Datasets:
JoaoJunior
/
formatted-java-preprocessed-code-APR

Dataset card Data Studio Files
xet
 Community
bugged
stringlengths
6
599k
fixed
stringlengths
10
599k
__index_level_0__
int64
0
1.13M
protected Project getProject() { ProjectTag tag = (ProjectTag) findAncestorWithClass(ProjectTag.class); if ( tag != null) { return tag.getProject(); } return (Project) context.findVariable( "org.apache.commons.jelly.werkz.Project" ); }
protected Project getProject() { ProjectTag tag = (ProjectTag) findAncestorWithClass(ProjectTag.class); if ( tag != null) { return tag.getProject(); } if (answer == null) { answer = (Project) context.findVariable( "org.apache.commons.jelly.werkz.Project" ); } return answer; ...
1,109,576
public void doAssociationTests(Vector affStatus, Vector permuteInd,Vector permuteDiscPar, Vector kidAffStatus) { if(fullProbMap == null || superdata == null || realAffectedStatus == null || realKidAffectedStatus == null) { return; } if(affStatus == null){ affStatus = realA...
public void doAssociationTests(Vector affStatus, Vector permuteInd,Vector permuteDiscPar, Vector kidAffStatus) { if(fullProbMap == null || superdata == null || realAffectedStatus == null || realKidAffectedStatus == null) { return; } if(affStatus == null){ affStatus = realA...
1,109,577
void guessBlocks(int method){ guessBlocks(method, new Vector()); }
void guessBlocks(int method){ guessBlocks(method, blocks); }
1,109,578
public Vector readBlocks(File infile) throws HaploViewException, IOException{ if (!infile.exists()){ throw new HaploViewException("File " + infile.getName() + " doesn't exist!"); } Vector cust = new Vector(); BufferedReader in = new BufferedReader(new FileReader(infile)); ...
public Vector readBlocks(File infile) throws HaploViewException, IOException{ if (!infile.exists()){ throw new HaploViewException("File " + infile.getName() + " doesn't exist!"); } Vector cust = new Vector(); BufferedReader in = new BufferedReader(new FileReader(infile)); ...
1,109,579
protected void computeBounds() { // XXX: should check for valid cached bounds before recomputing! TablePane pkTable = relationship.pkTable; TablePane fkTable = relationship.fkTable; if (!isOrientationLegal()) { // bestConnectionPoints also updates orientation as a side effect bestConnectionPoints(); } if (pk...
public void computeBounds() { // XXX: should check for valid cached bounds before recomputing! TablePane pkTable = relationship.pkTable; TablePane fkTable = relationship.fkTable; if (!isOrientationLegal()) { // bestConnectionPoints also updates orientation as a side effect bestConnectionPoints(); } if (pkTab...
1,109,580
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"); ...
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"); ...
1,109,581
public void run() { try { List<SQLTable> toBeProfiled = new ArrayList<SQLTable>(); for (SQLTable t: tables) { if (profileManager.getResult(t)== null) { toBeProfiled.add(t); ...
public void run() { try { List<SQLTable> toBeProfiled = new ArrayList<SQLTable>(); for (SQLTable t: tables) { if (profileManager.getResult(t)== null) { toBeProfiled.add(t); ...
1,109,582
public void actionPerformed(ActionEvent e) { Set<SQLTable> uniqueTables = new HashSet(); for (int i: viewTable.getSelectedRows()) { Object o = viewTable.getValueAt(i,3); ...
public void actionPerformed(ActionEvent e) { Set<SQLTable> uniqueTables = new HashSet(); for (int i: viewTable.getSelectedRows()) { Object o = viewTable.getValueAt(i,3); ...
1,109,583
public ColumnEditPanel(SQLTable table, int idx) throws ArchitectException { super(new BorderLayout(12,12)); JPanel westPanel = new JPanel(new BorderLayout()); columns = new JList(); columns.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); columns.addListSelectionListener(this); westPanel.add(new JScrollP...
public ColumnEditPanel(SQLTable table, int idx) throws ArchitectException { super(new BorderLayout(12,12)); JPanel westPanel = new JPanel(new BorderLayout()); columns = new JList(); columns.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); columns.addListSelectionListener(this); westPanel.add(new JScrollP...
1,109,584
public ColumnEditPanel(SQLTable table, int idx) throws ArchitectException { super(new BorderLayout(12,12)); JPanel westPanel = new JPanel(new BorderLayout()); columns = new JList(); columns.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); columns.addListSelectionListener(this); westPanel.add(new JScrollP...
public ColumnEditPanel(SQLTable table, int idx) throws ArchitectException { super(new BorderLayout(12,12)); JPanel westPanel = new JPanel(new BorderLayout()); columns = new JList(); columns.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); columns.addListSelectionListener(this); westPanel.add(new JScrollP...
