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coconut_java2006_preprocessed

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usedParents.add(mom); usedParents.add(dad);
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(currentInd.getZeroed(i) || dad.getZeroed(i) || mom.getZeroed(i)) { continue; } byte kid1 = currentInd.getMarkerA(i); byte kid2 = currentInd.getMarkerB(i); byte dad1 = dad.getMarkerA(i); byte dad2 = dad.getMarkerB(i); byte mom1 = mom.getMarkerA(i); byte mom2 = mom.getMarkerB(i);
if(currentInd.getZeroed(i) || dad.getZeroed(i) || mom.getZeroed(i)) { continue; } byte[] thisMarker = currentInd.getMarker(i); byte kid1 = thisMarker[0]; byte kid2 = thisMarker[1]; thisMarker = dad.getMarker(i); byte dad1 = thisMarker[0]; byte dad2 = thisMarker[1]; thisMarker = mom.getMarker(i); byte mom1 = thisMarker[...
private void buildTrioSet(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(); for ...
Object o = britr.next(); if(o != null) { HaplotypeAssociationResult har = (HaplotypeAssociationResult) o; res.add(har); }
HaplotypeAssociationResult har = (HaplotypeAssociationResult) britr.next(); res.add(har);
public void runFileTests(HaploData theData, Vector inputSNPResults) throws HaploViewException { Vector res = new Vector(); if(tests == null || theData == null) { return; } Vector blocks = new Vector(); Vector names = new Vector(); Vector alleles = new Vector(); ...
if (r.pkTable == null) { logger.error("addImportedRelationshipsToTable: Couldn't find exporting table " +rs.getString(1)+"."+rs.getString(2)+"."+rs.getString(3) +" in target database!"); continue; }
static void addImportedRelationshipsToTable(SQLTable table) throws ArchitectException { SQLDatabase db = table.getParentDatabase(); if (!db.isPopulated()) { throw new ArchitectException("relationship.unpopulatedTargetDatabase"); } Connection con = db.getConnection(); ResultSet rs = null; try { DatabaseMetaDa...
String text = textScript.getText(); text = text.trim(); textScript.setText(text);
textScript.trimWhitespace();
protected void trimBody() { if ( body instanceof ScriptBlock ) { ScriptBlock block = (ScriptBlock) body; List list = block.getScriptList(); for ( int i = list.size() - 1; i >= 0; i-- ) { Script script = (Script) list.get(i); if ( script instance...
String shortHapInputFileName;
public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); String shortHapInputFileName; if (command == READ_GENOTYPES){ ReadDataDialog readDialog = new ReadDataDialog("Open new data", this); readDialog.pack(); readDialog.setVisible(true); /**if (command == "Open Linkage Fil...
theBlocks.clearBlocks();
public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); String shortHapInputFileName; if (command == READ_GENOTYPES){ ReadDataDialog readDialog = new ReadDataDialog("Open new data", this); readDialog.pack(); readDialog.setVisible(true); /**if (command == "Open Linkage Fil...
String oldCatalog = null;
public void populate() throws ArchitectException { if (populated) return; logger.debug("SQLCatalog: populate starting"); int oldSize = children.size(); synchronized (parent) { Connection con = null; ResultSet rs = null; try { con = ((SQLDatabase) parent).getConnection(); DatabaseMetaData dbmd = ...
oldCatalog = con.getCatalog();
public void populate() throws ArchitectException { if (populated) return; logger.debug("SQLCatalog: populate starting"); int oldSize = children.size(); synchronized (parent) { Connection con = null; ResultSet rs = null; try { con = ((SQLDatabase) parent).getConnection(); DatabaseMetaData dbmd = ...
if (con != null) con.close();
if (con != null) { con.setCatalog(oldCatalog); con.close(); }
public void populate() throws ArchitectException { if (populated) return; logger.debug("SQLCatalog: populate starting"); int oldSize = children.size(); synchronized (parent) { Connection con = null; ResultSet rs = null; try { con = ((SQLDatabase) parent).getConnection(); DatabaseMetaData dbmd = ...
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 ( var == null ) { throw new IllegalArgumentException( "The var attribute cannot be null" ); } Document document = null; if ( source == null ) { SAXContentHandler handler = new SAXContentHandler...
String text = getBodyText( context );
String text = getBodyText();
public void run(Context context, XMLOutput output) throws Exception { if ( var == null ) { throw new IllegalArgumentException( "The var attribute cannot be null" ); } Document document = null; if ( source == null ) { SAXContentHandler handler = new SAXContentHandler...
if (items != null) { Iterator iter = items.evaluateAsIterator(context); if (log.isDebugEnabled()) { log.debug("Iterating through: " + iter);
try { if (items != null) { Iterator iter = items.evaluateAsIterator(context); if (log.isDebugEnabled()) { log.debug("Iterating through: " + iter); } for (index = 0; index < begin && iter.hasNext(); index++ ) { iter.next(); } while (iter.hasNext() && index < end) { Object value = iter.next(); if (var != null) { conte...
