JoaoJunior/formatted-java-preprocessed-code-APR

protected Object newInstance( Class theClass, Map attributes, XMLOutput output) throws JellyTagException { int style = getStyle(attributes); // now lets call the constructor with the parent Widget parent = getParentWidget(); Widget widget = (Widget) createWidget(theClass, parent, style); if (parent != null) {...

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private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable...

private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0, haploid = 0; //Hashtable allgenos = ...

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private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable...

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private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable...

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private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable...

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private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable...

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private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable...

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private double getGenoPercent(int het, int hom, int missing){ if (het+hom+missing == 0){ return 0; }else{ return 100.0*(het+hom)/(het+hom+missing); } }

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private double getGenoPercent(int het, int hom, int missing){ if (het+hom+missing == 0){ return 0; }else{ return 100.0*(het+hom)/(het+hom+missing); } }

private double getGenoPercent(int het, int hom, int missing){ if (het+hom+missing == 0){ return 0; }else{ return 100.0*(het+hom+haploid)/(het+hom+haploid+missing); } }

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public Expression createExpression( ExpressionFactory factory, String tagName, String attributeName, String attributeValue) throws JellyException { // #### may need to include some namespace URI information in the XPath instance? if (attributeName.equals("select")) ...

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public void doTag(final XMLOutput output) throws Exception { AttainTag attainTag = (AttainTag) findAncestorWithClass( AttainTag.class ); Session session = null; if ( attainTag == null ) { session = new JellySession( output ); } else { session = attainTag.get...

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public void flush() throws IOException { ((XMLWriter)contentHandler).flush(); }

public void flush() throws IOException { if( contentHandler instanceof XMLWriter ) { ((XMLWriter)contentHandler).flush(); } }

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public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) { WeblogicApplicationForm ap...

public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) { ApplicationForm appForm = ...

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public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) { WeblogicApplicationForm ap...

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public void setAttribute(String name, Object value) { if ( value == null ) { // should we send in null? super.setAttribute( name, "" ); } else { super.setAttribute( name, value.toString() ); } }

public void setAttribute(String name, Object value) { if ( value == null ) { // should we send in null? super.setAttribute( name, "" ); } else { if ( value instanceof Expression ) { super.setAttribute( name, ((Expression) value).evaluateAsValue(context) ); } els...

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private void applicationChanged(ApplicationConfig appConfig) { ApplicationHeartBeatThread associatedThread = null; for(ApplicationHeartBeatThread thread:threads){ if(thread.getApplicationConfig().equals(appConfig)){ associatedThread = thread; break; ...

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protected void configure() { // load the properties file of libraries available InputStream in = null; URL url = getClassLoader().getResource("org/apache/commons/jelly/jelly.properties"); if (url != null) { log.debug("Loading Jelly default tag libraries from: " + ur...

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public void doTag(XMLOutput output) throws Exception { value = false; if ( test != null ) { if ( test.evaluateAsBoolean( context ) ) { value = true; invokeBody(output); } } }

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public void doTag(XMLOutput output) throws Exception { value = false; if ( test != null ) { if ( test.evaluateAsBoolean( context ) ) { value = true; invokeBody(output); } } }

public void doTag(XMLOutput output) throws Exception { value = false; if ( test != null ) { if ( test.evaluateAsBoolean( context ) ) { tag.setBlockEvaluated(true); invokeBody(output); } } }

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public void doTag(final XMLOutput output) throws Exception { String name = getName(); if ( name == null ) { name = toString(); } // #### we need to redirect the output to a TestListener // or something? TestCase testCase = new TestCase(name) { ...

public void doTag(final XMLOutput output) throws JellyTagException { String name = getName(); if ( name == null ) { name = toString(); } // #### we need to redirect the output to a TestListener // or something? TestCase testCase = new TestCase(name) { ...

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public void doTag(final XMLOutput output) throws Exception { String name = getName(); if ( name == null ) { name = toString(); } // #### we need to redirect the output to a TestListener // or something? TestCase testCase = new TestCase(name) { ...

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private ListItem(final Document document) { super("DocumentListAvatar$ListItem", listItemBackground); this.document = document; this.selectionTimer = new Timer(500, new ActionListener() { public void actionPerformed(final ActionEvent e) { selectDocument(document.getId()); } }); setLayout(new GridB...