1,109,585
public void actionPerformed(ActionEvent e) { int idx = columns.getSelectedIndex(); if (idx < 0) { JOptionPane.showMessageDialog(ColumnEditPanel.this, "Please select a column, then click delete"); } else { try { model.removeColumn(idx); int size = model.getColumns().si...
public void actionPerformed(ActionEvent e) { int idx = columns.getSelectedIndex(); if (idx < 0) { JOptionPane.showMessageDialog(ColumnEditPanel.this, "Please select a column, then click delete"); } else { try { int size = model.getColumns().size(); if (size > 0...
1,109,586
public void actionPerformed(ActionEvent e) { int idx = columns.getSelectedIndex(); if (idx < 0) { JOptionPane.showMessageDialog(ColumnEditPanel.this, "Please select a column, then click delete"); } else { try { model.removeColumn(idx); int size = model.getColumns().si...
public void actionPerformed(ActionEvent e) { int idx = columns.getSelectedIndex(); if (idx < 0) { JOptionPane.showMessageDialog(ColumnEditPanel.this, "Please select a column, then click delete"); } else { try { model.removeColumn(idx); int size = model.getColumns().si...
1,109,587
public void runScript(String uri, XMLOutput output) throws Exception { URL url = getResource(uri); if (url == null) { throw new JellyException("Could not find Jelly script: " + url); } Script script = compileScript(url); URL newJellyContextURL = getJellyContextU...
public void runScript(String uri, XMLOutput output) throws Exception { URL url = getResource(uri); if (url == null) { throw new JellyException("Could not find Jelly script: " + url); } Script script = compileScript(url); URL newJellyContextURL = getJellyContextU...
1,109,588
private final void setDatabase(SQLDatabase newdb) { if (newdb == null) throw new NullPointerException("db must be non-null"); this.db = newdb; db.setIgnoreReset(true); if (db.getDataSource() == null) { ArchitectDataSource dbcs = new ArchitectDataSource(); dbcs.setName("Not Configured"); dbcs.setDisplayName("...
private final void setDatabase(SQLDatabase newdb) { if (newdb == null) throw new NullPointerException("db must be non-null"); this.db = newdb; db.setPlayPenDatabase(true); if (db.getDataSource() == null) { ArchitectDataSource dbcs = new ArchitectDataSource(); dbcs.setName("Not Configured"); dbcs.setDisplayNa...
1,109,589
protected static void addTablesToDatabase(SQLDatabase addTo) throws SQLException, ArchitectException { HashMap catalogs = new HashMap(); HashMap schemas = new HashMap(); synchronized (addTo) { Connection con = addTo.getConnection(); DatabaseMetaData dbmd = con.getMetaData(); ResultSet mdTables = null; try...
protected static void addTablesToDatabase(SQLDatabase addTo) throws SQLException, ArchitectException { HashMap catalogs = new HashMap(); HashMap schemas = new HashMap(); synchronized (addTo) { Connection con = addTo.getConnection(); DatabaseMetaData dbmd = con.getMetaData(); ResultSet rs = null; try { ...
1,109,590
protected static void addTablesToDatabase(SQLDatabase addTo) throws SQLException, ArchitectException { HashMap catalogs = new HashMap(); HashMap schemas = new HashMap(); synchronized (addTo) { Connection con = addTo.getConnection(); DatabaseMetaData dbmd = con.getMetaData(); ResultSet mdTables = null; try...
protected static void addTablesToDatabase(SQLDatabase addTo) throws SQLException, ArchitectException { HashMap catalogs = new HashMap(); HashMap schemas = new HashMap(); synchronized (addTo) { Connection con = addTo.getConnection(); DatabaseMetaData dbmd = con.getMetaData(); ResultSet mdTables = null; try...
1,109,591
protected static void addTablesToDatabase(SQLDatabase addTo) throws SQLException, ArchitectException { HashMap catalogs = new HashMap(); HashMap schemas = new HashMap(); synchronized (addTo) { Connection con = addTo.getConnection(); DatabaseMetaData dbmd = con.getMetaData(); ResultSet mdTables = null; try...
protected static void addTablesToDatabase(SQLDatabase addTo) throws SQLException, ArchitectException { HashMap catalogs = new HashMap(); HashMap schemas = new HashMap(); synchronized (addTo) { Connection con = addTo.getConnection(); DatabaseMetaData dbmd = con.getMetaData(); ResultSet mdTables = null; try...
1,109,592
protected static void addTablesToDatabase(SQLDatabase addTo) throws SQLException, ArchitectException { HashMap catalogs = new HashMap(); HashMap schemas = new HashMap(); synchronized (addTo) { Connection con = addTo.getConnection(); DatabaseMetaData dbmd = con.getMetaData(); ResultSet mdTables = null; try...
protected static void addTablesToDatabase(SQLDatabase addTo) throws SQLException, ArchitectException { HashMap catalogs = new HashMap(); HashMap schemas = new HashMap(); synchronized (addTo) { Connection con = addTo.getConnection(); DatabaseMetaData dbmd = con.getMetaData(); ResultSet mdTables = null; try...