public void doTag(XMLOutput output) throws Exception { if (log.isDebugEnabled()) { log.debug("running with items: " + items); } if (items != null) { Iterator iter = items.evaluateAsIterator(context); if (log.isDebugEnabled()) { log.debug("Iteratin...
for (index = 0; index < begin && iter.hasNext(); index++ ) { iter.next(); } while (iter.hasNext() && index < end) { Object value = iter.next(); if (var != null) { context.setVariable(var, value);
else { if ( end == Integer.MAX_VALUE && begin == 0 ) { throw new MissingAttributeException( "items" );
public void doTag(XMLOutput output) throws Exception { if (log.isDebugEnabled()) { log.debug("running with items: " + items); } if (items != null) { Iterator iter = items.evaluateAsIterator(context); if (log.isDebugEnabled()) { log.debug("Iteratin...
if (indexVar != null) { context.setVariable(indexVar, new Integer(index)); } invokeBody(output); index++; for ( int i = 1; i < step; i++, index++ ) { if ( ! iter.hasNext() ) { return;
else { String varName = var; if ( varName == null ) { varName = indexVar;
public void doTag(XMLOutput output) throws Exception { if (log.isDebugEnabled()) { log.debug("running with items: " + items); } if (items != null) { Iterator iter = items.evaluateAsIterator(context); if (log.isDebugEnabled()) { log.debug("Iteratin...
iter.next();
for (index = begin; index <= end; index += step ) { if (varName != null) { Object value = new Integer(index); context.setVariable(varName, value); } invokeBody(output); }
public void doTag(XMLOutput output) throws Exception { if (log.isDebugEnabled()) { log.debug("running with items: " + items); } if (items != null) { Iterator iter = items.evaluateAsIterator(context); if (log.isDebugEnabled()) { log.debug("Iteratin...
else { if ( end == Integer.MAX_VALUE && begin == 0 ) { throw new MissingAttributeException( "items" ); } else { String varName = var; if ( varName == null ) { varName = indexVar; } for (index = begin; index <= end; index += step ) { if (varName != null) { Object value = new Integer(index); context.setVariable(varName...
catch (BreakException e) { if (log.isDebugEnabled()) { log.debug("loop terminated by break: " + e, e);
public void doTag(XMLOutput output) throws Exception { if (log.isDebugEnabled()) { log.debug("running with items: " + items); } if (items != null) { Iterator iter = items.evaluateAsIterator(context); if (log.isDebugEnabled()) { log.debug("Iteratin...
logger.debug("dbchildrenadd. source="+e.getSource());
public void dbChildrenInserted(SQLObjectEvent e) { if (!SwingUtilities.isEventDispatchThread()) return; if (logger.isDebugEnabled()) { if (e.getSQLSource() instanceof SQLRelationship) { SQLRelationship r = (SQLRelationship) e.getSQLSource(); logger.debug("dbChildrenInserted SQLObjectEvent: "+e +"; pk ...
logger.debug("dbchildrenremove. source="+e.getSource());
public void dbChildrenRemoved(SQLObjectEvent e) { if (!SwingUtilities.isEventDispatchThread()) return; if (logger.isDebugEnabled()) logger.debug("dbChildrenRemoved SQLObjectEvent: "+e); try { SQLObject[] oldEventSources = e.getChildren(); for (int i = 0; i < oldEventSources.length; i++) { ArchitectUtils.unli...
if (e.getPropertyName().equals("name") && !e.getNewValue().equals(e.getSQLSource().getName()) ) { logger.error("Name change event has wrong new value. new="+e.getNewValue()+"; real="+e.getSQLSource().getName()); }
public void dbObjectChanged(SQLObjectEvent e) { if (!SwingUtilities.isEventDispatchThread()) return; if (logger.isDebugEnabled()) logger.debug("dbObjectChanged SQLObjectEvent: "+e); SQLObject source = e.getSQLSource(); if (source instanceof SQLRelationship) { SQLRelationship r = (SQLRelationship) source; fireT...
final TreeModelEvent ev =e;
logger.debug("firing TreeStructuredChanged. source="+e.getSource()); final TreeModelEvent ev =e;
protected void fireTreeStructureChanged(TreeModelEvent e) { final TreeModelEvent ev =e; Runnable notifier = new Runnable(){ public void run() { Iterator it = treeModelListeners.iterator(); while (it.hasNext()) { ((TreeModelListener) it.next()).treeStructureChanged(ev); } } };// TODO FIXME XXX Re...
