bugged stringlengths 6 599k | fixed stringlengths 10 599k | __index_level_0__ int64 0 1.13M |
|---|---|---|
public User getUser(String username){ return users.containsKey(username) ? (User)users.get(username) : null; } | public User getUser(String username){ return users.containsKey(username) ? (User)users.get(username) : null; } | 1,108,235 |
public JellyContext newJellyContext() { return createChildContext(); } | public JellyContext newJellyContext() { return createChildContext(); } | 1,108,236 |
public DataTypeTag(String name, DataType dataType) { this.name = name; this.dataType = dataType; setDynaBean( new ConvertingWrapDynaBean(dataType) ); } | public DataTypeTag(String name, DataType dataType) { this.name = name; this.dataType = dataType; setDynaBean( new ConvertingWrapDynaBean(dataType) ); } | 1,108,237 |
public TaskPropertyTag(String name) { setName(name); } | public TaskPropertyTag(String name) { setName(name); } | 1,108,238 |
public Object createNestedObject(Object object, String name) throws Exception { Object dataType = null; if ( object != null ) { IntrospectionHelper ih = IntrospectionHelper.getHelper( object.getClass() ); if ( ih != null ) { try { dataType = ih.c... | public Object createNestedObject(Object object, String name) throws Exception { Object dataType = null; if ( object != null ) { IntrospectionHelper ih = IntrospectionHelper.getHelper( object.getClass() ); if ( ih != null ) { try { dataType = ih.c... | 1,108,240 |
public BeanTag(Class defaultClass, String tagName) { this(defaultClass, tagName, null); } | public BeanTag(Class defaultClass, String tagName) { this(defaultClass, tagName, null); } | 1,108,241 |
public JellyTagException(String message, Throwable cause) { super(message,cause); } | public JellyTagException(String message, Throwable cause) { super(message,cause); } | 1,108,242 |
public DBCS_OkAction(DBCSPanel dbcsPanel, boolean isNew) { super("Ok"); this.dbcsPanel = dbcsPanel; this.isNew = isNew; dbcsPanel.setDbcs(new ArchitectDataSource()); } | public DBCS_OkAction(DBCSPanel dbcsPanel, boolean isNew) { super("Ok"); this.dbcsPanel = dbcsPanel; this.isNew = isNew; } | 1,108,244 |
public static JDialog createArchitectPanelDialog( final ArchitectPanel arch, final Window dialogParent, final String dialogTitle, final String actionButtonTitle, final Action okAction, final Action cancelAction) { final JDialog d; if (dialogParent instanceof Frame) { d = new JDialog((Frame) dial... | public static JDialog createArchitectPanelDialog( final ArchitectPanel arch, final Window dialogParent, final String dialogTitle, final String actionButtonTitle, final Action okAction, final Action cancelAction) { final JDialog d; if (dialogParent instanceof Frame) { d = new JDialog((Frame) dial... | 1,108,245 |
public static JDialog createArchitectPanelDialog( final ArchitectPanel arch, final Window dialogParent, final String dialogTitle, final String actionButtonTitle, final Action okAction, final Action cancelAction) { final JDialog d; if (dialogParent instanceof Frame) { d = new JDialog((Frame) dial... | public static JDialog createArchitectPanelDialog( final ArchitectPanel arch, final Window dialogParent, final String dialogTitle, final String actionButtonTitle, final Action okAction, final Action cancelAction) { final JDialog d; if (dialogParent instanceof Frame) { d = new JDialog((Frame) dial... | 1,108,246 |
public static void showExceptionDialog(Component parent, String message, Throwable throwable) { try { ExceptionReport er = new ExceptionReport(throwable); er.setNumObjectsInPlayPen(ArchitectFrame.getMainInstance().playpen.getTablePanes().size() + Archit... | public static void showExceptionDialog(Component parent, String message, Throwable throwable) { try { ExceptionReport er = new ExceptionReport(throwable); er.setNumObjectsInPlayPen(ArchitectFrame.getMainInstance().playpen.getTablePanes().size() + Archit... | 1,108,247 |
public List<DiffChunk<SQLObject>> generateTableDiffs() throws ArchitectException { try { Iterator sourceIter = sourceTableSet.iterator(); Iterator targetIter = targetTableSet.iterator(); SQLTable targetTable; SQLTable sourceTable; boolean sourceContinue; boolean targetContinue; //Checks if both lists of... | public List<DiffChunk<SQLObject>> generateTableDiffs() throws ArchitectException { try { Iterator sourceIter = sourceTableSet.iterator(); Iterator targetIter = targetTableSet.iterator(); SQLTable targetTable; SQLTable sourceTable; boolean sourceContinue; boolean targetContinue; //Checks if both lists of... | 1,108,248 |
public List<DiffChunk<SQLObject>> generateTableDiffs() throws ArchitectException { try { Iterator sourceIter = sourceTableSet.iterator(); Iterator targetIter = targetTableSet.iterator(); SQLTable targetTable; SQLTable sourceTable; boolean sourceContinue; boolean targetContinue; //Checks if both lists of... | public List<DiffChunk<SQLObject>> generateTableDiffs() throws ArchitectException { try { Iterator sourceIter = sourceTableSet.iterator(); Iterator targetIter = targetTableSet.iterator(); SQLTable targetTable; SQLTable sourceTable; boolean sourceContinue; boolean targetContinue; //Checks if both lists of... | 1,108,249 |
public List<DiffChunk<SQLObject>> generateTableDiffs() throws ArchitectException { try { Iterator sourceIter = sourceTableSet.iterator(); Iterator targetIter = targetTableSet.iterator(); SQLTable targetTable; SQLTable sourceTable; boolean sourceContinue; boolean targetContinue; //Checks if both lists of... | public List<DiffChunk<SQLObject>> generateTableDiffs() throws ArchitectException { try { Iterator sourceIter = sourceTableSet.iterator(); Iterator targetIter = targetTableSet.iterator(); SQLTable targetTable; SQLTable sourceTable; boolean sourceContinue; boolean targetContinue; //Checks if both lists of... | 1,108,250 |
