rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k |
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((Chromosome)chrom.lastElement()).setHaploid(true); | public Vector linkageToChrom(File infile, int type) throws IllegalArgumentException, HaploViewException, PedFileException, IOException{ pedFile = new PedFile(); if (type == PED_FILE){ pedFile.parseLinkage(infile); }else{ pedFile.parseHapMap(infile); } ... | |
}else{ ((Chromosome)chrom.lastElement()).setHaploid(true); | public Vector linkageToChrom(File infile, int type) throws IllegalArgumentException, HaploViewException, PedFileException, IOException{ pedFile = new PedFile(); if (type == PED_FILE){ pedFile.parseLinkage(infile); }else{ pedFile.parseHapMap(infile); } ... | |
return contentPane.getToolTipText(e); | Point zp = unzoomPoint(e.getPoint()); MouseEvent zoomedEvent = new MouseEvent((Component) e.getSource(), e.getID(), e.getWhen(), e.getModifiers(), zp.x, zp.y, e.getClickCount(), e.isPopupTrigger(), e.getButton()); return contentPane.getToolTipText(zoomedEvent); | public String getToolTipText(MouseEvent e) { return contentPane.getToolTipText(e); } |
ArchitectFrame.getMainInstance().getUserSettings().getPlDotIni().addDataSource(ds); | if (plDotIni.getDataSource(ds.getName()) != null) { plDotIni.removeDataSource(ds); } plDotIni.addDataSource(ds); | public void testSourceDropDownsWithOnlyCatalog() { ArchitectDataSource ds = new ArchitectDataSource(); ds.setDisplayName("testSourceDropDownsWithOnlyCatalog"); ds.setDriverClass("ca.sqlpower.architect.MockJDBCDriver"); ds.setUser("fake"); ds.setPass("fake"); //this creates a mock jdbc database with only catalogs... |
ArchitectFrame.getMainInstance().getUserSettings().getPlDotIni().addDataSource(ds); | if (plDotIni.getDataSource(ds.getName()) != null) { plDotIni.removeDataSource(ds); } plDotIni.addDataSource(ds); | public void testSourceDropDownsWithSchemaAndCatalog() { ArchitectDataSource ds = new ArchitectDataSource(); ds.setDisplayName("testSourceDropDownsWithSchemaAndCatalog"); ds.setDriverClass("ca.sqlpower.architect.MockJDBCDriver"); ds.setUser("fake"); ds.setPass("fake"); //this creates a mock jdbc database with cat... |
if (plDotIni.getDataSource(ds.getName()) != null) { plDotIni.removeDataSource(ds); } | public void testTargetDropDownsWithOnlyCatalog() { ArchitectDataSource ds = new ArchitectDataSource(); ds.setDisplayName("testTargetDropDownsWithOnlyCatalog"); ds.setDriverClass("ca.sqlpower.architect.MockJDBCDriver"); ds.setUser("fake"); ds.setPass("fake"); //this creates a mock jdbc database with schemas only ... | |
if (plDotIni.getDataSource(ds.getName()) != null) { plDotIni.removeDataSource(ds); } | public void testTargetDropDownsWithOnlySchema() { ArchitectDataSource ds = new ArchitectDataSource(); ds.setDisplayName("testTargetDropDownsWithOnlySchema"); ds.setDriverClass("ca.sqlpower.architect.MockJDBCDriver"); ds.setUser("fake"); ds.setPass("fake"); //this creates a mock jdbc database with only schemas d... | |
if (plDotIni.getDataSource(ds.getName()) != null) { plDotIni.removeDataSource(ds); } | public void testTargetDropDownsWithSchemaAndCatalog() { ArchitectDataSource ds = new ArchitectDataSource(); ds.setDisplayName("testTargetDropDownsWithSchemaAndCatalog"); ds.setDriverClass("ca.sqlpower.architect.MockJDBCDriver"); ds.setUser("fake"); ds.setPass("fake"); //this creates a mock jdbc database with sch... | |
if (plDotIni.getDataSource(ds.getName()) != null) { plDotIni.removeDataSource(ds); } | public void testTargetSchemaUpdateByCatalogChange(){ ArchitectDataSource ds = new ArchitectDataSource(); ds.setDisplayName("testTargetSchemaUpdateByCatalogChange"); ds.setDriverClass("ca.sqlpower.architect.MockJDBCDriver"); ds.setUser("fake"); ds.setPass("fake"); //this creates a mock jdbc database with catalogs... | |
InputStream schemaIS = getClass().getClassLoader().getResourceAsStream( "photovault_schema.xml" ); Database dbModel = new DatabaseIO().read( new InputStreamReader( schemaIS ) ); String driverName = "com.mysql.jdbc.Driver"; String dbUrl = "jdbc:mysql: DataSource ds = null; if ( instanceType == TYPE_EMBEDDED ) { if (... | createDatabase( user, passwd, null ); | public void createDatabase( String user, String passwd ) { // Get the database schema XML file InputStream schemaIS = getClass().getClassLoader().getResourceAsStream( "photovault_schema.xml" ); Database dbModel = new DatabaseIO().read( new InputStreamReader( schemaIS ) ); ... |
fc.setSelectedFile(null); | 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_... | |