public PhotoFolderTreeModel() {
public PhotoFolderTreeModel( FolderNodeMapper mapper ) {
public PhotoFolderTreeModel() { super(); nodeMapper = new DefaultFolderNodeMapper(); }
nodeMapper = new DefaultFolderNodeMapper();
nodeMapper = mapper;
public PhotoFolderTreeModel() { super(); nodeMapper = new DefaultFolderNodeMapper(); }
TreeModelListener l = (TreeModelListener) iter.next();
final TreeModelListener l = (TreeModelListener) iter.next(); SwingUtilities.invokeLater( new Runnable() { public void run() { l.treeStructureChanged( fe ); } });
protected void fireTreeModelEvent( TreeModelEvent e ) { Iterator iter = treeModelListeners.iterator(); while ( iter.hasNext() ) { TreeModelListener l = (TreeModelListener) iter.next(); log.warn( "Sending treeModelEvent" ); l.treeStructureChanged( e ); } }
l.treeStructureChanged( e );
protected void fireTreeModelEvent( TreeModelEvent e ) { Iterator iter = treeModelListeners.iterator(); while ( iter.hasNext() ) { TreeModelListener l = (TreeModelListener) iter.next(); log.warn( "Sending treeModelEvent" ); l.treeStructureChanged( e ); } }
hv.export(tab,format,0,Chromosome.getSize());
hv.export(tab,format,0,Chromosome.getFilteredSize());
public void actionPerformed (ActionEvent e){ String command = e.getActionCommand(); if (dpButton.isSelected()){ if(txtButton.isSelected()){ adjButton.setEnabled(true); compressCheckBox.setEnabled(false); }else{ compressCheckBox.setEnab...
public SQLSchema(SQLObject parent, String name) { this.parent = parent; this.schemaName = name; this.children = new LinkedList();
public SQLSchema() { this(null, null);
public SQLSchema(SQLObject parent, String name) { this.parent = parent; this.schemaName = name; this.children = new LinkedList(); }
int format, tab;
int format; HaploviewTab tab;
public void actionPerformed (ActionEvent e){ String command = e.getActionCommand(); if (dpButton.isSelected()){ if(txtButton.isSelected()){ adjButton.setEnabled(true); compressCheckBox.setEnabled(false); }else{ compressCheckBox.setEnab...
tab = VIEW_D_NUM;
tab = hv.ldTab;
public void actionPerformed (ActionEvent e){ String command = e.getActionCommand(); if (dpButton.isSelected()){ if(txtButton.isSelected()){ adjButton.setEnabled(true); compressCheckBox.setEnabled(false); }else{ compressCheckBox.setEnab...
tab = VIEW_HAP_NUM;
tab = hv.hapsTab;
public void actionPerformed (ActionEvent e){ String command = e.getActionCommand(); if (dpButton.isSelected()){ if(txtButton.isSelected()){ adjButton.setEnabled(true); compressCheckBox.setEnabled(false); }else{ compressCheckBox.setEnab...
tab = VIEW_CHECK_NUM;
tab = hv.checkTab;
public void actionPerformed (ActionEvent e){ String command = e.getActionCommand(); if (dpButton.isSelected()){ if(txtButton.isSelected()){ adjButton.setEnabled(true); compressCheckBox.setEnabled(false); }else{ compressCheckBox.setEnab...
tab = VIEW_ASSOC_NUM; ((JTabbedPane)hv.tabs.getComponent(tab)).setSelectedComponent(hv.tdtPanel);
tab = hv.associationTab; ((JTabbedPane)tab.getComponent(0)).setSelectedComponent(hv.tdtPanel);
public void actionPerformed (ActionEvent e){ String command = e.getActionCommand(); if (dpButton.isSelected()){ if(txtButton.isSelected()){ adjButton.setEnabled(true); compressCheckBox.setEnabled(false); }else{ compressCheckBox.setEnab...
tab = VIEW_ASSOC_NUM; ((JTabbedPane)hv.tabs.getComponent(tab)).setSelectedComponent(hv.hapAssocPanel);
tab = hv.associationTab; ((JTabbedPane)tab.getComponent(0)).setSelectedComponent(hv.hapAssocPanel);
public void actionPerformed (ActionEvent e){ String command = e.getActionCommand(); if (dpButton.isSelected()){ if(txtButton.isSelected()){ adjButton.setEnabled(true); compressCheckBox.setEnabled(false); }else{ compressCheckBox.setEnab...
tab = VIEW_ASSOC_NUM; ((JTabbedPane)hv.tabs.getComponent(tab)).setSelectedComponent(hv.permutationPanel);
tab = hv.associationTab; ((JTabbedPane)tab.getComponent(0)).setSelectedComponent(hv.permutationPanel);
public void actionPerformed (ActionEvent e){ String command = e.getActionCommand(); if (dpButton.isSelected()){ if(txtButton.isSelected()){ adjButton.setEnabled(true); compressCheckBox.setEnabled(false); }else{ compressCheckBox.setEnab...
new TextMethods().linkageToHaps(markerResultArray,checkPanel.getPedFile(),filenames[0]+".haps");
new TextMethods().linkageToHaps(markerResultArray,checkPanel.getPedFile(),inputOptions[0]+".haps");
public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == READ_GENOTYPES){ ReadDataDialog readDialog = new ReadDataDialog("Open new data", this); readDialog.pack(); readDialog.setVisible(true); }else if (command == "Conti...
hapScroller.setViewportView(hapDisplay);
void defineBlocks(){ String[] methodStrings = {"95% of informative pairwise comparisons show strong LD via confidence intervals (SFS)", "Four Gamete Rule", "Solid block of strong LD via D prime (MJD)"}; JComboBox methodList = new JCombo...