public List<DiffChunk<SQLObject>> generateTableDiffs() throws ArchitectException { try { Iterator sourceIter = sourceTableSet.iterator(); Iterator targetIter = targetTableSet.iterator(); SQLTable targetTable; SQLTable sourceTable; boolean sourceContinue; boolean targetContinue; //Checks if both lists of... | public List<DiffChunk<SQLObject>> generateTableDiffs() throws ArchitectException { try { Iterator sourceIter = sourceTableSet.iterator(); Iterator targetIter = targetTableSet.iterator(); SQLTable targetTable; SQLTable sourceTable; boolean sourceContinue; boolean targetContinue; //Checks if both lists of... | 1,108,251 |
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 < 12){boxSize=1... | 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 < 12){boxSize=1... | 1,108,252 |
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 < 12){boxSize=1... | 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 < 12){boxSize=1... | 1,108,253 |
public JellyContext runScript(URL url, XMLOutput output) throws Exception { Script script = compileScript(url); URL newJellyContextURL = getJellyContextURL(url); JellyContext newJellyContext = new JellyContext(this, newJellyContextURL); if (log.isDebugEnabled() ) { ... | public JellyContext runScript(URL url, XMLOutput output) throws Exception { Script script = compileScript(url); URL newJellyContextURL = getJellyContextURL(url); JellyContext newJellyContext = new JellyContext(this, newJellyContextURL); if (log.isDebugEnabled() ) { ... | 1,108,254 |
private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_blocks = block_size.length; int num_h... | private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_blocks = block_size.length; int num_h... | 1,108,255 |
public UseBeanTag(Class defaultClass) { this.defaultClass = defaultClass; } | public UseBeanTag(Class defaultClass) { this.defaultClass = defaultClass; } | 1,108,256 |
public Point parse(String text) { StringTokenizer items = new StringTokenizer( text, "," ); int x = 0; int y = 0; if ( items.hasMoreTokens() ) { x = parseNumber( items.nextToken() ); } if ( enum.hasMoreTokens() ) { y = parseNumber( items.nextToken() ); ... | public Point parse(String text) { StringTokenizer items = new StringTokenizer( text, "," ); int x = 0; int y = 0; if ( items.hasMoreTokens() ) { x = parseNumber( items.nextToken() ); } if ( items.hasMoreTokens() ) { y = parseNumber( items.nextToken() ); ... | 1,108,257 |
public Point parse(String text) { StringTokenizer items = new StringTokenizer( text, "," ); int x = 0; int y = 0; if ( items.hasMoreTokens() ) { x = parseNumber( items.nextToken() ); } if ( enum.hasMoreTokens() ) { y = parseNumber( items.nextToken() ); ... | public Point parse(String text) { StringTokenizer items = new StringTokenizer( text, "," ); int x = 0; int y = 0; if ( items.hasMoreTokens() ) { x = parseNumber( items.nextToken() ); } return new Point( x, y ); } if ( enum.hasMoreTokens() ) { y = parseNum... | 1,108,258 |
public String evaluateAsString(Context context); | public String evaluateAsString(JellyContext context); | 1,108,259 |
public static void main( String[] args ) { org.apache.log4j.BasicConfigurator.configure(); log.setLevel( org.apache.log4j.Level.DEBUG ); org.apache.log4j.Logger folderLog = org.apache.log4j.Logger.getLogger( PhotoFolder.class.getName() ); folderLog.setLevel( org.apache.log4j.Level.DEBUG ); junit.textui.TestRunner.r... | public static void main( String[] args ) { log.setLevel( org.apache.log4j.Level.DEBUG ); org.apache.log4j.Logger folderLog = org.apache.log4j.Logger.getLogger( PhotoFolder.class.getName() ); folderLog.setLevel( org.apache.log4j.Level.DEBUG ); junit.textui.TestRunner.run( suite() ); } | 1,108,260 |
public void setUp() { odmg = OJB.getInstance(); db = odmg.newDatabase(); try { db.open( "repository.xml", Database.OPEN_READ_WRITE ); } catch ( ODMGException e ) { // log.warn( "Could not open database: " + e.getMessage() ); db = null; } tx = odmg.newTransaction(); tx.begin(); } | public void setUp() { odmg = OJB.getInstance(); db = odmg.newDatabase(); try { db.open( "repository.xml", Database.OPEN_READ_WRITE ); } catch ( ODMGException e ) { // log.warn( "Could not open database: " + e.getMessage() ); db = null; } tx = odmg.newTransaction(); tx.begin(); } | 1,108,261 |
public void testCreate() { PhotoFolder folder = PhotoFolder.create( "Top", null ); // Try to find the object from DB DList folders = null; Transaction tx = odmg.newTransaction(); tx.begin(); try { OQLQuery query = odmg.newOQLQuery(); query.create( "select folders from " + PhotoFolder.class.getName() + " wh... | public void testCreate() { PhotoFolder folder = PhotoFolder.create( "Top", null ); // Try to find the object from DB DList folders = null; Transaction tx = odmg.newTransaction(); tx.begin(); try { OQLQuery query = odmg.newOQLQuery(); query.create( "select folders from " + PhotoFolder.class.getName() + " wh... | 1,108,263 |
public void testCreate() { PhotoFolder folder = PhotoFolder.create( "Top", null ); // Try to find the object from DB DList folders = null; Transaction tx = odmg.newTransaction(); tx.begin(); try { OQLQuery query = odmg.newOQLQuery(); query.create( "select folders from " + PhotoFolder.class.getName() + " wh... | public void testCreate() { PhotoFolder folder = PhotoFolder.create( "Top", null ); // Try to find the object from DB DList folders = null; Transaction tx = odmg.newTransaction(); tx.begin(); try { OQLQuery query = odmg.newOQLQuery(); query.create( "select folders from " + PhotoFolder.class.getName() + " wh... | 1,108,264 |