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public void mouseEntered(final MouseEvent e) { startSelectionTimer(); }

public void mouseEntered(final MouseEvent e) { selectDocument(document.getId()); }

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public void mouseExited(final MouseEvent e) { stopSelectionTimer(); unselect(); }

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private void select() { selectionTimer.stop(); setBackground(listItemBackgroundSelect); repaint(); }

private void select() { setBackground(listItemBackgroundSelect); repaint(); }

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private void selectDocument(final UUID documentId) { Assert.assertNotNull("Cannot select null document.", documentId); // if it's the same do nothing if(this.currentSelection == documentId || documentId.equals(currentSelection)) { return; } final Collection<Component> listItems = documentItemMap.values(); for(...

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public void drop(DropTargetDropEvent dtde) { if (tpTarget != null) { tpTarget.getDropTarget().drop(dtde); return; } Transferable t = dtde.getTransferable(); PlayPen c = (PlayPen) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if...

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public void drop(DropTargetDropEvent dtde) { if (tpTarget != null) { tpTarget.getDropTarget().drop(dtde); return; } Transferable t = dtde.getTransferable(); PlayPen c = (PlayPen) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if...

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public void drop(DropTargetDropEvent dtde) { if (tpTarget != null) { tpTarget.getDropTarget().drop(dtde); return; } Transferable t = dtde.getTransferable(); PlayPen c = (PlayPen) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if...

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public void drop(DropTargetDropEvent dtde) { if (tpTarget != null) { tpTarget.getDropTarget().drop(dtde); return; } Transferable t = dtde.getTransferable(); PlayPen c = (PlayPen) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if...

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public void drop(DropTargetDropEvent dtde) { if (tpTarget != null) { tpTarget.getDropTarget().drop(dtde); return; } Transferable t = dtde.getTransferable(); PlayPen c = (PlayPen) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if...

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public void drop(DropTargetDropEvent dtde) { if (tpTarget != null) { tpTarget.getDropTarget().drop(dtde); return; } Transferable t = dtde.getTransferable(); PlayPen c = (PlayPen) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if...

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public void drop(DropTargetDropEvent dtde) { if (tpTarget != null) { tpTarget.getDropTarget().drop(dtde); return; } Transferable t = dtde.getTransferable(); PlayPen c = (PlayPen) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if...

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public void setAttribute(String name, Object value) { // Catch the normal setAttribute, and call throw Ant's // normal property-deref routines. Project project = task.getProject(); String newValue = project.replaceProperties( (String) value ); super....

public void setAttribute(String name, Object value) { // Catch the normal setAttribute, and call throw Ant's // normal property-deref routines. Project project = task.getProject(); String newValue = ProjectHelper.replaceProperties( project, (String) value, ...

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protected void trimBody() { synchronized(body) { // #### should refactor this code into // #### trimWhitespace() methods on the Script objects if ( body instanceof CompositeTextScriptBlock ) { CompositeTextScriptBlock block = (CompositeTextScriptBlock) body; ...

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protected void trimBody() { synchronized(body) { // #### should refactor this code into // #### trimWhitespace() methods on the Script objects if ( body instanceof CompositeTextScriptBlock ) { CompositeTextScriptBlock block = (CompositeTextScriptBlock) body; ...

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public void parseHapMap(Vector rawLines) throws PedFileException { int colNum = -1; int numLines = rawLines.size(); Individual ind; this.order = new Vector(); //sort first Vector lines = new Vector(); Hashtable sortHelp = new Hashtable(numLines-1,1.0f); long[]...

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public void compoundEditEnd(UndoCompoundEvent e) { if (compoundDepth == 0) throw new IllegalStateException("Not in a compound edit"); compoundDepth--; if (compoundDepth == 0) { log.add(currentCompoundLog); currentCompoundLog = null; } ...

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public void compoundEditStart(UndoCompoundEvent e) { compoundDepth++; if (compoundDepth == 1) { currentCompoundLog = new ArrayList(); } }

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public void dbChildrenInserted(SQLObjectEvent e) { log.add(e); }

public void dbChildrenInserted(SQLObjectEvent e) { addToLog(LogItemType.INSERT, e); }

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public void dbChildrenRemoved(SQLObjectEvent e) { log.add(e); }

public void dbChildrenRemoved(SQLObjectEvent e) { addToLog(LogItemType.REMOVE, e); }

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public void dbObjectChanged(SQLObjectEvent e) { log.add(e); }

public void dbObjectChanged(SQLObjectEvent e) { addToLog(LogItemType.CHANGE, e); }