JScrollPane hapScroller = new JScrollPane(hapDisplay);
hapScroller = new JScrollPane(hapDisplay);
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 ...
maxCompDist = Long.parseLong(filenames[2])*1000;
maxCompDist = Long.parseLong(inputOptions[2])*1000;
void processData(){ maxCompDist = Long.parseLong(filenames[2])*1000; try{ this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); final SwingWorker worker = new SwingWorker(){ public Object construct(){ dPrimeDisplay=null; ...
if (!(filenames[1].equals(""))){ readMarkers(new File(filenames[1]));
if (!(inputOptions[1].equals(""))){ readMarkers(new File(inputOptions[1]));
void processData(){ maxCompDist = Long.parseLong(filenames[2])*1000; try{ this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); final SwingWorker worker = new SwingWorker(){ public Object construct(){ dPrimeDisplay=null; ...
if (!(filenames[1].equals(""))){ readMarkers(new File(filenames[1]));
if (!(inputOptions[1].equals(""))){ readMarkers(new File(inputOptions[1]));
public Object construct(){ dPrimeDisplay=null; infoKnown = false; if (!(filenames[1].equals(""))){ readMarkers(new File(filenames[1])); } theData.generateDPrimeTable(maxCompDist); ...
filenames = f; File pedFile = new File(filenames[0]);
inputOptions = f; File pedFile = new File(inputOptions[0]);
void readPedGenotypes(String[] f){ //input is a 3 element array with //filenames[0] = ped file //filenames[1] = info file (null if none) //filenames[2] = max comparison distance (don't compute d' if markers are greater than this dist apart) filenames = f; File pedFile = new...
filenames = f;
inputOptions = f;
void readPhasedGenotypes(String[] f){ //input is a 3 element array with //filenames[0] = haps file //filenames[1] = info file (null if none) //filenames[2] = max comparison distance (don't compute d' if markers are greater than this dist apart) filenames = f; theData = new ...
theData.prepareHapsInput(new File(filenames[0]));
theData.prepareHapsInput(new File(inputOptions[0]));
void readPhasedGenotypes(String[] f){ //input is a 3 element array with //filenames[0] = haps file //filenames[1] = info file (null if none) //filenames[2] = max comparison distance (don't compute d' if markers are greater than this dist apart) filenames = f; theData = new ...
while (comparator.compare(sourceColumn, targetColumn) < 0) {
if (comparator.compare(sourceColumn, targetColumn) < 0) {
private List<DiffChunk<SQLObject>> generateColumnDiffs( SQLTable sourceTable, SQLTable targetTable) throws ArchitectException { TreeSet<SQLColumn> sourceColumnList; TreeSet<SQLColumn> targetColumnList; Iterator<SQLColumn> sourceColIter; Iterator<SQLColumn> targetColIter; SQLColumn sourceColumn; SQLColumn tar...
break;
private List<DiffChunk<SQLObject>> generateColumnDiffs( SQLTable sourceTable, SQLTable targetTable) throws ArchitectException { TreeSet<SQLColumn> sourceColumnList; TreeSet<SQLColumn> targetColumnList; Iterator<SQLColumn> sourceColIter; Iterator<SQLColumn> targetColIter; SQLColumn sourceColumn; SQLColumn tar...
while (comparator.compare(sourceColumn, targetColumn) > 0) {
if (comparator.compare(sourceColumn, targetColumn) > 0) {
private List<DiffChunk<SQLObject>> generateColumnDiffs( SQLTable sourceTable, SQLTable targetTable) throws ArchitectException { TreeSet<SQLColumn> sourceColumnList; TreeSet<SQLColumn> targetColumnList; Iterator<SQLColumn> sourceColIter; Iterator<SQLColumn> targetColIter; SQLColumn sourceColumn; SQLColumn tar...
while (comparator.compare(sourceColumn, targetColumn) == 0) {
if (comparator.compare(sourceColumn, targetColumn) == 0) {
private List<DiffChunk<SQLObject>> generateColumnDiffs( SQLTable sourceTable, SQLTable targetTable) throws ArchitectException { TreeSet<SQLColumn> sourceColumnList; TreeSet<SQLColumn> targetColumnList; Iterator<SQLColumn> sourceColIter; Iterator<SQLColumn> targetColIter; SQLColumn sourceColumn; SQLColumn tar...
SQLRelationshipComparator relComparator = new SQLRelationshipComparator();
private List<DiffChunk<SQLObject>> generateRelationshipDiffs( Collection<SQLTable> sourceTables, Collection<SQLTable> targetTables) throws ArchitectException { //XXX: This is using an incorrect comparator, it only checks by relationship //names and does not get into a deeper level of checking the mappings. Set<...