public void testCreate() { PhotoFolder folder = PhotoFolder.create( "Top", null ); // Try to find the object from DB DList folders = null; Transaction tx = odmg.newTransaction(); tx.begin(); try { OQLQuery query = odmg.newOQLQuery(); query.create( "select folders from " + PhotoFolder.class.getName() + " wh... | public void testCreate() { PhotoFolder folder = PhotoFolder.create( "Top", null ); // Try to find the object from DB DList folders = null; Transaction tx = odmg.newTransaction(); tx.begin(); try { OQLQuery query = odmg.newOQLQuery(); query.create( "select folders from " + PhotoFolder.class.getName() + " wh... | 1,108,265 |
public void testCreate() { PhotoFolder folder = PhotoFolder.create( "Top", null ); // Try to find the object from DB DList folders = null; Transaction tx = odmg.newTransaction(); tx.begin(); try { OQLQuery query = odmg.newOQLQuery(); query.create( "select folders from " + PhotoFolder.class.getName() + " wh... | public void testCreate() { PhotoFolder folder = PhotoFolder.create( "Top", null ); // Try to find the object from DB DList folders = null; Transaction tx = odmg.newTransaction(); tx.begin(); try { OQLQuery query = odmg.newOQLQuery(); query.create( "select folders from " + PhotoFolder.class.getName() + " wh... | 1,108,266 |
public void testCreate() { PhotoFolder folder = PhotoFolder.create( "Top", null ); // Try to find the object from DB DList folders = null; Transaction tx = odmg.newTransaction(); tx.begin(); try { OQLQuery query = odmg.newOQLQuery(); query.create( "select folders from " + PhotoFolder.class.getName() + " wh... | public void testCreate() { PhotoFolder folder = PhotoFolder.create( "Top", null ); // Try to find the object from DB DList folders = null; Transaction tx = odmg.newTransaction(); tx.begin(); try { OQLQuery query = odmg.newOQLQuery(); query.create( "select folders from " + PhotoFolder.class.getName() + " wh... | 1,108,267 |
public WidgetTag(Class widgetClass, int style) { super(widgetClass); this.style = style; } | public WidgetTag(Class widgetClass, int style) { super(widgetClass); this.style = style; } | 1,108,270 |
public void registerBean(String name, Class type, Method method) { registerBean(name, type); if (method != null) { invokeMethods.put(name, method); } else { invokeMethods.remove(name); } } | public void registerBean(String name, Class type, Method method) { registerBean(name, type); if (method != null) { invokeMethods.put(name, method); } else { invokeMethods.remove(name); } } | 1,108,272 |
public Object createObject(Attributes attributes) { SQLTable tab = new SQLTable(); String id = attributes.getValue("id"); if (id != null) { objectIdMap.put(id, tab); } else { logger.warn("No ID found in table element while loading project!"); } String populated = attributes.getValue("populated"); ... | public Object createObject(Attributes attributes) { SQLTable tab = new SQLTable(); String id = attributes.getValue("id"); if (id != null) { objectIdMap.put(id, tab); } else { logger.warn("No ID found in table element while loading project!"); } String populated = attributes.getValue("populated"); ... | 1,108,273 |
protected Digester setupDigester() { Digester d = new Digester(); d.setValidating(false); d.push(this); // project name d.addCallMethod("architect-project/project-name", "setName", 0); // argument is element body text // source DB connection specs DBCSFactory dbcsFactory = new DBCSFactory(); d.addFactoryCreate... | protected Digester setupDigester() { Digester d = new Digester(); d.setValidating(false); d.push(this); // project name d.addCallMethod("architect-project/project-name", "setName", 0); // argument is element body text // source DB connection specs DBCSFactory dbcsFactory = new DBCSFactory(); d.addFactoryCreate... | 1,108,275 |
public Relationship(PlayPen parentPP, SQLRelationship model) throws ArchitectException { super(parentPP.getPlayPenContentPane()); this.model = model; setPkTable(getPlayPen().findTablePane(model.getPkTable())); setFkTable(getPlayPen().findTablePane(model.getFkTable())); setup(); } | public Relationship(PlayPen parentPP, SQLRelationship model) throws ArchitectException { super(parentPP.getPlayPenContentPane()); this.model = model; setPkTable(getPlayPen().findTablePane(model.getPkTable())); setFkTable(getPlayPen().findTablePane(model.getFkTable())); setup(); } | 1,108,276 |
public SQLTable() { //columnsPopulated = true; //relationshipsPopulated = true; children = new ArrayList(); } | public SQLTable() { //columnsPopulated = true; //relationshipsPopulated = true; children = new ArrayList(); } | 1,108,277 |
public PlayPen(SQLDatabase db) { this(); setDatabase(db); } | public PlayPen(SQLDatabase db) { this(); setDatabase(db); } | 1,108,278 |
public DBTree(List initialDatabases) throws ArchitectException { this(); setDatabaseList(initialDatabases); } | public DBTree(List initialDatabases) throws ArchitectException { this(); setDatabaseList(initialDatabases); } | 1,108,279 |
public DBTreeModel(Collection initialDatabases) throws ArchitectException { this.root = new DBTreeRoot(); if (initialDatabases != null) { Iterator it = initialDatabases.iterator(); while (it.hasNext()) { root.addChild((SQLDatabase) it.next()); } } this.treeModelListeners = new LinkedList(); ArchitectUtil... | public DBTreeModel(Collection initialDatabases) throws ArchitectException { this.root = new DBTreeRoot(); if (initialDatabases != null) { Iterator it = initialDatabases.iterator(); while (it.hasNext()) { root.addChild((SQLDatabase) it.next()); } } this.treeModelListeners = new LinkedList(); ArchitectUtil... | 1,108,280 |
public XMLOutput( ContentHandler contentHandler, LexicalHandler lexicalHandler) { this.contentHandler = contentHandler; this.lexicalHandler = lexicalHandler; } | public XMLOutput( ContentHandler contentHandler, LexicalHandler lexicalHandler) { this.contentHandler = contentHandler; this.lexicalHandler = lexicalHandler; } | 1,108,281 |