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public void dbStructureChanged(SQLObjectEvent e) { log.add(e); }

public void dbStructureChanged(SQLObjectEvent e) { throw new UnsupportedOperationException("Structure changes are not undoable"); }

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public List<Map<String,Object>> makeTableSnapshot(SQLTable t) { return null; //TODO: finish method }

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public void testChangeFifthColumnKey() throws ArchitectException{ SQLColumn col5 = table.getColumnByName("five"); assertNotNull(col5); col5.setPrimaryKeySeq(0); assertEquals(4, table.getPkSize()); assertEquals(0, table.getColumnIndex(table.getColumnByName("one"))); ...

public void testChangeFifthColumnKey() throws Exception { EventLogger l = new EventLogger(); SQLColumn col5 = table.getColumnByName("five"); assertNotNull(col5); col5.setPrimaryKeySeq(0); assertEquals(4, table.getPkSize()); assertEquals(0, table.getColumnIndex(table...

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public void testChangeFifthColumnKey() throws ArchitectException{ SQLColumn col5 = table.getColumnByName("five"); assertNotNull(col5); col5.setPrimaryKeySeq(0); assertEquals(4, table.getPkSize()); assertEquals(0, table.getColumnIndex(table.getColumnByName("one"))); ...

public void testChangeFifthColumnKey() throws ArchitectException{ SQLColumn col5 = table.getColumnByName("five"); assertNotNull(col5); TableSnapshot original = l.makeTableSnapshot(table); ArchitectUtils.listenToHierarchy(l, table); col5.setPrimaryKeySeq(0); ArchitectUtils.unlistenToHierarchy(l...

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public void testChangeFifthColumnKey() throws ArchitectException{ SQLColumn col5 = table.getColumnByName("five"); assertNotNull(col5); col5.setPrimaryKeySeq(0); assertEquals(4, table.getPkSize()); assertEquals(0, table.getColumnIndex(table.getColumnByName("one"))); ...

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protected TagScript createTag( String namespaceURI, String localName, Attributes list) throws SAXException { try { // use the URI to load a taglib TagLibrary taglib = context.getTagLibrary(namespaceURI); if (taglib == null) { if (nam...

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protected TagScript createTag( String namespaceURI, String localName, Attributes list) throws SAXException { try { // use the URI to load a taglib TagLibrary taglib = context.getTagLibrary(namespaceURI); if (taglib == null) { if (nam...

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public Vector check() throws PedFileException{ //before we perform the check we want to prune out individuals with too much missing data //or trios which contain individuals with too much missing data Vector indList = getOrder(); Individual currentInd; Family currentFamily; ...

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public Vector check() throws PedFileException{ //before we perform the check we want to prune out individuals with too much missing data //or trios which contain individuals with too much missing data Vector indList = getOrder(); Individual currentInd; Family currentFamily; ...

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public Vector check() throws PedFileException{ //before we perform the check we want to prune out individuals with too much missing data //or trios which contain individuals with too much missing data Vector indList = getOrder(); Individual currentInd; Family currentFamily; ...

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public Vector check() throws PedFileException{ //before we perform the check we want to prune out individuals with too much missing data //or trios which contain individuals with too much missing data Vector indList = getOrder(); Individual currentInd; Family currentFamily; ...

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public Vector check() throws PedFileException{ //before we perform the check we want to prune out individuals with too much missing data //or trios which contain individuals with too much missing data Vector indList = getOrder(); Individual currentInd; Family currentFamily; ...

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public void parseHapMap(Vector rawLines) throws PedFileException { int colNum = -1; int numLines = rawLines.size(); Individual ind; this.order = new Vector(); //sort first Vector lines = new Vector(); Hashtable sortHelp = new Hashtable(numLines-1,1.0f); long[]...

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public void parseLinkage(Vector pedigrees) throws PedFileException { int colNum = -1; boolean withOptionalColumn = false; int numLines = pedigrees.size(); Individual ind; this.order = new Vector(); for(int k=0; k<numLines; k++){ StringTokenizer tokenizer = new St...

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public void parseLinkage(Vector pedigrees) throws PedFileException { int colNum = -1; boolean withOptionalColumn = false; int numLines = pedigrees.size(); Individual ind; this.order = new Vector(); for(int k=0; k<numLines; k++){ StringTokenizer tokenizer = new St...