1,109,593
protected static void addTablesToDatabase(SQLDatabase addTo) throws SQLException, ArchitectException { HashMap catalogs = new HashMap(); HashMap schemas = new HashMap(); synchronized (addTo) { Connection con = addTo.getConnection(); DatabaseMetaData dbmd = con.getMetaData(); ResultSet mdTables = null; try...
protected static void addTablesToDatabase(SQLDatabase addTo) throws SQLException, ArchitectException { HashMap catalogs = new HashMap(); HashMap schemas = new HashMap(); synchronized (addTo) { Connection con = addTo.getConnection(); DatabaseMetaData dbmd = con.getMetaData(); ResultSet mdTables = null; try...
1,109,594
protected static void addTablesToDatabase(SQLDatabase addTo) throws SQLException, ArchitectException { HashMap catalogs = new HashMap(); HashMap schemas = new HashMap(); synchronized (addTo) { Connection con = addTo.getConnection(); DatabaseMetaData dbmd = con.getMetaData(); ResultSet mdTables = null; try...
protected static void addTablesToDatabase(SQLDatabase addTo) throws SQLException, ArchitectException { HashMap catalogs = new HashMap(); HashMap schemas = new HashMap(); synchronized (addTo) { Connection con = addTo.getConnection(); DatabaseMetaData dbmd = con.getMetaData(); ResultSet mdTables = null; try...
1,109,595
public void dbChildrenRemoved(SQLObjectEvent e) { if (e.getSource() == this.model.getColumnsFolder()) { int ci[] = e.getChangedIndices(); for (int i = 0; i < ci.length; i++) { columnSelection.remove(ci[i]); } if (columnSelection.size() > 0) { selectNone(); columnSelection.set(Math.min(ci[0], columnSe...
public void dbChildrenRemoved(SQLObjectEvent e) { if (e.getSource() == this.model.getColumnsFolder()) { int ci[] = e.getChangedIndices(); for (int i = 0; i < ci.length; i++) { columnSelection.remove(ci[i]); } if (columnSelection.size() > 0) { selectNone(); columnSelection.set(Math.min(ci[0], columnSe...
1,109,596
void resyncEntries(S replicaEntry, S masterEntry) throws FetchException, PersistException { if (replicaEntry == null && masterEntry == null) { return; } Log log = LogFactory.getLog(ReplicatedRepository.class); setReplicationDisabled(true); try { Transaction t...
void resyncEntries(S replicaEntry, S masterEntry) throws FetchException, PersistException { if (replicaEntry == null && masterEntry == null) { return; } Log log = LogFactory.getLog(ReplicatedRepository.class); setReplicationDisabled(true); try { Transaction t...
1,109,598
void resyncEntries(S replicaEntry, S masterEntry) throws FetchException, PersistException { if (replicaEntry == null && masterEntry == null) { return; } Log log = LogFactory.getLog(ReplicatedRepository.class); setReplicationDisabled(true); try { Transaction t...
void resyncEntries(S replicaEntry, S masterEntry) throws FetchException, PersistException { if (replicaEntry == null && masterEntry == null) { return; } Log log = LogFactory.getLog(ReplicatedRepository.class); setReplicationDisabled(true); try { Transaction t...
1,109,599
void resyncEntries(S replicaEntry, S masterEntry) throws FetchException, PersistException { if (replicaEntry == null && masterEntry == null) { return; } Log log = LogFactory.getLog(ReplicatedRepository.class); setReplicationDisabled(true); try { Transaction t...
void resyncEntries(S replicaEntry, S masterEntry) throws FetchException, PersistException { if (replicaEntry == null && masterEntry == null) { return; } Log log = LogFactory.getLog(ReplicatedRepository.class); setReplicationDisabled(true); try { Transaction t...
1,109,600
void resyncEntries(S replicaEntry, S masterEntry) throws FetchException, PersistException { if (replicaEntry == null && masterEntry == null) { return; } Log log = LogFactory.getLog(ReplicatedRepository.class); setReplicationDisabled(true); try { Transaction t...
void resyncEntries(S replicaEntry, S masterEntry) throws FetchException, PersistException { if (replicaEntry == null && masterEntry == null) { return; } Log log = LogFactory.getLog(ReplicatedRepository.class); setReplicationDisabled(true); try { Transaction t...
1,109,601
void resyncEntries(S replicaEntry, S masterEntry) throws FetchException, PersistException { if (replicaEntry == null && masterEntry == null) { return; } Log log = LogFactory.getLog(ReplicatedRepository.class); setReplicationDisabled(true); try { Transaction t...
void resyncEntries(S replicaEntry, S masterEntry) throws FetchException, PersistException { if (replicaEntry == null && masterEntry == null) { return; } Log log = LogFactory.getLog(ReplicatedRepository.class); setReplicationDisabled(true); try { Transaction t...