prefs.putInt(SwingUserSettings.DIVIDER_LOCATION, splitPane.getDividerLocation()); | public void actionPerformed(ActionEvent e) { if (promptForUnsavedModifications()) { JFileChooser chooser = new JFileChooser(); chooser.addChoosableFileFilter(ASUtils.ARCHITECT_FILE_FILTER); int returnVal = chooser.showOpenDialog(ArchitectFrame.this); if (returnVal == JFileChoo... | |
splitPane.setDividerLocation (sprefs.getInt(SwingUserSettings.DIVIDER_LOCATION, 150)); | splitPane.setDividerLocation(prefs.getInt(SwingUserSettings.DIVIDER_LOCATION,150)); | protected void init() throws ArchitectException { int accelMask = Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(); prefs = PrefsUtils.getUserPrefsNode(architectSession); UserSettings us; // must be done right away, because a static // initializer in this class effects BeanUtils // behaviour whi... |
prefs.putInt(SwingUserSettings.DIVIDER_LOCATION, splitPane.getDividerLocation()); | public void actionPerformed(ActionEvent e) { if (promptForUnsavedModifications()) { try { closeProject(getProject()); setProject(new SwingUIProject("New Project")); logger.debug("Glass pane is "+getGlassPane()); } catch (Exception ex) { ... | |
splitPane.setRightComponent(new JScrollPane(playpen)); | splitPane.setRightComponent(new JScrollPane(playpen)); splitPane.setDividerLocation(prefs.getInt(SwingUserSettings.DIVIDER_LOCATION,150)); | public void setProject(SwingUIProject p) throws ArchitectException { this.project = p; logger.debug("Setting project to "+project); setTitle(project.getName()+" - Power*Architect"); playpen = project.getPlayPen(); dbTree = project.getSourceDatabases(); setupActions(); setupConnectionsMenu(); splitPane.setL... |
RMINotificationListener notifListener = toRMINotificationListener(listener); notifications.put(listener, notifListener); NotificationFilter notifFilter = toJMXNotificationFilter(filter); | public void addNotificationListener(ObjectName objectName, ObjectNotificationListener listener, ObjectNotificationFilter filter, Object handback){ RMINotificationListener notifListener = ... | |
notifListener, notifFilter, handback); | notifListener, notifFilter, new String()); | public void addNotificationListener(ObjectName objectName, ObjectNotificationListener listener, ObjectNotificationFilter filter, Object handback){ RMINotificationListener notifListener = ... |
RMINotificationListener notifListener = (RMINotificationListener)notifications.remove(listener); | MyRMINotificationListener notifListener = (MyRMINotificationListener) notifications.remove(listener); | public void removeNotificationListener(ObjectName objectName, ObjectNotificationListener listener, ObjectNotificationFilter filter, Object handback){ RMINotificationListener notifList... |
notifListener.unexport(); | public void removeNotificationListener(ObjectName objectName, ObjectNotificationListener listener, ObjectNotificationFilter filter, Object handback){ RMINotificationListener notifList... | |
private static RMINotificationListener toRMINotificationListener( final ObjectNotificationListener listener){ | private static MyRMINotificationListener toRMINotificationListener( final ObjectNotificationListener listener) { | private static RMINotificationListener toRMINotificationListener( final ObjectNotificationListener listener){ return new MyRMINotificationListener(listener); } |
throw new RuntimeException("Notifications not supported"); | NotificationListener notifListener = toJMXNotificationListener(listener); notifications.put(listener, notifListener); NotificationFilter notifFilter = toJMXNotificationFilter(filter); notifFilters.put(filter, notifFilter); Class[] methodSignature = new Class[]{javax.management.ObjectName.class, NotificationListener.cl... | public void addNotificationListener(ObjectName objectName, ObjectNotificationListener listener, ObjectNotificationFilter filter, Object handback){ throw new RuntimeException("Notifications not... |
if ( !testFile.exists() ) { fail( "could not find test file " + testFile ); } | public void testThumbWithNoInstances() { PhotoInfo photo = PhotoInfo.create(); Thumbnail thumb = photo.getThumbnail(); assertTrue( "getThumbnail should return default thumbnail", thumb == Thumbnail.getDefaultThumbnail() ) ; assertEquals( "No new instances should have been created", 0, photo.getNumInstances() )... | |
for (int i = 0; i < viewItems.length; i++) { if (command.equals(viewItems[i])) tabs.setSelectedIndex(i); | for (int i = 0; i < tabs.getTabCount(); i++) { if (command.equals(tabs.getTitleAt(i))){ tabs.setSelectedIndex(i); break; } | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command.equals(READ_GENOTYPES)){ ReadDataDialog readDialog = new ReadDataDialog("Open new data", this); readDialog.pack(); readDialog.setVisible(true); } else if (command.equ... |
