObject children got removed: "+e); SQLObject o = e.getSQLSource(); SQLObject[] c = e.getChildren(); for (int i = 0; i < c.length; i++) { if (c[i] instanceof SQLTable) { for (int j = 0; j < getComponentCount(); j++) { TablePane tp = (Ta... | 1,109,018 |
public void dbChildrenRemoved(SQLObjectEvent e) { logger.debug("SQLObject children got removed: "+e); SQLObject o = e.getSQLSource(); SQLObject[] c = e.getChildren(); for (int i = 0; i < c.length; i++) { if (c[i] instanceof SQLTable) { c[i].removeSQLObjectListener(this); for (int j = 0; j < getComponentCou... | public void dbChildrenRemoved(SQLObjectEvent e) { logger.debug("SQLObject children got removed: "+e); SQLObject o = e.getSQLSource(); SQLObject[] c = e.getChildren(); for (int i = 0; i < c.length; i++) { if (c[i] instanceof SQLTable) { c[i].removeSQLObjectListener(this); for (int j = 0; j < getComponentCou... | 1,109,019 |
protected void configure() { // load the properties file of libraries available InputStream in = null; URL url = getClassLoader().getResource("org/apache/commons/jelly/jelly.properties"); if (url != null) { log.debug("Loading Jelly default tag libraries from: " + ur... | protected void configure() { // load the properties file of libraries available InputStream in = null; URL url = getClassLoader().getResource("org/apache/commons/jelly/jelly.properties"); if (url != null) { log.debug("Loading Jelly default tag libraries from: " + ur... | 1,109,020 |
public ExpressionScript(Expression expression) { this.expression = expression; } | public ExpressionScript(Expression expression) { this.expression = expression; } | 1,109,021 |
public ConstantExpression(Object value) { this.value = value; } | public ConstantExpression(Object value) { this.value = value; } | 1,109,022 |
public StaticTagScript(TagFactory tagFactory) { super(tagFactory); } | public StaticTagScript(TagFactory tagFactory) { super(tagFactory); } | 1,109,023 |
public String getOverTransmittedAllele(int type) { String[] alleleCodes = new String[5]; alleleCodes[0] = "X"; alleleCodes[1] = "A"; alleleCodes[2] = "C"; alleleCodes[3] = "G"; alleleCodes[4] = "T"; String retStr; if (this.counts[0][0] >= this.counts[0][1]){ ... | public String getOverTransmittedAllele(int type) { String[] alleleCodes = new String[5]; alleleCodes[0] = "X"; alleleCodes[1] = "A"; alleleCodes[2] = "C"; alleleCodes[3] = "G"; alleleCodes[4] = "T"; String retStr; if (this.counts[0][0] > this.counts[0][1]){ ... | 1,109,024 |
public String getOverTransmittedAllele(int type) { String[] alleleCodes = new String[5]; alleleCodes[0] = "X"; alleleCodes[1] = "A"; alleleCodes[2] = "C"; alleleCodes[3] = "G"; alleleCodes[4] = "T"; String retStr; if (this.counts[0][0] >= this.counts[0][1]){ ... | public String getOverTransmittedAllele(int type) { String[] alleleCodes = new String[5]; alleleCodes[0] = "X"; alleleCodes[1] = "A"; alleleCodes[2] = "C"; alleleCodes[3] = "G"; alleleCodes[4] = "T"; String retStr; if (this.counts[0][0] >= this.counts[0][1]){ ... | 1,109,025 |
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 = ""... | 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 = ""... | 1,109,027 |
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 = ""... | 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 = ""... | 1,109,028 |
public void paintComponent(Graphics g){ Graphics2D g2 = (Graphics2D) g; Dimension size = getSize(); Dimension pref = getPreferredSize(); Rectangle visRect = getVisibleRect(); /* boxSize = ((clipRect.width-2*H_BORDER)/dPrimeTable.length-1); if (boxSize... | public void paintComponent(Graphics g){ Graphics2D g2 = (Graphics2D) g; Dimension size = getSize(); Dimension pref = getPreferredSize(); Rectangle visRect = getVisibleRect(); /* boxSize = ((clipRect.width-2*H_BORDER)/dPrimeTable.length-1); if (boxSize... | 1,109,029 |
public void setModel( Object model ) { setModel( model, false ); } | public void setModel( Object model ) { setModel( model, false ); } | 1,109,030 |
private boolean checkAttributeDataType(ObjectAttributeInfo[] objAttrInfo, String[] dataTypes, ApplicationConfig appConfig, List attributesList){ boolean result = false; outerlo... | private boolean checkAttributeDataType(ObjectAttributeInfo[] objAttrInfo, String[] dataTypes, ApplicationConfig appConfig, List attributesList){ boolean result = false; outerlo... | 1,109,031 |