public void endPrefixMapping(String prefix) throws SAXException { namespaceStack.popNamespace(prefix); // End prefix mapping was already called after endElement // contentHandler.endPrefixMapping(prefix); } | public void endPrefixMapping(String prefix) throws SAXException { // End prefix mapping was already called after endElement // contentHandler.endPrefixMapping(prefix); } | 1,108,282 |
public void setContext(JellyContext context); | public void setContext(JellyContext context) throws Exception; | 1,108,283 |
public Object evaluate(Context context); | public Object evaluate(JellyContext context); | 1,108,284 |
public StartupException(String message, Throwable cause) { super(message, cause); } | public StartupException(String message, Throwable cause) { super(message, cause); } | 1,108,285 |
public SamplingException(String message, Throwable cause) { super(message, cause); } | public SamplingException(String message, Throwable cause) { super(message, cause); } | 1,108,286 |
public CheckDataPanel(PedFile pf) throws IOException, PedFileException{ setLayout(new BoxLayout(this,BoxLayout.Y_AXIS)); pedfile = pf; Vector result = pedfile.getResults(); int numResults = result.size(); Vector tableColumnNames = new Vector(); tableColumnNames.add("#"); ... | public CheckDataPanel(HaploData hd) throws IOException, PedFileException{ STATUS_COL = 8; setLayout(new BoxLayout(this,BoxLayout.Y_AXIS)); pedfile = pf; Vector result = pedfile.getResults(); int numResults = result.size(); Vector tableColumnNames = new Vector(); tableColumn... | 1,108,288 |
public CheckDataPanel(PedFile pf) throws IOException, PedFileException{ setLayout(new BoxLayout(this,BoxLayout.Y_AXIS)); pedfile = pf; Vector result = pedfile.getResults(); int numResults = result.size(); Vector tableColumnNames = new Vector(); tableColumnNames.add("#"); ... | public CheckDataPanel(PedFile pf) throws IOException, PedFileException{ setLayout(new BoxLayout(this,BoxLayout.Y_AXIS)); pedfile = hd.getPedFile(); theData = hd; Vector result = pedfile.getResults(); int numResults = result.size(); Vector tableColumnNames = new Vector(); ta... | 1,108,289 |
public CheckDataPanel(PedFile pf) throws IOException, PedFileException{ setLayout(new BoxLayout(this,BoxLayout.Y_AXIS)); pedfile = pf; Vector result = pedfile.getResults(); int numResults = result.size(); Vector tableColumnNames = new Vector(); tableColumnNames.add("#"); ... | public CheckDataPanel(PedFile pf) throws IOException, PedFileException{ setLayout(new BoxLayout(this,BoxLayout.Y_AXIS)); pedfile = pf; Vector result = pedfile.getResults(); int numResults = result.size(); Vector tableColumnNames = new Vector(); tableColumnNames.add("#"); ... | 1,108,290 |
public CheckDataPanel(PedFile pf) throws IOException, PedFileException{ setLayout(new BoxLayout(this,BoxLayout.Y_AXIS)); pedfile = pf; Vector result = pedfile.getResults(); int numResults = result.size(); Vector tableColumnNames = new Vector(); tableColumnNames.add("#"); ... | public CheckDataPanel(PedFile pf) throws IOException, PedFileException{ setLayout(new BoxLayout(this,BoxLayout.Y_AXIS)); pedfile = pf; Vector result = pedfile.getResults(); int numResults = result.size(); Vector tableColumnNames = new Vector(); tableColumnNames.add("#"); ... | 1,108,291 |
public CheckDataPanel(PedFile pf) throws IOException, PedFileException{ setLayout(new BoxLayout(this,BoxLayout.Y_AXIS)); pedfile = pf; Vector result = pedfile.getResults(); int numResults = result.size(); Vector tableColumnNames = new Vector(); tableColumnNames.add("#"); ... | public CheckDataPanel(PedFile pf) throws IOException, PedFileException{ setLayout(new BoxLayout(this,BoxLayout.Y_AXIS)); pedfile = pf; Vector result = pedfile.getResults(); int numResults = result.size(); Vector tableColumnNames = new Vector(); tableColumnNames.add("#"); ... | 1,108,292 |
protected void attachWidgets(Widget parent, Widget widget) { // set the content that will be scrolled if the parent is a ScrolledComposite if (parent instanceof ScrolledComposite && widget instanceof Control) { ScrolledComposite scrolledComposite = (ScrolledComposite) parent; scrolledComposite.setContent((Contro... | protected void attachWidgets(Widget parent, Widget widget) { // set the content that will be scrolled if the parent is a ScrolledComposite if (parent instanceof ScrolledComposite && widget instanceof Control) { ScrolledComposite scrolledComposite = (ScrolledComposite) parent; scrolledComposite.setContent((Contro... | 1,108,293 |
public Widget getParentWidget() { if (parent == null) { WidgetTag tag = (WidgetTag) findAncestorWithClass(WidgetTag.class); if (tag != null) { parent = tag.getWidget(); } } return parent; } | public Widget getParentWidget() { if (parent == null) { WidgetTag tag = (WidgetTag) findAncestorWithClass(WidgetTag.class); if (tag != null) { parent = tag.getWidget(); } } return parent; } | 1,108,294 |
private void argHandler(String[] args){ argHandlerMessages = new Vector(); int maxDistance = -1; //this means that user didn't specify any output type if it doesn't get changed below blockOutputType = -1; double hapThresh = -1; double minimumMAF=-1; double spacingThr... | private void argHandler(String[] args){ argHandlerMessages = new Vector(); int maxDistance = -1; //this means that user didn't specify any output type if it doesn't get changed below blockOutputType = -1; double hapThresh = -1; double minimumMAF=-1; double spacingThr... | 1,108,296 |
private void argHandler(String[] args){ argHandlerMessages = new Vector(); int maxDistance = -1; //this means that user didn't specify any output type if it doesn't get changed below blockOutputType = -1; double hapThresh = -1; double minimumMAF=-1; double spacingThr... | private void argHandler(String[] args){ argHandlerMessages = new Vector(); int maxDistance = -1; //this means that user didn't specify any output type if it doesn't get changed below blockOutputType = -1; double hapThresh = -1; double minimumMAF=-1; double spacingThr... | 1,108,297 |