return "Exit from jManage command prompt mode"; | return "Exits from jManage command prompt mode"; | public String getShortHelp(){ return "Exit from jManage command prompt mode"; } |
series[i].setMaximumItemCount(100); | private void poll() { Properties properties = getNewValues(); if(properties == null) return; long timestamp = Long.parseLong(properties.getProperty("timestamp")); // todo: this is not used String attributes = properties.getProperty("attributes"); String values = properties.... | |
if(authorizedList == null || authorizedList.isEmpty()) return false; | public boolean isAuthorized(ACLContext context, User user) { List authorizedList = getAuthorizedList(context); for(Iterator it=authorizedList.iterator(); it.hasNext(); ){ String authorized = (String)it.next(); if(user.getName().equals(authorized) || user.hasRole(authorized)){ ... | |
if (!(thisAllele-5 == a1)){ | if (!(thisAllele-4 == a1)){ | void prepareMarkerInput(File infile, long md, String[][] hapmapGoodies) throws IOException, HaploViewException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position. the... |
public void adjustDisplay() { | public void adjustDisplay(int dt){ | public void adjustDisplay() { //this is called when the controller wants to change the haps //displayed, instead of directly repainting so that none of this math //is done when the screen repaints for other reasons (resizing, focus change, etc) //first filter haps on displaythresh ... |
filteredHaplos = new Haplotype[orderedHaplos.length][]; boolean atLeastOneHap = false; | Haplotype[][] filts; filts = new Haplotype[orderedHaplos.length][]; int numhaps = 0; | public void adjustDisplay() { //this is called when the controller wants to change the haps //displayed, instead of directly repainting so that none of this math //is done when the screen repaints for other reasons (resizing, focus change, etc) //first filter haps on displaythresh ... |
if (orderedHaplos[i][j].getPercentage()*100 > displayThresh){ | if (orderedHaplos[i][j].getPercentage()*100 > dt){ | public void adjustDisplay() { //this is called when the controller wants to change the haps //displayed, instead of directly repainting so that none of this math //is done when the screen repaints for other reasons (resizing, focus change, etc) //first filter haps on displaythresh ... |
atLeastOneHap=true; | numhaps++; | public void adjustDisplay() { //this is called when the controller wants to change the haps //displayed, instead of directly repainting so that none of this math //is done when the screen repaints for other reasons (resizing, focus change, etc) //first filter haps on displaythresh ... |
if (atLeastOneHap){ printable++; atLeastOneHap=false; | if (numhaps > 1){ printable++; numhaps=0; | public void adjustDisplay() { //this is called when the controller wants to change the haps //displayed, instead of directly repainting so that none of this math //is done when the screen repaints for other reasons (resizing, focus change, etc) //first filter haps on displaythresh ... |
filteredHaplos[i] = new Haplotype[tempVector.size()]; tempVector.copyInto(filteredHaplos[i]); | filts[i] = new Haplotype[tempVector.size()]; tempVector.copyInto(filts[i]); | public void adjustDisplay() { //this is called when the controller wants to change the haps //displayed, instead of directly repainting so that none of this math //is done when the screen repaints for other reasons (resizing, focus change, etc) //first filter haps on displaythresh ... |
if (!(printable == filteredHaplos.length)) return; | if (!(printable == filts.length)){ JOptionPane.showMessageDialog(this.getParent(), "Error: At least one block has too few haplotypes of frequency > " + dt, "Error", JOptionPane.ERROR_MESSAGE); return; } | public void adjustDisplay() { //this is called when the controller wants to change the haps //displayed, instead of directly repainting so that none of this math //is done when the screen repaints for other reasons (resizing, focus change, etc) //first filter haps on displaythresh ... |
displayThresh = dt; filteredHaplos = filts; | public void adjustDisplay() { //this is called when the controller wants to change the haps //displayed, instead of directly repainting so that none of this math //is done when the screen repaints for other reasons (resizing, focus change, etc) //first filter haps on displaythresh ... | |
adjustDisplay(); | adjustDisplay(displayThresh); | public void getHaps() throws HaploViewException{ if (theData.blocks == null) {return;} Haplotype[][] haplos = theData.generateHaplotypes(theData.blocks, 0); orderedHaplos = new Haplotype[haplos.length][]; for (int i = 0; i < haplos.length; i++) { Vector orderedHaps = new Vecto... |