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public void parseLinkage(Vector pedigrees) throws PedFileException { int colNum = -1; boolean withOptionalColumn = false; int numLines = pedigrees.size(); Individual ind; this.order = new Vector(); for(int k=0; k<numLines; k++){ StringTokenizer tokenizer = new St...

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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 TagScript( ...

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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 TagScript( ...

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public Tag createTag() throws Exception { if ( factory instanceof TagFactory ) { return ((TagFactory) factory).createTag(); } else { return new ComponentTag(factory); } ...

public Tag createTag(String name, Attributes attributes) throws Exception { if ( factory instanceof TagFactory ) { return ((TagFactory) factory).createTag(); } else { return new ComponentTag(factory); ...

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public Tag createTag() throws Exception { if ( factory instanceof TagFactory ) { return ((TagFactory) factory).createTag(); } else { return new ComponentTag(factory); } ...

public Tag createTag() throws Exception { if ( factory instanceof TagFactory ) { return ((TagFactory) factory).createTag(name, attributes); } else { return new ComponentTag(factory); } ...

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public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); Object parentObject = findBeanAncestor(); // lets assume that Task instances are not nested inside other Task instances // for example <manifest> inside a <jar>...

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public void doTag(XMLOutput output) throws Exception { if (!maxRowsSpecified) { Object obj = context.getVariable("org.apache.commons.jelly.sql.maxRows"); if (obj != null) { if (obj instanceof Integer) { maxRows = ((Integer) obj).intValue(); ...

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public void doTag(XMLOutput output) throws Exception { if (!maxRowsSpecified) { Object obj = context.getVariable("org.apache.commons.jelly.sql.maxRows"); if (obj != null) { if (obj instanceof Integer) { maxRows = ((Integer) obj).intValue(); ...

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public void doTag(XMLOutput output) throws Exception { if (!maxRowsSpecified) { Object obj = context.getVariable("org.apache.commons.jelly.sql.maxRows"); if (obj != null) { if (obj instanceof Integer) { maxRows = ((Integer) obj).intValue(); ...

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public void addChild(Component component, Object constraints) throws JellyTagException { BorderLayoutTag tag = (BorderLayoutTag) findAncestorWithClass( BorderLayoutTag.class ); if (tag == null) { throw new JellyTagException( "this tag must be nested within a <tr> tag" ); } tag...

public void addChild(Component component, Object constraints) throws JellyTagException { BorderLayoutTag tag = (BorderLayoutTag) findAncestorWithClass( BorderLayoutTag.class ); if (tag == null) { throw new JellyTagException( "this tag must be nested within a <borderLayout> tag" ); } ...

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static Vector doSpine(DPrimeTable dPrime){ // find blocks by searching for stretches between two markers A,B where // D prime is > a threshold for all informative combinations of A, (A+1...B) int baddies; int verticalExtent=0; int horizontalExtent=0; Vector blocks = new Ve...

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public void doTag(XMLOutput output) throws Exception { Object answer = null; if ( value != null ) { answer = value.evaluate(context); } else { answer = getBodyText(); } if ( var != null ) { context.setVariable(var, answer); } ...

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protected void setPropertyValue( Object target, String property, Object value ) throws Exception { if ( target instanceof Map ) { Map map = (Map) target; map.put( property, value ); } else { BeanUtils.setProperty( target, property, value ); } }

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protected void setPropertyValue( Object target, String property, Object value ) throws Exception { if ( target instanceof Map ) { Map map = (Map) target; map.put( property, value ); } else { BeanUtils.setProperty( target, property, value ); } }

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public void addColumn(SQLColumn c, SQLTable t) throws ArchitectDiffException { Map colNameMap = new HashMap(); print("\n ALTER TABLE "); print( toQualifiedName(t) ); print(" ADD COLUMN "); print(columnDefinition(c,colNameMap)); endStatement(DDLStatement.StatementType.CREATE, c); }

public void addColumn(SQLColumn c) { Map colNameMap = new HashMap(); print("\n ALTER TABLE "); print( toQualifiedName(t) ); print(" ADD COLUMN "); print(columnDefinition(c,colNameMap)); endStatement(DDLStatement.StatementType.CREATE, c); }