private void argHandler(String[] args){ argHandlerMessages = new Vector(); int maxDistance = -1; //this means that user didn't specify any output type if it doesn't get changed below blockOutputType = -1; double hapThresh = -1; double minimumMAF=-1; double spacingThr... | private void argHandler(String[] args){ argHandlerMessages = new Vector(); int maxDistance = -1; //this means that user didn't specify any output type if it doesn't get changed below blockOutputType = -1; double hapThresh = -1; double minimumMAF=-1; double spacingThr... | 1,108,298 |
public AssociationTestSet(String fileName) throws IOException, HaploViewException{ tests = new Vector(); whitelist = new HashSet(); File testListFile = new File(fileName); BufferedReader in = new BufferedReader(new FileReader(testListFile)); String currentLine; int lineCoun... | public AssociationTestSet(String fileName) throws IOException, HaploViewException{ tests = new Vector(); whitelist = new HashSet(); File testListFile = new File(fileName); BufferedReader in = new BufferedReader(new FileReader(testListFile)); String currentLine; int lineCoun... | 1,108,299 |
public AssociationTestSet(String fileName) throws IOException, HaploViewException{ tests = new Vector(); whitelist = new HashSet(); File testListFile = new File(fileName); BufferedReader in = new BufferedReader(new FileReader(testListFile)); String currentLine; int lineCoun... | public AssociationTestSet(String fileName) throws IOException, HaploViewException{ tests = new Vector(); whitelist = new HashSet(); File testListFile = new File(fileName); BufferedReader in = new BufferedReader(new FileReader(testListFile)); String currentLine; int lineCoun... | 1,108,300 |
public IndividualDialog (HaploData hd){ Vector people = hd.getPedFile().getAllIndividuals(); Vector colNames = new Vector(); colNames.add("FamilyID"); colNames.add("IndividualID"); colNames.add("Geno%"); Vector data = new Vector(); for(int i=0;i<people.size();i++) { ... | public IndividualDialog (HaploView h, String title) { super(h,title); Vector people = hd.getPedFile().getAllIndividuals(); Vector colNames = new Vector(); colNames.add("FamilyID"); colNames.add("IndividualID"); colNames.add("Geno%"); Vector data = new Vector(); for(i... | 1,108,301 |
public IndividualDialog (HaploData hd){ Vector people = hd.getPedFile().getAllIndividuals(); Vector colNames = new Vector(); colNames.add("FamilyID"); colNames.add("IndividualID"); colNames.add("Geno%"); Vector data = new Vector(); for(int i=0;i<people.size();i++) { ... | public IndividualDialog (HaploData hd){ JPanel contents = new JPanel(); JTable table; contents.setLayout(new BoxLayout(contents,BoxLayout.Y_AXIS)); Vector people = h.theData.getPedFile().getAllIndividuals(); Vector excludedPeople = h.theData.getPedFile().getAxedPeople(); Vector colNames = new Vector... | 1,108,302 |
public MendelDialog(HaploData hd){ Vector results = hd.getPedFile().getResults(); Vector colNames = new Vector(); colNames.add("FamilyID"); colNames.add("ChildID"); colNames.add("Marker"); colNames.add("Position"); Vector data = new Vector(); for(int i=0;i<res... | public MendelDialog(HaploData hd){ Vector results = hd.getPedFile().getResults(); Vector colNames = new Vector(); colNames.add("FamilyID"); colNames.add("ChildID"); colNames.add("Marker"); colNames.add("Position"); Vector data = new Vector(); for(int i=0;i<res... | 1,108,304 |
public MendelDialog(HaploData hd){ Vector results = hd.getPedFile().getResults(); Vector colNames = new Vector(); colNames.add("FamilyID"); colNames.add("ChildID"); colNames.add("Marker"); colNames.add("Position"); Vector data = new Vector(); for(int i=0;i<res... | public MendelDialog(HaploData hd){ Vector results = hd.getPedFile().getResults(); Vector colNames = new Vector(); colNames.add("FamilyID"); colNames.add("ChildID"); colNames.add("Marker"); colNames.add("Position"); Vector data = new Vector(); for(int i=0;i<res... | 1,108,305 |
public MendelDialog(HaploData hd){ Vector results = hd.getPedFile().getResults(); Vector colNames = new Vector(); colNames.add("FamilyID"); colNames.add("ChildID"); colNames.add("Marker"); colNames.add("Position"); Vector data = new Vector(); for(int i=0;i<res... | public MendelDialog(HaploData hd){ Vector results = hd.getPedFile().getResults(); Vector colNames = new Vector(); colNames.add("FamilyID"); colNames.add("ChildID"); colNames.add("Marker"); colNames.add("Position"); Vector data = new Vector(); for(int i=0;i<res... | 1,108,306 |
DPrimeDisplay(HaploData hd){ //called when in cmd line mode, used to dump pngs theData = hd; this.computePreferredSize(); this.colorDPrime(); } | DPrimeDisplay(HaploData hd){ //called when in cmd line mode, used to dump pngs theData = hd; this.computePreferredSize(); this.colorDPrime(); } | 1,108,307 |
public BufferedImage export(int start, int stop, boolean compress) throws HaploViewException { forExport = true; exportStart = start; if (exportStart < 0){ exportStart = 0; } exportStop = stop; if (exportStop > Chromosome.getSize()){ exportStop = Chrom... | public BufferedImage export(int start, int stop, boolean compress) throws HaploViewException { forExport = true; exportStart = Chromosome.filterIndex[start]; if (exportStart < 0){ exportStart = 0; } exportStop = stop; if (exportStop > Chromosome.getSize()){ ... | 1,108,309 |
public BufferedImage export(int start, int stop, boolean compress) throws HaploViewException { forExport = true; exportStart = start; if (exportStart < 0){ exportStart = 0; } exportStop = stop; if (exportStop > Chromosome.getSize()){ exportStop = Chrom... | public BufferedImage export(int start, int stop, boolean compress) throws HaploViewException { forExport = true; exportStart = start; if (exportStart < 0){ exportStart = 0; } exportStop = stop; if (exportStop > Chromosome.getSize()){ exportStop = Chrom... | 1,108,310 |