result = FilteringScore.rangeComparator() .compare(first.getFilteringScore(), second.getFilteringScore()); | FilteringScore<?> firstScore = first.getFilteringScore(); FilteringScore<?> secondScore = second.getFilteringScore(); result = FilteringScore.rangeComparator().compare(firstScore, secondScore); | public int compare(CompositeScore<?> first, CompositeScore<?> second) { int result = FilteringScore.nullCompare(first, second); if (result != 0) { return result; } result = FilteringScore.rangeComparator() .compare(first.getFilteringScore... |
result = OrderingScore.fullComparator() .compare(first.getOrderingScore(), second.getOrderingScore()); | if (considerOrdering(firstScore) && considerOrdering(secondScore)) { | public int compare(CompositeScore<?> first, CompositeScore<?> second) { int result = FilteringScore.nullCompare(first, second); if (result != 0) { return result; } result = FilteringScore.rangeComparator() .compare(first.getFilteringScore... |
if (result != 0) { return result; | result = OrderingScore.fullComparator() .compare(first.getOrderingScore(), second.getOrderingScore()); if (result != 0) { return result; } | public int compare(CompositeScore<?> first, CompositeScore<?> second) { int result = FilteringScore.nullCompare(first, second); if (result != 0) { return result; } result = FilteringScore.rangeComparator() .compare(first.getFilteringScore... |
result = FilteringScore.fullComparator() .compare(first.getFilteringScore(), second.getFilteringScore()); | result = FilteringScore.fullComparator().compare(firstScore, secondScore); | public int compare(CompositeScore<?> first, CompositeScore<?> second) { int result = FilteringScore.nullCompare(first, second); if (result != 0) { return result; } result = FilteringScore.rangeComparator() .compare(first.getFilteringScore... |
(OrderedProperty<S>[] indexProperties, boolean unique, boolean clustered, | (StorableIndex<S> index, | public static <S extends Storable> OrderingScore<S> evaluate (OrderedProperty<S>[] indexProperties, boolean unique, boolean clustered, Filter<S> filter, OrderingList<S> ordering) { if (indexProperties == null) { throw new IllegalArgumentException("Index pr... |
if (indexProperties == null) { throw new IllegalArgumentException("Index properties required"); | if (index == null) { throw new IllegalArgumentException("Index required"); | public static <S extends Storable> OrderingScore<S> evaluate (OrderedProperty<S>[] indexProperties, boolean unique, boolean clustered, Filter<S> filter, OrderingList<S> ordering) { if (indexProperties == null) { throw new IllegalArgumentException("Index pr... |
List<PropertyFilter<S>> filterList = PropertyFilterList.get(filter); if (ordering == null) { ordering = OrderingList.emptyList(); } Set<ChainedProperty<S>> identityPropSet = new HashSet<ChainedProperty<S>>(filterList.size()); for (PropertyFilter<S> propFilter : filterList) { if (propFilter.getOperator() == RelOp.E... | return evaluate(index.getOrderedProperties(), index.isUnique(), index.isClustered(), filter, ordering); | public static <S extends Storable> OrderingScore<S> evaluate (OrderedProperty<S>[] indexProperties, boolean unique, boolean clustered, Filter<S> filter, OrderingList<S> ordering) { if (indexProperties == null) { throw new IllegalArgumentException("Index pr... |
registerTag("break", BreakTag.class); | public CoreTagLibrary() { registerTag("jelly", JellyTag.class); // core tags registerTag("out", ExprTag.class); registerTag("catch", CatchTag.class); registerTag("forEach", ForEachTag.class); registerTag("set", SetTag.class); registerTag("remove", RemoveTag.c... | |
removeChild(m); | protected void ensureNotInMapping(SQLColumn pkcol) throws ArchitectException { if (containsPkColumn(pkcol)) { ColumnMapping m = getMappingByPkCol(pkcol); List fkTies = fkTable.keysOfColumn(m.getFkColumn()); if (fkTies == null || fkTies.size() <= 1) { fkTable.removeColumn(m.getFkColumn()); } remov... | |
public void populate() throws ArchitectException { | public void populate() { | public void populate() throws ArchitectException { logger.debug("SQLRelationship: populate is a no-op"); } |
System.out.println(o.getClass()); | 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"); ... | |
System.out.println(o.getClass()); | public void run() { try { List<SQLTable> toBeProfiled = new ArrayList<SQLTable>(); for (SQLTable t: tables) { if (profileManager.getResult(t)== null) { toBeProfiled.add(t); ... | |
System.out.println(o.getClass()); | public void actionPerformed(ActionEvent e) { Set<SQLTable> uniqueTables = new HashSet(); for (int i: viewTable.getSelectedRows()) { Object o = viewTable.getValueAt(i,3); ... | |