Set<SQLRelationship> sourceRels = new TreeSet<SQLRelationship>(comparator); Set<SQLRelationship> targetRels = new TreeSet<SQLRelationship>(comparator);
Set<SQLRelationship> sourceRels = new TreeSet<SQLRelationship>(relComparator); Set<SQLRelationship> targetRels = new TreeSet<SQLRelationship>(relComparator);
private List<DiffChunk<SQLObject>> generateRelationshipDiffs( Collection<SQLTable> sourceTables, Collection<SQLTable> targetTables) throws ArchitectException { //XXX: This is using an incorrect comparator, it only checks by relationship //names and does not get into a deeper level of checking the mappings. Set<...
for (SQLTable t : sourceTables) { sourceRels.addAll(t.getImportedKeys()); }
for (SQLTable t : sourceTables) { if (t.getImportedKeys() != null){ sourceRels.addAll(t.getImportedKeys()); } } for (SQLTable t : targetTables) { if (t.getImportedKeys() != null){ targetRels.addAll(t.getImportedKeys()); } }
private List<DiffChunk<SQLObject>> generateRelationshipDiffs( Collection<SQLTable> sourceTables, Collection<SQLTable> targetTables) throws ArchitectException { //XXX: This is using an incorrect comparator, it only checks by relationship //names and does not get into a deeper level of checking the mappings. Set<...
for (SQLTable t : targetTables) { targetRels.addAll(t.getImportedKeys()); }
private List<DiffChunk<SQLObject>> generateRelationshipDiffs( Collection<SQLTable> sourceTables, Collection<SQLTable> targetTables) throws ArchitectException { //XXX: This is using an incorrect comparator, it only checks by relationship //names and does not get into a deeper level of checking the mappings. Set<...
while (comparator.compare(sourceRel, targetRel) < 0) { diffs.add(new DiffChunk<SQLObject>(sourceRel, DiffType.LEFTONLY)); diffs.addAll(generateMappingDiffs(sourceRel, null));
if (relComparator.compare(sourceRel, targetRel) < 0) { diffs.add(new DiffChunk<SQLObject>(sourceRel, DiffType.LEFTONLY));
private List<DiffChunk<SQLObject>> generateRelationshipDiffs( Collection<SQLTable> sourceTables, Collection<SQLTable> targetTables) throws ArchitectException { //XXX: This is using an incorrect comparator, it only checks by relationship //names and does not get into a deeper level of checking the mappings. Set<...
break;
private List<DiffChunk<SQLObject>> generateRelationshipDiffs( Collection<SQLTable> sourceTables, Collection<SQLTable> targetTables) throws ArchitectException { //XXX: This is using an incorrect comparator, it only checks by relationship //names and does not get into a deeper level of checking the mappings. Set<...
while (comparator.compare(sourceRel, targetRel) > 0) {
if (relComparator.compare(sourceRel, targetRel) > 0) {
private List<DiffChunk<SQLObject>> generateRelationshipDiffs( Collection<SQLTable> sourceTables, Collection<SQLTable> targetTables) throws ArchitectException { //XXX: This is using an incorrect comparator, it only checks by relationship //names and does not get into a deeper level of checking the mappings. Set<...
diffs.addAll(generateMappingDiffs(null, targetRel));
private List<DiffChunk<SQLObject>> generateRelationshipDiffs( Collection<SQLTable> sourceTables, Collection<SQLTable> targetTables) throws ArchitectException { //XXX: This is using an incorrect comparator, it only checks by relationship //names and does not get into a deeper level of checking the mappings. Set<...
while (comparator.compare(sourceRel, targetRel) == 0) {
if (relComparator.compare(sourceRel, targetRel) == 0) {
private List<DiffChunk<SQLObject>> generateRelationshipDiffs( Collection<SQLTable> sourceTables, Collection<SQLTable> targetTables) throws ArchitectException { //XXX: This is using an incorrect comparator, it only checks by relationship //names and does not get into a deeper level of checking the mappings. Set<...
diffs.addAll(generateMappingDiffs(sourceRel, targetRel));
private List<DiffChunk<SQLObject>> generateRelationshipDiffs( Collection<SQLTable> sourceTables, Collection<SQLTable> targetTables) throws ArchitectException { //XXX: This is using an incorrect comparator, it only checks by relationship //names and does not get into a deeper level of checking the mappings. Set<...
targetContinue = false; break;
targetContinue = false;
private List<DiffChunk<SQLObject>> generateRelationshipDiffs( Collection<SQLTable> sourceTables, Collection<SQLTable> targetTables) throws ArchitectException { //XXX: This is using an incorrect comparator, it only checks by relationship //names and does not get into a deeper level of checking the mappings. Set<...
diffs.addAll(generateMappingDiffs(sourceRel, null));
private List<DiffChunk<SQLObject>> generateRelationshipDiffs( Collection<SQLTable> sourceTables, Collection<SQLTable> targetTables) throws ArchitectException { //XXX: This is using an incorrect comparator, it only checks by relationship //names and does not get into a deeper level of checking the mappings. Set<...
diffs.add(new DiffChunk<SQLObject>(targetRel, DiffType.RIGHTONLY)); diffs.addAll(generateMappingDiffs(null, targetRel));
diffs.add(new DiffChunk<SQLObject>(targetRel, DiffType.RIGHTONLY));
private List<DiffChunk<SQLObject>> generateRelationshipDiffs( Collection<SQLTable> sourceTables, Collection<SQLTable> targetTables) throws ArchitectException { //XXX: This is using an incorrect comparator, it only checks by relationship //names and does not get into a deeper level of checking the mappings. Set<...