public void doPermutations(int selection) { selectionType = selection; stopProcessing = false; Vector curResults = null; if (selectionType == CUSTOM){ activeAssocTestSet = custAssocTestSet; }else{ activeAssocTestSet = defaultAssocTestSet; } doub... | public void doPermutations(int selection) { selectionType = selection; stopProcessing = false; Vector curResults = null; if (selectionType == CUSTOM){ activeAssocTestSet = custAssocTestSet; }else{ activeAssocTestSet = defaultAssocTestSet; } doub... | 1,108,312 |
protected void indexDir() { IndexerFileChooser fc = new IndexerFileChooser(); fc.setFileSelectionMode( JFileChooser.DIRECTORIES_ONLY ); int retval = fc.showDialog( this, "Select directory to index" ); if ( retval == JFileChooser.APPROVE_OPTION ) { File dir = fc.getSelectedFile(); ... | protected void indexDir() { IndexerFileChooser fc = new IndexerFileChooser(); fc.setFileSelectionMode( JFileChooser.DIRECTORIES_ONLY ); int retval = fc.showDialog( this, "Select directory to index" ); if ( retval == JFileChooser.APPROVE_OPTION ) { File dir = fc.getSelectedFile(); ... | 1,108,314 |
public void setPhoto( PhotoInfo photo ) throws FileNotFoundException { if ( this.photo != null ) { this.photo.removeChangeListener( this ); } this.photo = photo; if ( photo == null ) { setImage( null ); return; } log.debug( "JAIPhotoViewer.setPhoto() photo=" + photo.getUid() ); photo.addChangeLi... | public void setPhoto( PhotoInfo photo ) throws FileNotFoundException { if ( this.photo != null ) { this.photo.removeChangeListener( this ); } this.photo = photo; if ( photo == null ) { setImage( null ); return; } log.debug( "JAIPhotoViewer.setPhoto() photo=" + photo.getUid() ); photo.addChangeLi... | 1,108,316 |
public void setPhoto( PhotoInfo photo ) throws FileNotFoundException { if ( this.photo != null ) { this.photo.removeChangeListener( this ); } this.photo = photo; if ( photo == null ) { setImage( null ); return; } log.debug( "JAIPhotoViewer.setPhoto() photo=" + photo.getUid() ); photo.addChangeLi... | public void setPhoto( PhotoInfo photo ) throws FileNotFoundException { if ( this.photo != null ) { this.photo.removeChangeListener( this ); } this.photo = photo; if ( photo == null ) { setImage( null ); return; } log.debug( "JAIPhotoViewer.setPhoto() photo=" + photo.getUid() ); photo.addChangeLi... | 1,108,317 |
public DelegatedQueryExecutor(Storage<S> rootStorage, Filter<S> filter, OrderingList<S> ordering) throws FetchException { check(rootStorage); Query<S> query; if (filter == null) { query = rootStorage.query(); } else { query... | public DelegatedQueryExecutor(Storage<S> rootStorage, Filter<S> filter, OrderingList<S> ordering) throws FetchException { check(rootStorage); Query<S> query; if (filter == null) { query = rootStorage.query(); } else { query... | 1,108,318 |
public DelegatedQueryExecutor(Storage<S> rootStorage, Filter<S> filter, OrderingList<S> ordering) throws FetchException { check(rootStorage); Query<S> query; if (filter == null) { query = rootStorage.query(); } else { query... | public DelegatedQueryExecutor(Storage<S> rootStorage, Filter<S> filter, OrderingList<S> ordering) throws FetchException { check(rootStorage); Query<S> query; if (filter == null) { query = rootStorage.query(); } else { query... | 1,108,319 |
public JoinedQueryExecutor(Repository repo, ChainedProperty<B> bToAProperty, QueryExecutor<A> aExecutor) throws SupportException, FetchException, RepositoryException { mFactory = new JoinedCursorFactory<A, B> (repo, bToAProperty... | public JoinedQueryExecutor(Repository repo, Class<B> bType, String bToAProperty, QueryExecutor<A> aExecutor) throws SupportException, FetchException, RepositoryException { mFactory = new JoinedCursorFactory<A, B> (repo, bToAProp... | 1,108,320 |
public JoinedQueryExecutor(Repository repo, ChainedProperty<B> bToAProperty, QueryExecutor<A> aExecutor) throws SupportException, FetchException, RepositoryException { mFactory = new JoinedCursorFactory<A, B> (repo, bToAProperty... | public JoinedQueryExecutor(Repository repo, ChainedProperty<B> bToAProperty, QueryExecutor<A> aExecutor) throws SupportException, FetchException, RepositoryException { mFactory = new JoinedCursorFactory<A, B> (repo, bType, bToAP... | 1,108,321 |
public JoinedQueryExecutor(Repository repo, ChainedProperty<B> bToAProperty, QueryExecutor<A> aExecutor) throws SupportException, FetchException, RepositoryException { mFactory = new JoinedCursorFactory<A, B> (repo, bToAProperty... | public JoinedQueryExecutor(Repository repo, ChainedProperty<B> bToAProperty, QueryExecutor<A> aExecutor) throws SupportException, FetchException, RepositoryException { mFactory = new JoinedCursorFactory<A, B> (repo, bToAProperty... | 1,108,322 |
public JoinedQueryExecutor(Repository repo, ChainedProperty<B> bToAProperty, QueryExecutor<A> aExecutor) throws SupportException, FetchException, RepositoryException { mFactory = new JoinedCursorFactory<A, B> (repo, bToAProperty... | public JoinedQueryExecutor(Repository repo, ChainedProperty<B> bToAProperty, QueryExecutor<A> aExecutor) throws SupportException, FetchException, RepositoryException { mFactory = new JoinedCursorFactory<A, B> (repo, bToAProperty... | 1,108,323 |
public ServerConnection getServerConnection(ApplicationConfig config) throws ConnectionFailedException { try { MBeanHome home = findExternal(config.getURL(), config.getUsername(), config.getPassword()); return new WLServerConnection(home.getMBeanServer()); ... | public ServerConnection getServerConnection(ApplicationConfig config) throws ConnectionFailedException { try { MBeanHome home = findExternal(config.getURL(), config.getUsername(), config.getPassword()); return new WLServerConnection(home.getMBeanServer()); ... | 1,108,324 |