super.setUp(); | public void setUp() { // Create several photos with different shooting dates // Add them to a collection so that they are easy to delete afterwards Calendar cal = Calendar.getInstance(); photos = new Vector(); uids = new Vector(); cal.set( 2002, 11, 23 ); makePhoto( cal ); cal.set( 2002, 11, 24 ); makePhoto( cal );... | |
playPenInstance.children = new ArrayList(); | public static synchronized SQLDatabase getPlayPenInstance() { if (playPenInstance == null) { playPenInstance = new SQLDatabase(); playPenInstance.populated = true; } return playPenInstance; } | |
getBody().run(context, newOutput); | invokeBody( newOutput); | public void doTag(XMLOutput output) throws Exception { if (var == null) { throw new IllegalArgumentException("The var attribute cannot be null"); } Document document = null; if (xml == null) { SAXContentHandler handler = new SAXContentHandler(); XMLOutput... |
g2.setColor(this.getBackground()); | g2.setColor(BG_GREY); | public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... |
id = Integer.parseInt(acc.toString()); | id = acc.getIdentifier().intValue(); | public PresentationObject getAccounts(IWContext iwc) { DataTable T = new DataTable(); T.setWidth("100%"); String styp = ""; Collection accounts = null; if (topic > 0) { accounts = MailFinder.getInstance().getTopicAccounts(topic); styp = iwrb.getLocalizedString("list.topic", "topic"); Ema... |
T.add(getAccountLink(topicID,Integer.parseInt( account.toString()),account.getHost()),3,row); | T.add(getAccountLink(topicID,( account.getIdentifier().intValue()),account.getHost()),3,row); | public PresentationObject getTopicsOverView(IWContext iwc){ Table T = new Table(); int row = 1; T.add(getTopicLink(-1,iwrb.getLocalizedString("new_topic","New topic")),1,row); row++; T.add(tf.format(iwrb.getLocalizedString("name","Name"),tf.HEADER),1,row); T.add(tf.format(iwrb.getLocalizedString("category",... |
T.add(getWelcomeLetterLink(Integer.parseInt(welcome.toString()),topicID,welcome.getSubject()),5,row); | T.add(getWelcomeLetterLink(welcome.getIdentifier().intValue()),topicID,welcome.getSubject()),5,row); | public PresentationObject getTopicsOverView(IWContext iwc){ Table T = new Table(); int row = 1; T.add(getTopicLink(-1,iwrb.getLocalizedString("new_topic","New topic")),1,row); row++; T.add(tf.format(iwrb.getLocalizedString("name","Name"),tf.HEADER),1,row); T.add(tf.format(iwrb.getLocalizedString("category",... |
SQLColumn col = (SQLColumn)t.getValueAt(t.getSelectedRow(),4); Set<SQLTable> tables = new HashSet<SQLTable>(); for (int i =0; i < t.getRowCount(); i++){ tables.add((SQLTable)t.getValueAt(i,3)); } profilePanel.setTables(new ArrayList(tables)); | SQLColumn col = (SQLColumn)t.getValueAt(t.getSelectedRow(), t.convertColumnIndexToView( ProfileColumn.valueOf("COLUMN").ordinal())); | public void mouseClicked(MouseEvent evt) { // TODO Auto-generated method stub Object obj = evt.getSource(); if (evt.getClickCount() == 2) { if ( obj instanceof JTable ) { JTable t = (JTable)obj; SQLColumn col = (SQLColumn)t.ge... |
Object o = viewTable.getValueAt(i,3); | Object o = viewTable.getValueAt(i, viewTable.convertColumnIndexToView( ProfileColumn.valueOf("TABLE").ordinal())); | 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"); ... |
logger.debug("Deleting row "+killMe[i]+": "+viewTable.getValueAt(killMe[i],4)); SQLColumn col = (SQLColumn) viewTable.getValueAt(killMe[i], 4); | logger.debug("Deleting row "+ killMe[i]+ ": "+ viewTable.getValueAt(killMe[i], viewTable.convertColumnIndexToView( ProfileColumn.valueOf("COLUMN").ordinal()))); SQLColumn col = (SQLColumn) viewTable.getValueAt(killMe[i], viewTable.convertColumnIndexToView( ProfileColumn.valueOf("COLUMN").ordinal())); | 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"); ... |
SQLColumn col = (SQLColumn) viewTable.getValueAt(0, 4); | SQLColumn col = (SQLColumn) viewTable.getValueAt(0, viewTable.convertColumnIndexToView( ProfileColumn.valueOf("COLUMN").ordinal())); | 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"); ... |
List<SQLTable> list = new ArrayList(tables); p.setTables(list); | 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"); ... | |
if ( viewTable.getRowCount() > 0 ) { SQLColumn col = (SQLColumn)viewTable.getValueAt(0, viewTable.convertColumnIndexToView( ProfileColumn.valueOf("COLUMN").ordinal())); p.getTableSelector().setSelectedItem(col.getParentTable()); p.getColumnSelector().setSelectedValue(col,true); } | 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"); ... | |