private Class getClass(String type, ClassLoader classLoader){ if(type.equals("boolean")) return Boolean.class; if(type.equals("byte")) return Byte.TYPE; if(type.equals("char")) return Character.class; if(type.equals("double")) return Double... | private Class getClass(String type, ClassLoader classLoader){ if(type.equals("boolean")) return Boolean.class; if(type.equals("byte")) return Byte.TYPE; if(type.equals("char")) return Character.class; if(type.equals("double")) return Double... | 1,109,032 |
private List queryMBeansWithAttributes(ServiceContext context, String filter, String[] dataTypes) throws ServiceException{ ServerConnection serverConnection = context.getServerConnection(); List mbeans = queryMBeans(context, filter); List mbea... | private List queryMBeansWithAttributes(ServiceContext context, String filter, String[] dataTypes) throws ServiceException{ ServerConnection serverConnection = context.getServerConnection(); List mbeans = queryMBeans(context, filter); List mbea... | 1,109,033 |
private List queryMBeansWithAttributes(ServiceContext context, String filter, String[] dataTypes) throws ServiceException{ ServerConnection serverConnection = context.getServerConnection(); List mbeans = queryMBeans(context, filter); List mbea... | private List queryMBeansWithAttributes(ServiceContext context, String filter, String[] dataTypes) throws ServiceException{ ServerConnection serverConnection = context.getServerConnection(); List mbeans = queryMBeans(context, filter); List mbea... | 1,109,034 |
public Map queryMBeansWithNotifications(ServiceContext context) throws ServiceException { ServerConnection serverConnection = context.getServerConnection(); Set mbeans = serverConnection.queryNames(DEFAULT_FILTER_OBJECT_NAME); Map mbeanToNoficationsMap = new TreeMap();... | public Map queryMBeansWithNotifications(ServiceContext context) throws ServiceException { ServerConnection serverConnection = context.getServerConnection(); Set mbeans = serverConnection.queryNames(DEFAULT_FILTER_OBJECT_NAME); Map mbeanToNoficationsMap = new TreeMap();... | 1,109,036 |
public void addSQLObjectListener(SQLObjectListener l) { if (getSQLObjectListeners().contains(l)) { logger.warn("NOT Adding duplicate listener "+l+" to SQLObject "+this); return; } getSQLObjectListeners().add(l); } | public void addSQLObjectListener(SQLObjectListener l) { if (getSQLObjectListeners().contains(l)) { if (logger.isDebugEnabled()) { logger.debug("NOT Adding duplicate listener "+l+" to SQLObject "+this); } return; } getSQLObjectListeners().add(l); } | 1,109,037 |
public Object createNestedObject(String name) throws Exception { Object dataType = null; Object object = getObject(); if ( object != null ) { IntrospectionHelper ih = IntrospectionHelper.getHelper( object.getClass() ); if ( ih != null ) { try { ... | public Object createNestedObject(Object object, String name) throws Exception { Object dataType = null; Object object = getObject(); if ( object != null ) { IntrospectionHelper ih = IntrospectionHelper.getHelper( object.getClass() ); if ( ih != null ) { ... | 1,109,038 |
public Object createNestedObject(String name) throws Exception { Object dataType = null; Object object = getObject(); if ( object != null ) { IntrospectionHelper ih = IntrospectionHelper.getHelper( object.getClass() ); if ( ih != null ) { try { ... | public Object createNestedObject(String name) throws Exception { Object dataType = null; if ( object != null ) { IntrospectionHelper ih = IntrospectionHelper.getHelper( object.getClass() ); if ( ih != null ) { try { dataType =... | 1,109,039 |
public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); if ( project.getTaskDefinitions().containsKey( tagName ) ) { // the following algorithm follows the lifetime of a tag // http://jakarta.apac... | public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); if ( project.getTaskDefinitions().containsKey( tagName ) ) { // the following algorithm follows the lifetime of a tag // http://jakarta.apac... | 1,109,041 |
public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); if ( project.getTaskDefinitions().containsKey( tagName ) ) { // the following algorithm follows the lifetime of a tag // http://jakarta.apac... | public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); if ( project.getTaskDefinitions().containsKey( tagName ) ) { // the following algorithm follows the lifetime of a tag // http://jakarta.apac... | 1,109,042 |