1,109,602
public <S extends Storable> Storage<S> storageFor(Class<S> type) throws MalformedTypeException, SupportException, RepositoryException { Storage storage = mStorageMap.get(type); if (storage != null) { return storage; } Object lock; boolean doCreate; sync...
public <S extends Storable> Storage<S> storageFor(Class<S> type) throws MalformedTypeException, SupportException, RepositoryException { Storage storage = mStorageMap.get(type); if (storage != null) { return storage; } Object lock; boolean doCreate; sync...
1,109,603
public <S extends Storable> Storage<S> storageFor(Class<S> type) throws MalformedTypeException, SupportException, RepositoryException { Storage storage = mStorageMap.get(type); if (storage != null) { return storage; } Object lock; boolean doCreate; sync...
public <S extends Storable> Storage<S> storageFor(Class<S> type) throws MalformedTypeException, SupportException, RepositoryException { Storage storage = mStorageMap.get(type); if (storage != null) { return storage; } Object lock; boolean doCreate; sync...
1,109,604
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 ) ); ...
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 ) ); ...
1,109,606
public void doTag(XMLOutput output) throws Exception { String localName = null; int idx = name.indexOf(':'); if (idx >= 0) { localName = name.substring(idx + 1); } else { localName = name; } /** * @todo we should buffer up any S...
public void doTag(XMLOutput output) throws Exception { int idx = name.indexOf(':'); if (idx >= 0) { localName = name.substring(idx + 1); } else { localName = name; } /** * @todo we should buffer up any SAX events and replay the...
1,109,607
public void doTag(XMLOutput output) throws Exception { String localName = null; int idx = name.indexOf(':'); if (idx >= 0) { localName = name.substring(idx + 1); } else { localName = name; } /** * @todo we should buffer up any S...
public void doTag(XMLOutput output) throws Exception { String localName = null; int idx = name.indexOf(':'); if (idx >= 0) { localName = name.substring(idx + 1); } else { localName = name; } /** * @todo we should buffer up any S...
1,109,608
public void doTag(XMLOutput output) throws Exception { String localName = null; int idx = name.indexOf(':'); if (idx >= 0) { localName = name.substring(idx + 1); } else { localName = name; } /** * @todo we should buffer up any S...
public void doTag(XMLOutput output) throws Exception { String localName = null; int idx = name.indexOf(':'); if (idx >= 0) { localName = name.substring(idx + 1); } else { localName = name; } /** * @todo we should buffer up any S...
1,109,609
public void setAttributeValue( String name, String value ) { // ### we'll assume that all attributes are in no namespace! // ### this is severely limiting! // ### we should be namespace aware int index = attributes.getIndex("", name); if (index >= 0) { attributes.remove...
public void setAttributeValue( String name, String value ) throws JellyException { if (outputAttributes) { throw new JellyException( "Cannot set the value of attribute: " + name + " as we have already output the startElement() SAX event" ); } // ### we'll assume that all attributes are in no namespace! ...
1,109,610
public void drop(DropTargetDropEvent e) { hoverTimer.stop(); // Prevent hover timer from doing an unwanted expandPath or collapsePath if (!isDropAcceptable(e)) { e.rejectDrop(); return; } e.acceptDrop(e.getDropAction()); Transferable transferable = e.getTransferable(); DataFlavor[] flavors = tra...
public void drop(DropTargetDropEvent e) { hoverTimer.stop(); // Prevent hover timer from doing an unwanted expandPath or collapsePath if (!isDropAcceptable(e)) { e.rejectDrop(); return; } e.acceptDrop(e.getDropAction()); Transferable transferable = e.getTransferable(); DataFlavor[] flavors = tra...
1,109,613
public void drop(DropTargetDropEvent e) { hoverTimer.stop(); // Prevent hover timer from doing an unwanted expandPath or collapsePath if (!isDropAcceptable(e)) { e.rejectDrop(); return; } e.acceptDrop(e.getDropAction()); Transferable transferable = e.getTransferable(); DataFlavor[] flavors = tra...
public void drop(DropTargetDropEvent e) { hoverTimer.stop(); // Prevent hover timer from doing an unwanted expandPath or collapsePath if (!isDropAcceptable(e)) { e.rejectDrop(); return; } e.acceptDrop(e.getDropAction()); Transferable transferable = e.getTransferable(); DataFlavor[] flavors = tra...
1,109,614
public Object getVariable(String name) { Object value = variables.get(name); if ( value == null && getInherit() ) { value = getParent().findVariable( name ); } return value; }
public Object getVariable(String name) { Object value = variables.get(name); if ( value == null && isInherit() ) { value = getParent().findVariable( name ); } return value; }
1,109,617
public void setExport(boolean shouldExport) { this.shouldExport = shouldExport; }
public void setExport(boolean shouldExport) { this.shouldExport = shouldExport; }
1,109,618
public void setInherit(boolean shouldInherit) { this.shouldInherit = shouldInherit; }
public void setInherit(boolean shouldInherit) { this.shouldInherit = shouldInherit; }
1,109,619
public void setVariable(String name, Object value) { if ( getExport() ) { getParent().setVariable( name, value ); return; } if (value == null) { variables.remove(name); } else { variables.put(name, value); } }
public void setVariable(String name, Object value) { if ( isExport() ) { getParent().setVariable( name, value ); return; } if (value == null) { variables.remove(name); } else { variables.put(name, value); } }
1,109,620
public String getFreqString(int i ){ if (Options.getAssocTest() == ASSOC_TRIO){ return ""; } nf.setMinimumFractionDigits(3); nf.setMaximumFractionDigits(3); StringBuffer countSB = new StringBuffer(); Haplotype h = (Haplotype) alleles.get(i); double caseSum...