public String draw();
public String draw(String applicationName);
public String draw();
private void applicationChanged(ApplicationConfig appConfig) { removeApplication(appConfig); addApplication(appConfig);
private void applicationChanged(ApplicationEvent appEvent) { removeApplication(appEvent.getApplicationConfig()); addApplication(appEvent);
private void applicationChanged(ApplicationConfig appConfig) { removeApplication(appConfig); addApplication(appConfig); }
addApplication(((NewApplicationEvent)event).getApplicationConfig());
addApplication((NewApplicationEvent)event);
public void start() { for (ApplicationConfig appConfig : ApplicationConfigManager .getAllApplications()) { // only add non-cluster applications if(!appConfig.isCluster()) addApplication(appConfig); } // TODO: perfect dependency to be i...
applicationChanged(((ApplicationChangedEvent)event).getApplicationConfig());
applicationChanged((ApplicationChangedEvent)event);
public void start() { for (ApplicationConfig appConfig : ApplicationConfigManager .getAllApplications()) { // only add non-cluster applications if(!appConfig.isCluster()) addApplication(appConfig); } // TODO: perfect dependency to be i...
addApplication(((NewApplicationEvent)event).getApplicationConfig());
addApplication((NewApplicationEvent)event);
public void handleEvent(EventObject event) { if(!(event instanceof ApplicationEvent)){ throw new IllegalArgumentException("event must be of type ApplicationEvent"); } if(event instanceof NewApplicationEvent){ addApplication((...
applicationChanged(((ApplicationChangedEvent)event).getApplicationConfig());
applicationChanged((ApplicationChangedEvent)event);
public void handleEvent(EventObject event) { if(!(event instanceof ApplicationEvent)){ throw new IllegalArgumentException("event must be of type ApplicationEvent"); } if(event instanceof NewApplicationEvent){ addApplication((...
} catch (Exception e) {
} catch (ConnectionFailedException e){
public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) throws Exception { ...
super("Edit Table Properties...",
super("Table Properties...",
public EditTableAction() { super("Edit Table Properties...", ASUtils.createIcon("TableProperties", "Edit Table Properties", ArchitectFrame.getMainInstance().sprefs.getInt(SwingUserSettings.ICON_SIZE, 24))); }
"Edit Table Properties",
"Table Properties",
public EditTableAction() { super("Edit Table Properties...", ASUtils.createIcon("TableProperties", "Edit Table Properties", ArchitectFrame.getMainInstance().sprefs.getInt(SwingUserSettings.ICON_SIZE, 24))); }
putValue(SHORT_DESCRIPTION, "Table Properties");
public EditTableAction() { super("Edit Table Properties...", ASUtils.createIcon("TableProperties", "Edit Table Properties", ArchitectFrame.getMainInstance().sprefs.getInt(SwingUserSettings.ICON_SIZE, 24))); }
"match"
element
protected SAXReader createSAXReader() throws Exception { // installs the NekoHTML parser SAXParser parser = new SAXParser(); parser.setProperty( "http://cyberneko.org/html/properties/names/elems", "match" ); parser.setProperty( "http://cyberneko.or...
"match"
attribute
protected SAXReader createSAXReader() throws Exception { // installs the NekoHTML parser SAXParser parser = new SAXParser(); parser.setProperty( "http://cyberneko.org/html/properties/names/elems", "match" ); parser.setProperty( "http://cyberneko.or...
registerTag("sleep", SleepTag.class);
public UtilTagLibrary() { registerTag("loadText", LoadTextTag.class); registerTag("properties", PropertiesTag.class); registerTag("tokenize", TokenizeTag.class); }
suite.addTestSuite(TestCompareDMPanel.class);
public static Test suite() { TestSuite suite = new TestSuite("Test for Architect's Swing GUI"); //$JUnit-BEGIN$ suite.addTestSuite(TestSwingUIProject.class); suite.addTestSuite(TestArchitectFrame.class); suite.addTestSuite(TestAutoLayoutAction.class); suite.addTestSuite(TestPlayPen.class); suite.addTestSuite(...
if ( uri == null ) { throw new JellyException( "<j:include> must have a 'uri' attribute defined" );
if (uri == null) { throw new MissingAttributeException( "uri" );
public void doTag(XMLOutput output) throws Exception { if ( uri == null ) { throw new JellyException( "<j:include> must have a 'uri' attribute defined" ); } // we need to create a new JellyContext of the URI // take off the script name from the URL conte...
public Object getSource() {
public String getSource() {
public Object getSource() { return source; }
public void setSource(Object source) {
public void setSource(String source) {
public void setSource(Object source) { this.source = source; }
if (!isNew) { oldName = dbcsPanel.getDbcs().getName(); } else { oldName = null; }
public DBCS_OkAction(DBCSPanel dbcsPanel, boolean isNew) { super("Ok"); this.dbcsPanel = dbcsPanel; this.isNew = isNew; }
public void actionPerformed(ActionEvent e) { logger.debug(getValue(SHORT_DESCRIPTION) + " started"); dbcsPanel.applyChanges();
public void actionPerformed(ActionEvent e) {
public void actionPerformed(ActionEvent e) { logger.debug(getValue(SHORT_DESCRIPTION) + " started"); dbcsPanel.applyChanges(); ArchitectDataSource newDS = dbcsPanel.getDbcs(); if (isNew) { if ("".equals(newDS.getName().trim())) { JOptionPane.showMessageDialog(newConnectionDialog,"A connection must have at lea...