public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); if ( project.getTaskDefinitions().containsKey( tagName ) ) { // the following algorithm follows the lifetime of a tag // http://jakarta.apac... | public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); if ( project.getTaskDefinitions().containsKey( tagName ) ) { // the following algorithm follows the lifetime of a tag // http://jakarta.apac... | 1,109,043 |
public void setBeanProperties() throws Exception { Object object = getObject(); if ( object != null ) { Map map = getAttributes(); for ( Iterator iter = map.entrySet().iterator(); iter.hasNext(); ) { Map.Entry entry = (Map.Entry) iter.next(); String name = (String) entry.ge... | public void setBeanProperties() throws Exception { Object object = getTaskObject(); if ( object != null ) { Map map = getAttributes(); for ( Iterator iter = map.entrySet().iterator(); iter.hasNext(); ) { Map.Entry entry = (Map.Entry) iter.next(); String name = (String) entr... | 1,109,044 |
public Expression createExpression(ExpressionFactory factory, String tagName, String attributeName, String attributeValue) throws Exception { if (attributeName.equals( "value" ) || attributeName.equals( "items" ) || attributeName.equals( "test" ) ) { return factory.createExpression( attributeValu... | public Expression createExpression(ExpressionFactory factory, String tagName, String attributeName, String attributeValue) throws Exception { if (attributeName.equals( "value" ) || attributeName.equals( "items" ) || attributeName.equals( "test" ) ) { return factory.createExpression( attributeValu... | 1,109,048 |
public static Object unmarshal(Class clazz, String str){ try { return org.exolab.castor.xml.Unmarshaller.unmarshal(clazz, new StringReader(str)); } catch (Exception e) { throw new RuntimeException("Error while unmarshalling obj of type:" + cl... | public static Object unmarshal(String className, String str){ try { return org.exolab.castor.xml.Unmarshaller.unmarshal(clazz, new StringReader(str)); } catch (Exception e) { throw new RuntimeException("Error while unmarshalling obj of type:" + ... | 1,109,050 |
public static Object unmarshal(Class clazz, String str){ try { return org.exolab.castor.xml.Unmarshaller.unmarshal(clazz, new StringReader(str)); } catch (Exception e) { throw new RuntimeException("Error while unmarshalling obj of type:" + cl... | public static Object unmarshal(Class clazz, String str){ try { return org.exolab.castor.xml.Unmarshaller.unmarshal(clazz, new StringReader(str)); } catch (Exception e) { throw new RuntimeException("Error while unmarshalling obj of type:" + cl... | 1,109,051 |
public static String marshal(Object obj){ StringWriter writer = new StringWriter(); try { org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(writer); marshaller.setRootElement("marshalledObject"); marshaller.setMarshal... | public static String marshal(Object obj){ StringWriter writer = new StringWriter(); try { org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(writer); marshaller.setRootElement("marshalledObject"); marshaller.setMarshal... | 1,109,052 |
public static String marshal(Object obj){ StringWriter writer = new StringWriter(); try { org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(writer); marshaller.setRootElement("marshalledObject"); marshaller.setMarshal... | public static String marshal(Object obj){ StringWriter writer = new StringWriter(); try { org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(writer); marshaller.setRootElement("marshalledObject"); marshaller.setMarshal... | 1,109,053 |
public synchronized void populate() throws ArchitectException { if (populated) return; int oldSize = children.size(); Connection con = null; ResultSet rs = null; try { con = getConnection(); DatabaseMetaData dbmd = con.getMetaData(); logger.debug("MetaData class is: " + dbmd.getClass().getName()); rs = ... | public synchronized void populate() throws ArchitectException { if (populated) return; int oldSize = children.size(); Connection con = null; ResultSet rs = null; try { con = getConnection(); DatabaseMetaData dbmd = con.getMetaData(); rs = dbmd.getCatalogs(); while (rs.next()) { String catName = ... | 1,109,054 |
void generateDPrimeTable(long maxdist){ //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset dPrimeTable = new PairwiseLinkage[Chromosome.getSize()][Chromosome.getSize()]; int doublehet; long negMaxdist = -1*maxdist; int[][] twoMark... | void generateDPrimeTable(long maxdist){ //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset dPrimeTable = new PairwiseLinkage[Chromosome.getSize()][Chromosome.getSize()]; int doublehet; long negMaxdist = -1*maxdist; int[][] twoMark... | 1,109,056 |