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public void addColumn(SQLColumn c, SQLTable t) throws ArchitectDiffException { Map colNameMap = new HashMap(); print("\n ALTER TABLE "); print( toQualifiedName(t) ); print(" ADD COLUMN "); print(columnDefinition(c,colNameMap)); endStatement(DDLStatement.StatementType.CREATE, c); }

public void addColumn(SQLColumn c, SQLTable t) throws ArchitectDiffException { Map colNameMap = new HashMap(); print("\n ALTER TABLE "); print(toQualifiedName(c.getParentTable())); print(" ADD COLUMN "); print(columnDefinition(c,colNameMap)); endStatement(DDLStatement.StatementType.CREATE, c); }

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public void addPrimaryKey(SQLTable t, String primaryKeyName) throws ArchitectException { Map colNameMap = new HashMap(); StringBuffer sqlStatement = new StringBuffer(); boolean first = true; sqlStatement.append("ALTER TABLE "+ toQualifiedName(t.getCatalogName(),t.getSchemaName(),t.getName()) + " ADD PRIMARY K...

public void addPrimaryKey(SQLTable t) throws ArchitectException { Map colNameMap = new HashMap(); StringBuffer sqlStatement = new StringBuffer(); boolean first = true; sqlStatement.append("ALTER TABLE "+ toQualifiedName(t.getCatalogName(),t.getSchemaName(),t.getName()) + " ADD PRIMARY KEY ("); for (SQLColumn...

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public void addPrimaryKey(SQLTable t, String primaryKeyName) throws ArchitectException { Map colNameMap = new HashMap(); StringBuffer sqlStatement = new StringBuffer(); boolean first = true; sqlStatement.append("ALTER TABLE "+ toQualifiedName(t.getCatalogName(),t.getSchemaName(),t.getName()) + " ADD PRIMARY K...

public void addPrimaryKey(SQLTable t, String primaryKeyName) throws ArchitectException { Map colNameMap = new HashMap(); StringBuffer sqlStatement = new StringBuffer(); boolean first = true; sqlStatement.append("ALTER TABLE "+ toQualifiedName(t.getName()) + " ADD PRIMARY KEY ("); for (SQLColumn c : t.getColu...

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public void addRelationship(SQLRelationship r) throws ArchitectDiffException { print("\n ALTER TABLE "); print( toQualifiedName(r.getFkTable()) ); print(" ADD CONSTRAINT "); print(r.getName()); print(" FOREIGN KEY ( "); Map<String, SQLColumn> colNameMap = new HashMap<String, SQLColumn> (); boolean firstCol...

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protected String columnDefinition(SQLColumn c, Map colNameMap) throws ArchitectDiffException { StringBuffer def = new StringBuffer(); // Column name def.append(createPhysicalName(colNameMap, c)); def.append(" "); def.append(columnType(c)); def.append(" "); // Column nul...

protected String columnDefinition(SQLColumn c, Map colNameMap) { StringBuffer def = new StringBuffer(); // Column name def.append(createPhysicalName(colNameMap, c)); def.append(" "); def.append(columnType(c)); def.append(" "); // Column nullability def.append(col...

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public void dropColumn(SQLColumn c, SQLTable t) throws ArchitectDiffException { Map colNameMap = new HashMap(); print("\n ALTER TABLE "); print( toQualifiedName(t) ); print(" DROP COLUMN "); print(createPhysicalName(colNameMap,c)); endStatement(DDLStatement.StatementType.DROP, c); }

public void dropColumn(SQLColumn c) { Map colNameMap = new HashMap(); print("\n ALTER TABLE "); print( toQualifiedName(t) ); print(" DROP COLUMN "); print(createPhysicalName(colNameMap,c)); endStatement(DDLStatement.StatementType.DROP, c); }

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public void dropColumn(SQLColumn c, SQLTable t) throws ArchitectDiffException { Map colNameMap = new HashMap(); print("\n ALTER TABLE "); print( toQualifiedName(t) ); print(" DROP COLUMN "); print(createPhysicalName(colNameMap,c)); endStatement(DDLStatement.StatementType.DROP, c); }

public void dropColumn(SQLColumn c, SQLTable t) throws ArchitectDiffException { Map colNameMap = new HashMap(); print("\n ALTER TABLE "); print(toQualifiedName(c.getParentTable())); print(" DROP COLUMN "); print(createPhysicalName(colNameMap,c)); endStatement(DDLStatement.StatementType.DROP, c); }