JOptionPane.showMessageDialog(newConnectionDialog,"A connection with the name \""+newDS.getName()+"\" already exists");
JOptionPane.showMessageDialog(newConnectionDialog,"A connection with the name \""+curName+"\" already exists");
public void actionPerformed(ActionEvent e) { logger.debug(getValue(SHORT_DESCRIPTION) + " started"); dbcsPanel.applyChanges(); ArchitectDataSource newDS = dbcsPanel.getDbcs(); if (isNew) { if ("".equals(newDS.getName().trim())) { JOptionPane.showMessageDialog(newConnectionDialog,"A connection must have at lea...
}
} else if (curName.equals(oldName)) { System.out.println("The current Name is the same as the old name"); dbcsPanel.applyChanges(); } else { PlDotIni plDotIni = ArchitectFrame.getMainInstance().getUserSettings().getPlDotIni(); if (plDotIni.getDataSource(newDS.getName()) == null ) { dbcsPanel.applyChanges(); } else { ...
public void actionPerformed(ActionEvent e) { logger.debug(getValue(SHORT_DESCRIPTION) + " started"); dbcsPanel.applyChanges(); ArchitectDataSource newDS = dbcsPanel.getDbcs(); if (isNew) { if ("".equals(newDS.getName().trim())) { JOptionPane.showMessageDialog(newConnectionDialog,"A connection must have at lea...
}
} else { g2.setBackground( this.getBackground() ); }
private void paintThumbnail( Graphics2D g2, PhotoInfo photo, int startx, int starty, boolean isSelected ) { log.debug( "paintThumbnail entry " + photo.getUid() ); long startTime = System.currentTimeMillis(); long thumbReadyTime = 0; long thumbDrawnTime = 0; long endTime = 0; // Cu...
Date lower = new Date( date.getTime() - lAccuracy ); Date upper = new Date( date.getTime() + (lAccuracy-1) ); if ( fdParsers == null ) { createParsers(); }
public String format() { long lAccuracy = (long) (accuracy * 24 * 3600 * 1000); String dateStr = ""; if ( date == null ) { return ""; } if ( accuracy > 0 ) { // Find the correct format to use String formatStr =accuracyFormatStrings[0]; for ( int i = 1; i < accuracyFormatLimits.length; i++ ) {...
String formatStr =accuracyFormatStrings[0]; for ( int i = 1; i < accuracyFormatLimits.length; i++ ) { if ( accuracy < accuracyFormatLimits[i] ) {
FuzzyDateParser parser = fdParsers[0]; for ( int i = 0; i < fdParsers.length; i++ ) { if ( (2 * lAccuracy) < fdParsers[i].getFuzzyPeriodLength( lower ) ) {
public String format() { long lAccuracy = (long) (accuracy * 24 * 3600 * 1000); String dateStr = ""; if ( date == null ) { return ""; } if ( accuracy > 0 ) { // Find the correct format to use String formatStr =accuracyFormatStrings[0]; for ( int i = 1; i < accuracyFormatLimits.length; i++ ) {...
formatStr =accuracyFormatStrings[i];
parser = fdParsers[i];
public String format() { long lAccuracy = (long) (accuracy * 24 * 3600 * 1000); String dateStr = ""; if ( date == null ) { return ""; } if ( accuracy > 0 ) { // Find the correct format to use String formatStr =accuracyFormatStrings[0]; for ( int i = 1; i < accuracyFormatLimits.length; i++ ) {...
DateFormat df = new SimpleDateFormat( formatStr ); Date lower = new Date( date.getTime() - lAccuracy ); Date upper = new Date( date.getTime() + lAccuracy ); String lowerStr = df.format( lower ); String upperStr = df.format( upper );
String lowerStr = parser.format( lower ); String upperStr = parser.format( upper );
public String format() { long lAccuracy = (long) (accuracy * 24 * 3600 * 1000); String dateStr = ""; if ( date == null ) { return ""; } if ( accuracy > 0 ) { // Find the correct format to use String formatStr =accuracyFormatStrings[0]; for ( int i = 1; i < accuracyFormatLimits.length; i++ ) {...
showInPlayPenAction = new ShowInPlayPenAction();
public DBTree() { setUI(new MultiDragTreeUI()); setRootVisible(false); setShowsRootHandles(true); ds = new DragSource(); DragGestureRecognizer dgr = ds.createDefaultDragGestureRecognizer (this, DnDConstants.ACTION_COPY, new DBTreeDragGestureListener()); newDBCSAction = new NewDBCSAction(); dbcsPropertiesActio...
mi = new JMenuItem(); mi.setAction(showInPlayPenAction); newMenu.add(mi);
protected JPopupMenu refreshMenu(TreePath p) { logger.debug("refreshMenu is being called."); JPopupMenu newMenu = new JPopupMenu(); if (isTargetDatabaseNode(p)) { // two menu items: "Set Target Database" and "Connection Properties newMenu.add(connectionsMenu = new JMenu("Set Target Database")); if (Archit...
public Object evaluate(Context context) { try {
public Object evaluate(JellyContext context) {
public Object evaluate(Context context) { try { JexlContext jexlContext = new JexlContext() { Map ctx; public void setVars(Map vars) { ctx = vars; } public Map getVars() { return ctx; } }; jexlContext.setVars(context.getVariables()); if ( log.isDebugEnab...