Object o = viewTable.getValueAt(i,3); | Object o = viewTable.getValueAt(i, viewTable.convertColumnIndexToView( ProfileColumn.valueOf("TABLE").ordinal())); | public void run() { try { List<SQLTable> toBeProfiled = new ArrayList<SQLTable>(); for (SQLTable t: tables) { if (profileManager.getResult(t)== null) { toBeProfiled.add(t); ... |
logger.debug("Deleting row "+killMe[i]+": "+viewTable.getValueAt(killMe[i],4)); SQLColumn col = (SQLColumn) viewTable.getValueAt(killMe[i], 4); | logger.debug("Deleting row "+ killMe[i]+ ": "+ viewTable.getValueAt(killMe[i], viewTable.convertColumnIndexToView( ProfileColumn.valueOf("COLUMN").ordinal()))); SQLColumn col = (SQLColumn) viewTable.getValueAt(killMe[i], viewTable.convertColumnIndexToView( ProfileColumn.valueOf("COLUMN").ordinal())); | public void run() { try { List<SQLTable> toBeProfiled = new ArrayList<SQLTable>(); for (SQLTable t: tables) { if (profileManager.getResult(t)== null) { toBeProfiled.add(t); ... |
SQLColumn col = (SQLColumn) viewTable.getValueAt(0, 4); | SQLColumn col = (SQLColumn) viewTable.getValueAt(0, viewTable.convertColumnIndexToView( ProfileColumn.valueOf("COLUMN").ordinal())); | public void run() { try { List<SQLTable> toBeProfiled = new ArrayList<SQLTable>(); for (SQLTable t: tables) { if (profileManager.getResult(t)== null) { toBeProfiled.add(t); ... |
List<SQLTable> list = new ArrayList(tables); p.setTables(list); | public void run() { try { List<SQLTable> toBeProfiled = new ArrayList<SQLTable>(); for (SQLTable t: tables) { if (profileManager.getResult(t)== null) { toBeProfiled.add(t); ... | |
if ( viewTable.getRowCount() > 0 ) { SQLColumn col = (SQLColumn)viewTable.getValueAt(0, viewTable.convertColumnIndexToView( ProfileColumn.valueOf("COLUMN").ordinal())); p.getTableSelector().setSelectedItem(col.getParentTable()); p.getColumnSelector().setSelectedValue(col,true); } | public void run() { try { List<SQLTable> toBeProfiled = new ArrayList<SQLTable>(); for (SQLTable t: tables) { if (profileManager.getResult(t)== null) { toBeProfiled.add(t); ... | |
Object o = viewTable.getValueAt(i,3); | Object o = viewTable.getValueAt(i, viewTable.convertColumnIndexToView( ProfileColumn.valueOf("TABLE").ordinal())); | public void actionPerformed(ActionEvent e) { Set<SQLTable> uniqueTables = new HashSet(); for (int i: viewTable.getSelectedRows()) { Object o = viewTable.getValueAt(i,3); ... |
logger.debug("Deleting row "+killMe[i]+": "+viewTable.getValueAt(killMe[i],4)); SQLColumn col = (SQLColumn) viewTable.getValueAt(killMe[i], 4); | logger.debug("Deleting row "+ killMe[i]+ ": "+ viewTable.getValueAt(killMe[i], viewTable.convertColumnIndexToView( ProfileColumn.valueOf("COLUMN").ordinal()))); SQLColumn col = (SQLColumn) viewTable.getValueAt(killMe[i], viewTable.convertColumnIndexToView( ProfileColumn.valueOf("COLUMN").ordinal())); | public void actionPerformed(ActionEvent e) { int[] killMe = viewTable.getSelectedRows(); Arrays.sort(killMe); // iterate backwards so the rows don't shift away on us! f... |
SQLColumn col = (SQLColumn) viewTable.getValueAt(0, 4); | SQLColumn col = (SQLColumn) viewTable.getValueAt(0, viewTable.convertColumnIndexToView( ProfileColumn.valueOf("COLUMN").ordinal())); | public void actionPerformed(ActionEvent e) { while ( viewTable.getRowCount() > 0 ) { SQLColumn col = (SQLColumn) viewTable.getValueAt(0, 4); try { profi... |
if (value instanceof List) { if (xpCmp != null && (xpCmp.getXpath() != null)) { Collections.sort((List)value, xpCmp); } } | public void doTag(XMLOutput output) throws Exception { if (var == null) { throw new MissingAttributeException( "var" ); } if (select == null) { throw new MissingAttributeException( "select" ); } Object xpathContext = getXPathContext(); ... | |
g2.drawImage(gBrowseImage, H_BORDER,V_BORDER,this); | g2.drawImage(gBrowseImage,H_BORDER-GBROWSE_MARGIN,V_BORDER,this); | public void paintComponent(Graphics g){ DPrimeTable dPrimeTable = theData.dpTable; if (Chromosome.getSize() == 0){ //if there are no valid markers return; } Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming ... |
return "Count"; | return COUNT; | public String getColumnName(int column) { if ( column == 0 ) { return "Count"; } else if ( column == 1 ) { return "Value"; } else { throw new IllegalStateException("Unknown Column Index:"+column); } } |
return "Value"; | return VALUE; | public String getColumnName(int column) { if ( column == 0 ) { return "Count"; } else if ( column == 1 ) { return "Value"; } else { throw new IllegalStateException("Unknown Column Index:"+column); } } |