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public void dropPrimaryKey(SQLTable t, String primaryKeyName) { print("ALTER TABLE " + toQualifiedName(t.getCatalogName(),t.getSchemaName(),t.getName()) + " DROP PRIMARY KEY " + primaryKeyName); endStatement(DDLStatement.StatementType.DROP,t); }

public void dropPrimaryKey(SQLTable t) { print("ALTER TABLE " + toQualifiedName(t.getCatalogName(),t.getSchemaName(),t.getName()) + " DROP PRIMARY KEY " + primaryKeyName); endStatement(DDLStatement.StatementType.DROP,t); }

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public void dropPrimaryKey(SQLTable t, String primaryKeyName) { print("ALTER TABLE " + toQualifiedName(t.getCatalogName(),t.getSchemaName(),t.getName()) + " DROP PRIMARY KEY " + primaryKeyName); endStatement(DDLStatement.StatementType.DROP,t); }

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public void dropTable(SQLTable t) { print(makeDropTableSQL(t.getCatalogName(), t.getSchemaName(), t.getName())); endStatement(DDLStatement.StatementType.DROP, t); }

public void dropTable(SQLTable t) { print(makeDropTableSQL(t.getName())); endStatement(DDLStatement.StatementType.DROP, t); }

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public List generateDDLStatements(SQLDatabase source) throws SQLException, ArchitectException { warnings = new ArrayList(); ddlStatements = new ArrayList(); ddl = new StringBuffer(500); topLevelNames = new HashMap(); // for tracking dup table/relationship names try { if (allowConnection) { con = source.getC...

public List<DDLStatement> generateDDLStatements(SQLDatabase source) throws SQLException, ArchitectException { warnings = new ArrayList(); ddlStatements = new ArrayList(); ddl = new StringBuffer(500); topLevelNames = new HashMap(); // for tracking dup table/relationship names try { if (allowConnection) { con...

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public List generateDDLStatements(SQLDatabase source) throws SQLException, ArchitectException { warnings = new ArrayList(); ddlStatements = new ArrayList(); ddl = new StringBuffer(500); topLevelNames = new HashMap(); // for tracking dup table/relationship names try { if (allowConnection) { con = source.getC...

public List generateDDLStatements(SQLDatabase source) throws SQLException, ArchitectException { warnings = new ArrayList(); ddlStatements = new ArrayList<DDLStatement>(); ddl = new StringBuffer(500); topLevelNames = new HashMap(); // for tracking dup table/relationship names try { if (allowConnection) { con...

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public String makeDropForeignKeySQL(String fkCatalog, String fkSchema, String fkTable, String fkName) { return "ALTER TABLE " +toQualifiedName(fkCatalog, fkSchema, fkTable) +" DROP FOREIGN KEY " +fkName; }

public String makeDropForeignKeySQL(String fkTable, String fkName) { return "ALTER TABLE " +toQualifiedName(fkCatalog, fkSchema, fkTable) +" DROP FOREIGN KEY " +fkName; }

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public String makeDropForeignKeySQL(String fkCatalog, String fkSchema, String fkTable, String fkName) { return "ALTER TABLE " +toQualifiedName(fkCatalog, fkSchema, fkTable) +" DROP FOREIGN KEY " +fkName; }

public String makeDropForeignKeySQL(String fkCatalog, String fkSchema, String fkTable, String fkName) { return "ALTER TABLE " +toQualifiedName(fkTable) +" DROP FOREIGN KEY " +fkName; }

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public String makeDropTableSQL(String catalog, String schema, String table) { return "DROP TABLE "+toQualifiedName(catalog, schema, table); }

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public void modifyColumn(SQLColumn c) throws ArchitectDiffException { Map colNameMap = new HashMap(); SQLTable t = c.getParentTable(); print("\n ALTER TABLE "); print( toQualifiedName(t) ); print(" ALTER COLUMN "); print(columnDefinition(c,colNameMap)); endStatement(DDLStatement.StatementType.MODIFY, c); }

public void modifyColumn(SQLColumn c) { Map colNameMap = new HashMap(); SQLTable t = c.getParentTable(); print("\n ALTER TABLE "); print( toQualifiedName(t) ); print(" ALTER COLUMN "); print(columnDefinition(c,colNameMap)); endStatement(DDLStatement.StatementType.MODIFY, c); }

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public String toQualifiedName(SQLTable t) { String catalog = getTargetCatalog(); if ( catalog == null ) catalog = t.getCatalogName(); String schema = getTargetSchema(); if ( schema == null ) schema = t.getSchemaName(); return DDLUtils.toQualifiedName(catalog,schema,t.getPhysicalName()); }

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protected void writeExportedRelationships(SQLTable t) throws ArchitectException { Iterator it = t.getExportedKeys().iterator(); while (it.hasNext()) { SQLRelationship rel = (SQLRelationship) it.next(); // geneate a physical name for this relationship createPhysicalName(topLevelNames,rel); // println(""); ...