public WLServerConnection(MBeanServer mbeanServer){ super(mbeanServer, MBeanServer.class); assert mbeanServer != null; this.mbeanServer = (RemoteMBeanServer)mbeanServer; } | public WLServerConnection(MBeanServer mbeanServer, Context ctx){ super(mbeanServer, MBeanServer.class); assert mbeanServer != null; this.mbeanServer = (RemoteMBeanServer)mbeanServer; } | 1,108,325 |
public TagScript createTagScript(String name, Attributes attributes) throws Exception { TagScript answer = super.createTagScript(name, attributes); if ( answer == null ) { final Factory factory = getFactory( name ); if ( factory != null ) { return new DynaTagScript... | public TagScript createTagScript(String name, Attributes attributes) throws Exception { TagScript answer = super.createTagScript(name, attributes); if ( answer == null ) { final Factory factory = getFactory( name ); if ( factory != null ) { return new DynaTagScript... | 1,108,329 |
public Tag createTag() throws Exception { return new ComponentTag(factory); } | public Tag createTag() throws Exception { if ( factory instanceof TagFactory ) { return ((TagFactory) factory).createTag(); } else { return new ComponentTag(factory); } } | 1,108,330 |
public DynaTagScript(TagFactory tagFactory) { super(tagFactory); } | public DynaTagScript(TagFactory tagFactory) { super(tagFactory); } | 1,108,331 |
public void testJDBCClassLoader() throws Exception { // Side effect is to load my prefs; needed to avoid having to manually add jar to session. ArchitectFrame.getMainInstance(); ArchitectSession sess = ArchitectSession.getInstance(); JDBCClassLoader cl = sess.getJDBCClassLoader(); System.out.println("If... | public void testJDBCClassLoader() throws Exception { // Side effect is to load my prefs; needed to avoid having to manually add jar to session. ArchitectFrame.getMainInstance(); ArchitectSession sess = ArchitectSessionImpl.getInstance(); JDBCClassLoader cl = sess.getJDBCClassLoader(); System.out.println... | 1,108,332 |
public JDBCClassLoader getJDBCClassLoader() { return jdbcClassLoader; } | public JDBCClassLoader getJDBCClassLoader() { return jdbcClassLoader; } | 1,108,333 |
public void dbChildrenInserted(SQLObjectEvent e) { try { SQLObject[] newEventSources = e.getChildren(); for (int i = 0; i < newEventSources.length; i++) { listenToSQLObjectAndChildren(newEventSources[i]); } } catch (ArchitectException ex) { ex.printStackTrace(); } TreeModelEvent tme = new TreeModelEvent... | public void dbChildrenInserted(SQLObjectEvent e) { try { SQLObject[] newEventSources = e.getChildren(); for (int i = 0; i < newEventSources.length; i++) { listenToSQLObjectAndChildren(newEventSources[i]); } } catch (ArchitectException ex) { logger.error("Error listening to added object", ex); } TreeMode... | 1,108,334 |
public void dbChildrenRemoved(SQLObjectEvent e) { try { SQLObject[] oldEventSources = e.getChildren(); for (int i = 0; i < oldEventSources.length; i++) { unlistenToSQLObjectAndChildren(oldEventSources[i]); } } catch (ArchitectException ex) { ex.printStackTrace(); } TreeModelEvent tme = new TreeModelEven... | public void dbChildrenRemoved(SQLObjectEvent e) { try { SQLObject[] oldEventSources = e.getChildren(); for (int i = 0; i < oldEventSources.length; i++) { unlistenToSQLObjectAndChildren(oldEventSources[i]); } } catch (ArchitectException ex) { logger.error("Error unlistening to removed object", ex); } Tre... | 1,108,335 |
public static SQLObject[] getPathToNode(SQLObject node) { LinkedList path = new LinkedList(); while (node != null) { path.add(0, node); node = node.getParent(); } return (SQLObject[]) path.toArray(new SQLObject[path.size()]); } | public SQLObject[] getPathToNode(SQLObject node) { LinkedList path = new LinkedList(); while (node != null) { path.add(0, node); node = node.getParent(); } return (SQLObject[]) path.toArray(new SQLObject[path.size()]); } | 1,108,338 |
protected void listenToSQLObjectAndChildren(SQLObject o) throws ArchitectException { o.addSQLObjectListener(this); if (o.isPopulated()) { Iterator it = o.getChildren().iterator(); while (it.hasNext()) { listenToSQLObjectAndChildren((SQLObject) it.next()); } } } | protected void listenToSQLObjectAndChildren(SQLObject o) throws ArchitectException { o.addSQLObjectListener(this); if (o.isPopulated() && o.allowsChildren()) { Iterator it = o.getChildren().iterator(); while (it.hasNext()) { listenToSQLObjectAndChildren((SQLObject) it.next()); } } } | 1,108,340 |
protected void unlistenToSQLObjectAndChildren(SQLObject o) throws ArchitectException { o.removeSQLObjectListener(this); if (o.isPopulated()) { Iterator it = o.getChildren().iterator(); while (it.hasNext()) { SQLObject ob = (SQLObject) it.next(); unlistenToSQLObjectAndChildren(ob); } } } | protected void unlistenToSQLObjectAndChildren(SQLObject o) throws ArchitectException { o.removeSQLObjectListener(this); if (o.isPopulated() && o.allowsChildren()) { Iterator it = o.getChildren().iterator(); while (it.hasNext()) { SQLObject ob = (SQLObject) it.next(); unlistenToSQLObjectAndChildren(ob); }... | 1,108,341 |
public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command.equals("Filter")){ chromChoice = (String)chromChooser.getSelectedItem(); if (chromStart.getText().equals("")){ startPos = -1; }else{ startPos =... | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command.equals("Filter")){ chromChoice = (String)chromChooser.getSelectedItem(); if (chromStart.getText().equals("")){ startPos = -1; }else{ startPos =... | 1,108,342 |