public void characters(char ch[], int start, int length) throws SAXException { | public void characters(char[] ch, int start, int length) throws SAXException { | public void doTag(XMLOutput output) throws JellyTagException { int idx = name.indexOf(':'); final String localName = (idx >= 0) ? name.substring(idx + 1) : name; outputAttributes = false; XMLOutput newOutput = new XMLOutput(output) { // add an initialize ... |
public void ignorableWhitespace(char ch[], int start, int length) | public void ignorableWhitespace(char[] ch, int start, int length) | public void doTag(XMLOutput output) throws JellyTagException { int idx = name.indexOf(':'); final String localName = (idx >= 0) ? name.substring(idx + 1) : name; outputAttributes = false; XMLOutput newOutput = new XMLOutput(output) { // add an initialize ... |
* before any content is output | * before any content is output. | public void doTag(XMLOutput output) throws JellyTagException { int idx = name.indexOf(':'); final String localName = (idx >= 0) ? name.substring(idx + 1) : name; outputAttributes = false; XMLOutput newOutput = new XMLOutput(output) { // add an initialize ... |
public void characters(char ch[], int start, int length) throws SAXException { | public void characters(char[] ch, int start, int length) throws SAXException { | public void characters(char ch[], int start, int length) throws SAXException { initialize(); super.characters(ch, start, length); } |
public void ignorableWhitespace(char ch[], int start, int length) | public void ignorableWhitespace(char[] ch, int start, int length) | public void ignorableWhitespace(char ch[], int start, int length) throws SAXException { initialize(); super.ignorableWhitespace(ch, start, length); } |
public void setAttributeValue( String name, String value ) throws JellyTagException { | public void setAttributeValue(String name, String value, String uri) throws JellyTagException { | public void setAttributeValue( String name, String value ) throws JellyTagException { if (outputAttributes) { throw new JellyTagException( "Cannot set the value of attribute: " + name + " as we have already output the startElement() SAX event" ); } ... |
int index = attributes.getIndex("", name); | int idx = name.indexOf(':'); final String localName = (idx >= 0) ? name.substring(idx + 1) : name; final String nsUri = (uri != null) ? uri : ""; int index = attributes.getIndex(nsUri, localName); | public void setAttributeValue( String name, String value ) throws JellyTagException { if (outputAttributes) { throw new JellyTagException( "Cannot set the value of attribute: " + name + " as we have already output the startElement() SAX event" ); } ... |
attributes.addAttribute("", name, name, "CDATA", value); | attributes.addAttribute(nsUri, localName, name, "CDATA", value); | public void setAttributeValue( String name, String value ) throws JellyTagException { if (outputAttributes) { throw new JellyTagException( "Cannot set the value of attribute: " + name + " as we have already output the startElement() SAX event" ); } ... |
pp.contentPane.add(c, 0); | if (c instanceof Relationship) { pp.contentPane.add(c,pp.contentPane.getFirstRelationIndex()); } else { pp.contentPane.add(c, 0); } | public void actionPerformed(ActionEvent e) { List items = pp.getSelectedItems(); Iterator it = items.iterator(); while (it.hasNext()) { PlayPenComponent c = (PlayPenComponent) it.next(); pp.contentPane.remove(c); pp.contentPane.add(c, 0); } pp.repaint(); } |
contentPane.add(ppc, contentPane.getComponentCount()); | if (ppc instanceof Relationship) { contentPane.add(ppc, contentPane.getComponentCount()); } else { contentPane.add(ppc, contentPane.getFirstRelationIndex()); } | public void dbChildrenInserted(SQLObjectEvent e) { logger.debug("SQLObject children got inserted: "+e); boolean fireEvent = false; SQLObject[] c = e.getChildren(); for (int i = 0; i < c.length; i++) { try { addHierarcyListeners(c[i]); } catch (ArchitectException ex) { logger.error("Couldn't listen to add... |
dbcsPanel.setDbcs(db.getDataSource()); | public void showDbcsDialog() { final DBCSPanel dbcsPanel = new DBCSPanel(); DBCS_OkAction okAction = new DBCS_OkAction(dbcsPanel, false); dbcsPanel.setDbcs(db.getDataSource()); Action cancelAction = new AbstractAction() { public void actionPerformed(ActionEvent e) { dbcsPanel.discardChanges(); } }; ... | |
public PostageException(String message, Throwable cause) { super(message, cause); | public PostageException() { super(); | public PostageException(String message, Throwable cause) { super(message, cause); } |