public String getFreqString(int i ){ if (Options.getAssocTest() == ASSOC_TRIO){ return ""; } nf.setMinimumFractionDigits(3); nf.setMaximumFractionDigits(3); StringBuffer countSB = new StringBuffer(); Haplotype h = (Haplotype) filteredAlleles.get(i); double...
1,109,621
public JSR160ServerConnection(JMXConnector jmxc ) throws IOException { assert jmxc != null; this.jmxc = jmxc; this.mbeanServer = jmxc.getMBeanServerConnection(); }
public JSR160ServerConnection(JMXConnector jmxc, MBeanServerConnection mbeanServer) throws IOException { assert jmxc != null; this.jmxc = jmxc; this.mbeanServer = jmxc.getMBeanServerConnection(); }
1,109,622
public JSR160ServerConnection(JMXConnector jmxc ) throws IOException { assert jmxc != null; this.jmxc = jmxc; this.mbeanServer = jmxc.getMBeanServerConnection(); }
public JSR160ServerConnection(JMXConnector jmxc ) throws IOException { assert jmxc != null; this.jmxc = jmxc; this.mbeanServer = mbeanServer; }
1,109,623
public void createMBean(String className, ObjectName name, Object[] params, String[] signature){ throw new RuntimeException("Notifications not supported"); }
public void createMBean(String className, ObjectName name, Object[] params, String[] signature){ Class[] methodSignature = new Class[]{String.class, javax.management.ObjectName.class, new Object[0].getClass(), new String[0].getC...
1,109,624
public void unregisterMBean(ObjectName objectName){ throw new RuntimeException("unregisterMBean not supported"); }
public void unregisterMBean(ObjectName objectName){ Class[] methodSignature = new Class[]{javax.management.ObjectName.class}; Object[] methodArgs = new Object[]{toJMXObjectName(objectName)}; callMBeanServer("unregisterMBean", methodSignature, methodArgs); }
1,109,625
public String getAlleleName(int i) { return ((Haplotype) alleles.get(i)).toString(); }
public String getAlleleName(int i) { return ((Haplotype) filteredAlleles.get(i)).toString(); }
1,109,626
public String getFreq(int j) { double freq = ((Haplotype)alleles.get(j)).getPercentage(); if (freq < 0){ return (""); }else{ nf.setMinimumFractionDigits(3); nf.setMaximumFractionDigits(3); return nf.format(freq); } }
public String getFreq(int j) { double freq = ((Haplotype)alleles.get(j)).getPercentage(); if (freq < 0){ return (""); }else{ nf.setMinimumFractionDigits(3); nf.setMaximumFractionDigits(3); return nf.format(freq); } }
1,109,627
public String getNumericAlleleName(int i){ return ((Haplotype) alleles.get(i)).toNumericString(); }
public String getNumericAlleleName(int i){ return ((Haplotype) filteredAlleles.get(i)).toNumericString(); }
1,109,628
private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus, Vector kidAffStatus, boolean[] haploid) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_bloc...
private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus, Vector kidAffStatus, boolean[] haploid) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_bloc...
1,109,629
private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus, Vector kidAffStatus, boolean[] haploid) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_bloc...
private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus, Vector kidAffStatus, boolean[] haploid) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_bloc...
1,109,630
public void zeroOutMarker(int i){ byte zeroArray[] = {0,0}; this.markers.set(i, zeroArray); }
public void zeroOutMarker(int i){ byte zeroArray[] = {0,0}; this.markers.set(i, zeroArray); }
1,109,633
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...
public TagScript createTagScript(final 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...
1,109,634
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...
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...
1,109,635
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...
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...
1,109,636
public JeezTagLibrary() { this( AntTagLibrary.createProject() ); }
public JeezTagLibrary() { this.antTagLib = new AntTagLibrary(); }
1,109,637
public TagScript createTagScript(String name, Attributes attrs) throws Exception { TagScript script = super.createTagScript( name, attrs ); if ( script == null ) { // script = this.coreTagLib.createTagScript( name, attrs ); if ( script == nu...
public TagScript createTagScript(String name, Attributes attrs) throws Exception { TagScript script = super.createTagScript( name, attrs ); if ( script == null ) { // script = this.coreTagLib.createTagScript( name, attrs ); if ( script == nu...