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public void delete() { Implementation odmg = ODMG.getODMGImplementation(); Database db = ODMG.getODMGDatabase(); ODMGXAWrapper txw = new ODMGXAWrapper(); db.deletePersistent( this ); if ( imageFile != null && !imageFile.delete() ) { log.error( "File " + imageFile.getAbsolutePath() + " could not be delet...

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public void delete() { Implementation odmg = ODMG.getODMGImplementation(); Database db = ODMG.getODMGDatabase(); ODMGXAWrapper txw = new ODMGXAWrapper(); db.deletePersistent( this ); if ( imageFile != null && !imageFile.delete() ) { log.error( "File " + imageFile.getAbsolutePath() + " could not be delet...

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public java.util.Date getCheckTime() { ODMGXAWrapper txw = new ODMGXAWrapper(); txw.lock( this, Transaction.READ ); txw.commit(); return checkTime; }

public java.util.Date getCheckTime() { ODMGXAWrapper txw = new ODMGXAWrapper(); txw.lock( this, Transaction.READ ); txw.commit(); return checkTime != null ? (java.util.Date) checkTime.clone() : null; }

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public byte[] getHash() { if ( hash == null && imageFile != null ) { calcHash(); } return (byte[]) hash.clone(); }

public byte[] getHash() { if ( hash == null && imageFile != null ) { calcHash(); } return (hash != null) ? (byte[]) hash.clone() : null; }

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protected void readImageFile() throws IOException { // Find the JPEG image reader // TODO: THis shoud decode also other readers from fname Iterator readers = ImageIO.getImageReadersByFormatName("jpg"); ImageReader reader = (ImageReader)readers.next(); ImageInputStream iis = ImageIO.createImageInputStream( imageFile...

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public String getProperty(String name) { if (name == null) { return null; } return (String) this.context.getVariable(name); }

public String getProperty(String name) { if (name == null) { return null; } Object value = this.context.getVariable(name); if (value == null) { return null; } else { return value.toString(); } }

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protected Rectangle getPhotoBounds( int photoNum ) { if ( photoNum < photoCollection.getPhotoCount() ) { PhotoInfo photoCandidate = photoCollection.getPhoto( photoNum ); log.warn( "Checking bounds" ); // Check whether the click was inside the thumbnail or not int w...

protected Rectangle getPhotoBounds( int photoNum ) { if ( photoNum < photoCollection.getPhotoCount() ) { PhotoInfo photoCandidate = photoCollection.getPhoto( photoNum ); log.debug( "Checking bounds" ); // Check whether the click was inside the thumbnail or not int ...

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protected Rectangle getPhotoBounds( int photoNum ) { if ( photoNum < photoCollection.getPhotoCount() ) { PhotoInfo photoCandidate = photoCollection.getPhoto( photoNum ); log.warn( "Checking bounds" ); // Check whether the click was inside the thumbnail or not int w...

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public void doTag(XMLOutput output) throws Exception { invokeBody(output); }

public void doTag(XMLOutput output) throws Exception { ChooseTag tag = (ChooseTag) findAncestorWithClass( ChooseTag.class ); if ( tag == null ) { throw new JellyException( "This tag must be enclosed inside a <choose> tag" ); } if ( ! tag.isBlockEvaluated() ) { tag.setBlockEvaluated(true); invokeBody(output);...

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public static Vector calcCCTDT(Vector chromosomes){ Vector results = new Vector(); int numMarkers = Chromosome.getSize(); for (int i = 0; i < numMarkers; i++){ TDTResult thisResult = new TDTResult(Chromosome.getMarker(i)); for (int j = 0; j < chromosomes.size()-1; j++){ ...

public static Vector calcCCTDT(Vector chromosomes){ Vector results = new Vector(); int numMarkers = Chromosome.getFilteredSize(); for (int i = 0; i < numMarkers; i++){ TDTResult thisResult = new TDTResult(Chromosome.getMarker(i)); for (int j = 0; j < chromosomes.size()-1; ...

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