Iterator iter = selectedPhotos.iterator(); | if ( selectedPhotos.size() > 1 ) { int n = JOptionPane.showConfirmDialog( parentFrame, "You have selected " + selectedPhotos.size() + " photos\n" + "Are you sure that you want to\ndisplay all of them at once?", "Open multiple photos", JOptionPane.YES_NO_OPTION ); if ( n != JOptionPane.YES_OPTION ) { return; } } Curs... | public void actionPerformed( ActionEvent ev ) { try { Collection selectedPhotos = view.getSelection(); Iterator iter = selectedPhotos.iterator(); while ( iter.hasNext() ) { PhotoInfo photo = (PhotoInfo) iter.next(); JFrame frame = new JFrame( "Ph... |
c.setCursor( oldCursor ); | public void actionPerformed( ActionEvent ev ) { try { Collection selectedPhotos = view.getSelection(); Iterator iter = selectedPhotos.iterator(); while ( iter.hasNext() ) { PhotoInfo photo = (PhotoInfo) iter.next(); JFrame frame = new JFrame( "Ph... | |
addComponentListener( this ); | public JAIPhotoViewer() { super(); createUI(); addComponentListener( this ); } | |
String expressions = "\nExpected expression: " + expected + "\nActual expression: " + actual; | String expressions = "\nExpected expression: " + expected.getExpressionText() + "\nActual expression: " + actual.getExpressionText(); | public void doTag(XMLOutput output) throws Exception { String message = getBodyText(); Object expectedValue = expected.evaluate(context); Object actualValue = actual.evaluate(context); if (expectedValue == null && actualValue == null) { ... |
if (left.isBound() && right.isBound()) { markBound(); } | BinaryOpFilter(Filter<S> left, Filter<S> right) { super(left == null ? null : left.getStorableType()); if (right == null) { throw new IllegalArgumentException(); } if (left.getStorableType() != right.getStorableType()) { throw new IllegalArgumentException("Type mism... | |
abstract void dumpTree(Appendable app, int indentLevel) throws IOException; | public void dumpTree(Appendable app) throws IOException { dumpTree(app, 0); } | abstract void dumpTree(Appendable app, int indentLevel) throws IOException; |
Tag answer = DynamicTagLibrary.this.createTag(name, attributes); if ( answer == null && parent != null ) { return parent.createTag(name, attributes); } return answer; | return DynamicTagLibrary.this.createTag(name, attributes); | public TagScript createTagScript(final String name, final Attributes attributes) throws Exception { return new TagScript( new TagFactory() { public Tag createTag(String name, Attributes attributes) throws Exception { Tag answer = DynamicTagLibrary.this.crea... |
Tag answer = DynamicTagLibrary.this.createTag(name, attributes); if ( answer == null && parent != null ) { return parent.createTag(name, attributes); } return answer; | return DynamicTagLibrary.this.createTag(name, attributes); | public Tag createTag(String name, Attributes attributes) throws Exception { Tag answer = DynamicTagLibrary.this.createTag(name, attributes); // delegate to my parent instead if ( answer == null && parent != null ) { ... |
public DynamicTag(Script template) { this.template = template; | public DynamicTag() { | public DynamicTag(Script template) { this.template = template; } |
long blockSize = Chromosome.getMarker(last).getPosition() - Chromosome.getMarker(first).getPosition(); | long blockSize = Chromosome.getFilteredMarker(last).getPosition() - Chromosome.getFilteredMarker(first).getPosition(); | public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... |
public boolean addDriverJar(String fullPath) { return driverJarList.add(fullPath); } | public boolean addDriverJar(String fullPath); | public boolean addDriverJar(String fullPath) { return driverJarList.add(fullPath); } |
System.out.println("start"); | public Vector findTags() { tags = new Vector(); untagged = new Vector(); taggedSoFar = 0; //potentialTagsHash stores the PotentialTag objects keyed on the corresponding sequences Hashtable potentialTagHash = new Hashtable(); PotentialTagComparator ptcomp = new PotentialTagC... | |
System.out.println("tagged " + countTagged + " SNPS using " + tags.size() +" tags" ); System.out.println("# of SNPs that could not be tagged: " + untagged.size()); | debugPrint("tagged " + countTagged + " SNPS using " + tags.size() +" tags" ); debugPrint("# of SNPs that could not be tagged: " + untagged.size()); | public Vector findTags() { tags = new Vector(); untagged = new Vector(); taggedSoFar = 0; //potentialTagsHash stores the PotentialTag objects keyed on the corresponding sequences Hashtable potentialTagHash = new Hashtable(); PotentialTagComparator ptcomp = new PotentialTagC... |
/* | public TagScript createTagScript(String name, Attributes attributes) throws Exception { Project project = getProject(); // custom Ant tags if ( name.equals("fileScanner") ) { Tag tag = new FileScannerTag(new FileScanner(project)); return TagScript.newIn... |
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