JexlContext jexlContext = new JexlContext() { Map ctx;
try {
public Object evaluate(Context context) { try { JexlContext jexlContext = new JexlContext() { Map ctx; public void setVars(Map vars) { ctx = vars; } public Map getVars() { return ctx; } }; jexlContext.setVars(context.getVariables()); if ( log.isDebugEnab...
public void setVars(Map vars) { ctx = vars; }
JexlContext jexlContext = new JexlContext() {
public Object evaluate(Context context) { try { JexlContext jexlContext = new JexlContext() { Map ctx; public void setVars(Map vars) { ctx = vars; } public Map getVars() { return ctx; } }; jexlContext.setVars(context.getVariables()); if ( log.isDebugEnab...
public Map getVars() { return ctx; } };
Map ctx;
public Object evaluate(Context context) { try { JexlContext jexlContext = new JexlContext() { Map ctx; public void setVars(Map vars) { ctx = vars; } public Map getVars() { return ctx; } }; jexlContext.setVars(context.getVariables()); if ( log.isDebugEnab...
jexlContext.setVars(context.getVariables());
public void setVars(Map vars) {
public Object evaluate(Context context) { try { JexlContext jexlContext = new JexlContext() { Map ctx; public void setVars(Map vars) { ctx = vars; } public Map getVars() { return ctx; } }; jexlContext.setVars(context.getVariables()); if ( log.isDebugEnab...
if ( log.isDebugEnabled() ) { log.debug( "Evaluating EL: " + expression ); } return expression.evaluate( jexlContext ); } catch (Exception e) { log.warn( "Caught exception evaluating: " + expression + ". Reason: " + e, e ); return null; } }
ctx = vars; } public Map getVars() { return ctx; } }; jexlContext.setVars(context.getVariables()); if (log.isDebugEnabled()) { log.debug("Evaluating EL: " + expression); } return expression.evaluate(jexlContext); } catch (Exception e) { log.warn("Caught exception evaluating: " + expression + ". Reason: " +...
public Object evaluate(Context context) { try { JexlContext jexlContext = new JexlContext() { Map ctx; public void setVars(Map vars) { ctx = vars; } public Map getVars() { return ctx; } }; jexlContext.setVars(context.getVariables()); if ( log.isDebugEnab...
unrelatedIndividuals = new Vector();
unrelatedIndividuals = useable;
public Vector check() throws PedFileException{ //before we perform the check we want to prune out individuals with too much missing data //or trios which contain individuals with too much missing data Iterator fitr = families.values().iterator(); Vector useable = new Vector(); whi...
return;
logger.debug("SQLColumn: populate is a no-op");
public void populate() throws ArchitectException { // SQLColumn doesn't have children, so populate does nothing! return; }
System.out.println(form.getField(0) + " " + form.getField(1) + ". " +
logger.info(form.getField(0) + " " + form.getField(1) + ". " +
public static void main(String[] args) { JTextField[] fields = { new JTextField(), new JTextField(), new JTextField(), new JTextField() }; String[] labels = { "First Name", "Middle Initial", "Last Name", "Age" }; char[] mnemonics = { 'F', 'M', 'L', 'A' }; int[] widths = { 15, 1, 15, 3 }; String[] descs = { "First...
System.out.println(form.getField(0) + " " + form.getField(1) + ". " +
logger.info(form.getField(0) + " " + form.getField(1) + ". " +
public void actionPerformed(ActionEvent e) { System.out.println(form.getField(0) + " " + form.getField(1) + ". " + form.getField(2) + ", age " + form.getField(3)); }
thumbReadyTime = System.currentTimeMillis();
private void paintThumbnail( Graphics2D g2, PhotoInfo photo, int startx, int starty, boolean isSelected ) { log.debug( "paintThumbnail entry " + photo.getUid() ); // Current position in which attributes can be drawn int ypos = starty + rowHeight/2; if ( photo != null ) { Thumbnail thumbnail...
log.debug( "Thumb fetch " + (thumbReadyTime - startTime ) + " ms" ); log.debug( "Thumb draw " + ( thumbDrawnTime - thumbReadyTime ) + " ms" ); log.debug( "Deacoration draw " + (endTime - thumbDrawnTime ) + " ms" ); log.debug( "Total " + (endTime - startTime ) + " ms" );
private void paintThumbnail( Graphics2D g2, PhotoInfo photo, int startx, int starty, boolean isSelected ) { log.debug( "paintThumbnail entry " + photo.getUid() ); // Current position in which attributes can be drawn int ypos = starty + rowHeight/2; if ( photo != null ) { Thumbnail thumbnail...