public void filterAll(String chr, int start, int end, String column, String s, String value){ resetFilters(); int rows = getRowCount(); Vector newFiltered = new Vector(); boolean chromPass = false; boolean genericPass = false; long realStart = start*1000; long realEn... | public void filterAll(String chr, int start, int end, String column, String s, String value){ resetFilters(); int rows = getRowCount(); Vector newFiltered = new Vector(); boolean chromPass = false; boolean genericPass = false; long realStart = start*1000; long realEn... | 1,108,343 |
public void doTag(XMLOutput output) throws Exception { TaskSource tag = (TaskSource) findAncestorWithClass( TaskSource.class ); if ( tag == null ) { throw new JellyException( "You should only use Ant DataType tags within an Ant Task" ); } Object task = tag.getT... | public void doTag(XMLOutput output) throws Exception { TaskSource tag = (TaskSource) findAncestorWithClass( TaskSource.class ); if ( tag == null ) { throw new JellyException( "You should only use Ant DataType tags within an Ant Task" ); } Object task = tag.getT... | 1,108,344 |
public void run(JellyContext context, XMLOutput output) throws Exception { // initialize all the properties of the tag before its used // if there is a problem abort this tag for (int i = 0, size = expressions.length; i < size; i++) { Expression expression = expressions[i]; ... | public void run(JellyContext context, XMLOutput output) throws Exception { // initialize all the properties of the tag before its used // if there is a problem abort this tag for (int i = 0, size = expressions.length; i < size; i++) { Expression expression = expressions[i]; ... | 1,108,345 |
public TagScript(TagFactory tagFactory) { this.tagFactory = tagFactory; } | public TagScript(TagFactory tagFactory) { this.tagFactory = tagFactory; } | 1,108,346 |
public TablePane(SQLTable m, PlayPen parentPP) { super(parentPP.getPlayPenContentPane()); setModel(m); setOpaque(true); setInsertionPoint(COLUMN_INDEX_NONE); //dt = new DropTarget(parentPP, new TablePaneDropListener(this)); dtl = new TablePaneDropListener(this); updateUI(); } | public TablePane(SQLTable m, PlayPen parentPP) { super(parentPP.getPlayPenContentPane()); setModel(m); setOpaque(true); setInsertionPoint(COLUMN_INDEX_NONE); //dt = new DropTarget(parentPP, new TablePaneDropListener(this)); dtl = new TablePaneDropListener(this); updateUI(); } | 1,108,348 |
public TablePane(SQLTable m, PlayPen parentPP) { super(parentPP.getPlayPenContentPane()); setModel(m); setOpaque(true); setInsertionPoint(COLUMN_INDEX_NONE); //dt = new DropTarget(parentPP, new TablePaneDropListener(this)); dtl = new TablePaneDropListener(this); updateUI(); } | public TablePane(SQLTable m, PlayPen parentPP) { super(parentPP.getPlayPenContentPane()); setModel(m); setOpaque(true); setInsertionPoint(COLUMN_INDEX_NONE); //dt = new DropTarget(parentPP, new TablePaneDropListener(this)); dtl = new TablePaneDropListener(this); updateUI(); } | 1,108,349 |
public JellyAssertionFailedError(String message) { super(message); } | public JellyAssertionFailedError(String message) { super(message); } | 1,108,350 |
public static void copyFile( File src, File dst ) throws IOException { FileInputStream in = new FileInputStream( src ); FileOutputStream out = new FileOutputStream( dst ); byte buf[] = new byte[1024]; int nRead = 0; int offset = 0; while ( (nRead = in.read( buf )) > 0 ) { out.write( buf, 0, nRead ); offset ... | public static void copyFile( File src, File dst ) throws IOException { FileInputStream in = new FileInputStream( src ); FileOutputStream out = new FileOutputStream( dst ); byte buf[] = new byte[1024]; int nRead = 0; int offset = 0; while ( (nRead = in.read( buf )) > 0 ) { out.write( buf, 0, nRead ); offset ... | 1,108,354 |
public static byte[] calcHash( File f ) { FileInputStream is = null; byte hash[] = null; try { is = new FileInputStream( f ); byte readBuffer[] = new byte[4096]; MessageDigest md = MessageDigest.getInstance("MD5"); int bytesRead = -1; while... | public static byte[] calcHash( File f ) { FileInputStream is = null; byte hash[] = null; try { is = new FileInputStream( f ); byte readBuffer[] = new byte[4096]; MessageDigest md = MessageDigest.getInstance("MD5"); int bytesRead = -1; while... | 1,108,355 |
public static byte[] calcHash( File f ) { FileInputStream is = null; byte hash[] = null; try { is = new FileInputStream( f ); byte readBuffer[] = new byte[4096]; MessageDigest md = MessageDigest.getInstance("MD5"); int bytesRead = -1; while... | public static byte[] calcHash( File f ) { FileInputStream is = null; byte hash[] = null; try { is = new FileInputStream( f ); byte readBuffer[] = new byte[4096]; MessageDigest md = MessageDigest.getInstance("MD5"); int bytesRead = -1; while... | 1,108,356 |
public static byte[] calcHash( File f ) { FileInputStream is = null; byte hash[] = null; try { is = new FileInputStream( f ); byte readBuffer[] = new byte[4096]; MessageDigest md = MessageDigest.getInstance("MD5"); int bytesRead = -1; while... | public static byte[] calcHash( File f ) { FileInputStream is = null; byte hash[] = null; try { is = new FileInputStream( f ); byte readBuffer[] = new byte[4096]; MessageDigest md = MessageDigest.getInstance("MD5"); int bytesRead = -1; while... | 1,108,357 |
public void save(ProgressMonitor pm) throws IOException, ArchitectException { // write to temp file and then rename (this preserves old project file // when there's problems) if (file.exists() && !file.canWrite()) { // write problems with architect file will muck up the save process throw new ArchitectExceptio... | public void save(ProgressMonitor pm) throws IOException, ArchitectException { // write to temp file and then rename (this preserves old project file // when there's problems) if (file.exists() && !file.canWrite()) { // write problems with architect file will muck up the save process throw new ArchitectExceptio... | 1,108,360 |
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