1,109,638
public TagScript createTagScript(String name, Attributes attrs) throws Exception { TagScript script = super.createTagScript( name, attrs ); if ( script == null ) { // script = this.coreTagLib.createTagScript( name, attrs ); if ( script == nu...
public TagScript createTagScript(String name, Attributes attrs) throws Exception { TagScript script = super.createTagScript( name, attrs ); if ( script == null ) { // script = this.coreTagLib.createTagScript( name, attrs ); if ( script == nu...
1,109,640
public TagScript createTagScript(String name, Attributes attrs) throws Exception { TagScript script = super.createTagScript( name, attrs ); if ( script == null ) { // script = this.coreTagLib.createTagScript( name, attrs ); if ( script == nu...
public TagScript createTagScript(String name, Attributes attrs) throws Exception { TagScript script = super.createTagScript( name, attrs ); if ( script == null ) { // script = this.coreTagLib.createTagScript( name, attrs ); if ( script == nu...
1,109,641
public TagScript createTagScript(String name, Attributes attributes) throws Exception { Object value = templates.get(name); if ( value instanceof Script ) { Script template = (Script) value; DynamicTag tag = new DynamicTag(template); // XXXX: somehow...
public TagScript createTagScript(final String name, Attributes attributes) throws Exception { Object value = templates.get(name); if ( value instanceof Script ) { Script template = (Script) value; DynamicTag tag = new DynamicTag(template); // XXXX: s...
1,109,642
public TagScript createTagScript(String name, Attributes attributes) throws Exception { Object value = templates.get(name); if ( value instanceof Script ) { Script template = (Script) value; DynamicTag tag = new DynamicTag(template); // XXXX: somehow...
public TagScript createTagScript(String name, Attributes attributes) throws Exception { Object value = templates.get(name); if ( value instanceof Script ) { Script template = (Script) value; DynamicTag tag = new DynamicTag(template); // XXXX: somehow...
1,109,643
public void setDisplayThresh(int amount) { parent.displayThresh = amount; parent.adjustDisplay(); }
public void setDisplayThresh(int amount) { parent.displayThresh = amount; parent.adjustDisplay(); }
1,109,644
public void testSetDisplayName() { CountingPropertyChangeListener l = new CountingPropertyChangeListener(); ds.addPropertyChangeListener(l); ds.setDisplayName("test"); assertEquals(1, l.getPropertyChangeCount()); assertEquals("displayName", l.getLastPropertyChange()); assertEquals("test", ds.getDisplayName());...
public void testSetDisplayName() { CountingPropertyChangeListener l = new CountingPropertyChangeListener(); ds.addPropertyChangeListener(l); ds.setDisplayName("test"); assertEquals(1, l.getPropertyChangeCount()); assertEquals("name", l.getLastPropertyChange()); assertEquals("test", ds.getDisplayName()); }
1,109,646
public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo...
public void dPrimeDraw(String[][] table, boolean info, Vector snps, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Fon...
1,109,649
public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo...
public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo...
1,109,650
public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo...
public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo...
1,109,651
public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo...
public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo...
1,109,653
public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo...
public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo...
1,109,654
public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo...
public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo...
1,109,655
public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo...
public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo...
1,109,656
public Dimension dPrimeGetPreferredSize(int size){ return new Dimension(size*30, size*30); }
public Dimension dPrimeGetPreferredSize(int size){ return new Dimension(size*30, size*30); }
1,109,657
public Hashtable getProperties() { Hashtable h = new Hashtable(); for (Iterator i = this.context.getVariableNames(); i.hasNext(); ) { String name = (String) i.next(); Object value = this.context.getVariable(name); if (value != null) { h.put(name, value);...
public Hashtable getProperties() { Hashtable h = new Hashtable(); for (Iterator i = this.context.getVariableNames(); i.hasNext(); ) { String name = (String) i.next(); Object value = this.context.getVariable(name); if (value != null) { h.put(name, value.t...
1,109,658
public ArchitectDataSource() { properties = new HashMap(); }
public ArchitectDataSource() { properties = new HashMap<String,String>(); }
1,109,659
public String get(String key) { return (String) properties.get(key); }
public String get(String key) { return properties.get(key); }
1,109,660
public String getOdbcDsn() { return (String) properties.get(PL_DSN); }
public String getOdbcDsn() { return properties.get(PL_DSN); }
1,109,661
protected PropertyChangeSupport getPcs() { if (pcs == null) pcs = new PropertyChangeSupport(this); return pcs; }
private PropertyChangeSupport getPcs() { if (pcs == null) pcs = new PropertyChangeSupport(this); return pcs; }
1,109,662
public String getPlDbType() { return (String) properties.get(PL_TYPE); }
public String getPlDbType() { return properties.get(PL_TYPE); }
1,109,663
public String getPlSchema() { return (String) properties.get(PL_SCHEMA_OWNER); }
public String getPlSchema() { return properties.get(PL_SCHEMA_OWNER); }
1,109,664
public Map getPropertiesMap() { return properties; }
public Map getPropertiesMap() { return properties; }
1,109,665
private void setWindowImage(Window window, Image image) { Window.setDefaultImage(image); }
private void setWindowImage(Window window, Image image) { window.getShell().setImage(image); }
1,109,666
public void doTag(XMLOutput output) throws JellyTagException { // invoke by body just in case some nested tag configures me invokeBody(output); Widget parent = getParentWidget(); if (parent == null) { throw new JellyTagException("This tag must be nested within a widget"); ...
public void doTag(XMLOutput output) throws JellyTagException { // invoke by body just in case some nested tag configures me invokeBody(output); Widget parent = getParentWidget(); if (parent == null) { throw new JellyTagException("This tag must be nested within a Widget or a ...