void generateDPrimeTable(long maxdist){ //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset dPrimeTable = new PairwiseLinkage[Chromosome.getSize()][Chromosome.getSize()]; int doublehet; long negMaxdist = -1*maxdist; int[][] twoMark... | void generateDPrimeTable(long maxdist){ //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset dPrimeTable = new PairwiseLinkage[Chromosome.getSize()][Chromosome.getSize()]; int doublehet; long negMaxdist = -1*maxdist; int[][] twoMark... | 1,109,057 |
Haplotype[][] generateHaplotypes(Vector blocks, int hapthresh) throws HaploViewException{ //TODO: output indiv hap estimates Haplotype[][] results = new Haplotype[blocks.size()][]; //String raw = new String(); //String currentLine; this.totalBlocks = blocks.size(); this.blo... | Haplotype[][] generateHaplotypes(Vector blocks, int hapthresh) throws HaploViewException{ //TODO: output indiv hap estimates Haplotype[][] results = new Haplotype[blocks.size()][]; //String raw = new String(); //String currentLine; this.totalBlocks = blocks.size(); this.blo... | 1,109,058 |
public ObjectName getObjectName() { try { final String objectNameString = request.getParameter(RequestParams.OBJECT_NAME); return new ObjectName(objectNameString); } catch (MalformedObjectNameException e) { throw new RuntimeException(e); } ... | public ObjectName getObjectName() { try { final String objectNameString = request.getParameter(RequestParams.OBJECT_NAME); if(objectNameString != null){ return new ObjectName(objectNameString); }else{ return null; } } catch (MalformedObjectNameException e) { ... | 1,109,060 |
public Config(List<ApplicationConfig> applications, List<DashboardConfig> dashboards){ this.applications = applications; this.dashboards = dashboards; } | public Config(List<ApplicationConfig> applications){ this.applications = applications; this.dashboards = dashboards; } | 1,109,061 |
public Config(List<ApplicationConfig> applications, List<DashboardConfig> dashboards){ this.applications = applications; this.dashboards = dashboards; } | public Config(List<ApplicationConfig> applications, List<DashboardConfig> dashboards){ this.applications = applications; } | 1,109,062 |
public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) throws Exception { ... | public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) throws Exception { ... | 1,109,063 |
public DBListClass(PropertyMetaClass wclass) { super("dblist", "DB List", wclass); } | public DBListClass(PropertyMetaClass wclass) { super("dblist", "DB List", wclass); } | 1,109,065 |
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_... | 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_... | 1,109,067 |
public Object evaluate(Context context) { try { interpreter.setContext(context); if ( log.isDebugEnabled() ) { log.debug( "Evaluating EL: " + text ); } return interpreter.eval( text ); } catch (Exception e) { ... | public Object evaluate(JellyContext context) { try { interpreter.setContext(context); if ( log.isDebugEnabled() ) { log.debug( "Evaluating EL: " + text ); } return interpreter.eval( text ); } catch (Exception e) ... | 1,109,068 |
public Object evaluate(Context context) { try { interpreter.setContext(context); if ( log.isDebugEnabled() ) { log.debug( "Evaluating EL: " + text ); } return interpreter.eval( text ); } catch (Exception e) { ... | public Object evaluate(Context context) { try { interpreter.setJellyContext(context); if ( log.isDebugEnabled() ) { log.debug( "Evaluating EL: " + text ); } return interpreter.eval( text ); } catch (Exception e) ... | 1,109,069 |
public void dragGestureRecognized(DragGestureEvent dge) { logger.info("Drag gesture event: "+dge); // we only start drags on left-click drags InputEvent ie = dge.getTriggerEvent(); if ( (ie.getModifiers() & InputEvent.BUTTON1_MASK) == 0) { return; } DBTree t = (DBTree) dge.getComponent(); TreePath[... | public void dragGestureRecognized(DragGestureEvent dge) { logger.info("Drag gesture event: "+dge); // we only start drags on left-click drags InputEvent ie = dge.getTriggerEvent(); if ( (ie.getModifiers() & InputEvent.BUTTON1_MASK) == 0) { return; } DBTree t = (DBTree) dge.getComponent(); TreePath[... | 1,109,070 |
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