1,109,667
public void doTag(XMLOutput output) throws JellyTagException { // invoke by body just in case some nested tag configures me invokeBody(output); Widget parent = getParentWidget(); if (parent == null) { throw new JellyTagException("This tag must be nested within a widget"); ...
public void doTag(XMLOutput output) throws JellyTagException { // invoke by body just in case some nested tag configures me invokeBody(output); Widget parent = getParentWidget(); if (parent == null) { throw new JellyTagException("This tag must be nested within a widget"); ...
1,109,668
public void doTag(XMLOutput output) throws JellyTagException { // invoke by body just in case some nested tag configures me invokeBody(output); Widget parent = getParentWidget(); if (parent == null) { throw new JellyTagException("This tag must be nested within a widget"); ...
public void doTag(XMLOutput output) throws JellyTagException { // invoke by body just in case some nested tag configures me invokeBody(output); Widget parent = getParentWidget(); if (parent == null) { throw new JellyTagException("This tag must be nested within a widget"); ...
1,109,669
public HaploView(){ try{ fc = new JFileChooser(System.getProperty("user.dir")); }catch(NullPointerException n){ try{ UIManager.setLookAndFeel(UIManager.getCrossPlatformLookAndFeelClassName()); fc = new JFileChooser(System.getProperty("user.dir")); ...
public HaploView(){ try{ fc = new JFileChooser(System.getProperty("user.dir")); }catch(NullPointerException n){ try{ UIManager.setLookAndFeel(UIManager.getCrossPlatformLookAndFeelClassName()); fc = new JFileChooser(System.getProperty("user.dir")); ...
1,109,670
public PresentationObject getLetterForm(IWContext iwc) { Table T = new Table(); TextInput fromAddress = new TextInput("from_address"); fromAddress.setLength(80); TextInput fromName = new TextInput("from_name"); fromName.setLength(80); TextInput subject = new TextInput("subject"); subject.setLength(80); TextAre...
public PresentationObject getLetterForm(IWContext iwc) { Table T = new Table(); TextInput fromAddress = new TextInput("from_address"); fromAddress.setLength(80); TextInput fromName = new TextInput("from_name"); fromName.setLength(80); TextInput subject = new TextInput("subject"); subject.setLength(80); TextAre...
1,109,671
public PresentationObject getLetterForm(IWContext iwc) { Table T = new Table(); TextInput fromAddress = new TextInput("from_address"); fromAddress.setLength(80); TextInput fromName = new TextInput("from_name"); fromName.setLength(80); TextInput subject = new TextInput("subject"); subject.setLength(80); TextAre...
public PresentationObject getLetterForm(IWContext iwc) { Table T = new Table(); TextInput fromAddress = new TextInput("from_address"); fromAddress.setLength(80); TextInput fromName = new TextInput("from_name"); fromName.setLength(80); TextInput subject = new TextInput("subject"); subject.setLength(80); TextAre...
1,109,672
public void doTag(XMLOutput output) throws Exception { if (test != null) { while (test.evaluateAsBoolean(getContext())) { if (log.isDebugEnabled()) { log.debug("evaluated to true! gonna keep on chuggin!"); } invokeBody(output); ...
public void doTag(XMLOutput output) throws MissingAttributeException, Exception { if (test != null) { while (test.evaluateAsBoolean(getContext())) { if (log.isDebugEnabled()) { log.debug("evaluated to true! gonna keep on chuggin!"); } ...
1,109,673
void processData(){ final long maxCompDist = Long.parseLong(filenames[2])*1000; try{ this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); final SwingWorker worker = new SwingWorker(){ public Object construct(){ dPrimeDisplay=null; ...
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; ...
1,109,674
void readMarkers(File inputFile){ try { int good = theData.prepareMarkerInput(inputFile); if (good == -1){ JOptionPane.showMessageDialog(this, "Number of markers in info file does not match number of markers in dataset.", "Err...
void readMarkers(File inputFile){ try { int good = theData.prepareMarkerInput(inputFile,maxCompDist); if (good == -1){ JOptionPane.showMessageDialog(this, "Number of markers in info file does not match number of markers in dataset.", ...
1,109,675
public void checkColumnLocked(SQLColumn col) throws LockedColumnException { for (SQLRelationship.ColumnMapping cm : getMappings()) { if (cm.getFkColumn() == col) { throw new LockedColumnException(this); } } }
public void checkColumnLocked(SQLColumn col) throws LockedColumnException { for (SQLRelationship.ColumnMapping cm : getMappings()) { if (cm.getFkColumn() == col) { throw new LockedColumnException(this,col); } } }
1,109,676
public void testParse() throws Exception { InputStream in = getClass().getResourceAsStream( "example.jelly" ); XMLParser parser = new XMLParser(); Script script = parser.parse( in ); script = script.compile(); log.debug( "Found: " + script ); assertTrue( "Script is ...
public void testParse() throws Exception { InputStream in = getClass().getResourceAsStream( "example.jelly" ); XMLParser parser = new XMLParser(); Script script = parser.parse( in ); script = script.compile(); log.debug( "Found: " + script ); assertTrue( "Script is ...
1,109,678
public void setDataType(Object dataType) { this.dataType = dataType; setDynaBean( new WrapDynaBean(dataType) ); }
public void setDataType(Object dataType) { this.dataType = dataType; setDynaBean( new ConvertingWrapDynaBean(dataType) ); }
1,109,679
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 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{ g...
1,109,680
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 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{ ...
1,109,681
public void tallyCCInd(byte a1, byte a2, int cc){ //case = 0, control = 1 for int cc if (a1 == 5 && a2 == 5){ counts[cc][0]++; counts[cc][1]++; }else{ //seed the alleles as soon as they're found if (allele1 == 0){ allele1 = a1; ...
public void tallyCCInd(byte a1, byte a2, int cc){ //case = 0, control = 1 for int cc if (a1 >= 5 && a2 >= 5){ counts[cc][0]++; counts[cc][1]++; }else{ //seed the alleles as soon as they're found if (allele1 == 0){ allele1 = a1; ...
1,109,682
public void tallyTrioInd(byte alleleT, byte alleleU) { if(alleleT == 5 && alleleU == 5) { if(tallyHet){ counts[0][0]++; counts[1][1]++; counts[0][1]++; counts[1][0]++; this.tallyHet = false; } else { ...
public void tallyTrioInd(byte alleleT, byte alleleU) { if(alleleT >= 5 && alleleU >= 5) { if(tallyHet){ counts[0][0]++; counts[1][1]++; counts[0][1]++; counts[1][0]++; this.tallyHet = false; } else { ...
1,109,683
private void findAllMatchingTestMail(String username) throws SamplingException { try { org.apache.commons.net.pop3.POP3Client pop3Client = openConnection(username); // retrieve all messages POP3MessageInfo[] entries = null; try { entries = pop3Client...
private void findAllMatchingTestMail(String username) throws SamplingException { try { org.apache.commons.net.pop3.POP3Client pop3Client = openConnection(username); // retrieve all messages POP3MessageInfo[] entries = null; try { entries = pop3Client...
1,109,684
private void findAllMatchingTestMail(String username) throws SamplingException { try { org.apache.commons.net.pop3.POP3Client pop3Client = openConnection(username); // retrieve all messages POP3MessageInfo[] entries = null; try { entries = pop3Client...
private void findAllMatchingTestMail(String username) throws SamplingException { try { org.apache.commons.net.pop3.POP3Client pop3Client = openConnection(username); // retrieve all messages POP3MessageInfo[] entries = null; try { entries = pop3Client...
1,109,685
private void findAllMatchingTestMail(String username) throws SamplingException { try { org.apache.commons.net.pop3.POP3Client pop3Client = openConnection(username); // retrieve all messages POP3MessageInfo[] entries = null; try { entries = pop3Client...
private void findAllMatchingTestMail(String username) throws SamplingException { try { org.apache.commons.net.pop3.POP3Client pop3Client = openConnection(username); // retrieve all messages POP3MessageInfo[] entries = null; try { entries = pop3Client...
1,109,686
public Expression createExpression(final String text) throws Exception {/* org.apache.commons.jexl.Expression expr = org.apache.commons.jexl.ExpressionFactory.createExpression(text); if ( isSupportAntVariables() ) { expr.addPostResolver(new FlatResolv...
public Expression createExpression(final String text) throws Exception {/* org.apache.commons.jexl.Expression expr = org.apache.commons.jexl.ExpressionFactory.createExpression(text); if ( isSupportAntVariables() ) { expr.addPostResolver(new FlatResolv...
1,109,687
public String getExpressionText() { return text; }
public String getExpressionText() { return "${" + text + "}"; }
1,109,688
public void doTag(final XMLOutput output) throws Exception { if ( this.var == null ) { throw new MissingAttributeException( "var" ); } if ( this.delim == null ) { throw new MissingAttributeException( "var" ); } StringTokenizer tokenizer = new...
public void doTag(final XMLOutput output) throws Exception { if ( this.var == null ) { throw new MissingAttributeException( "delim" ); } if ( this.delim == null ) { throw new MissingAttributeException( "delim" ); } StringTokenizer tokenizer =...
1,109,689