JoaoJunior/formatted-java-preprocessed-code-APR

public Vector linkageToChrom(File infile, int type) throws IllegalArgumentException, HaploViewException, PedFileException, IOException{ pedFile = new PedFile(); if (type == PED_FILE){ pedFile.parseLinkage(infile); }else{ pedFile.parseHapMap(infile); ...

1,110,802

public Vector linkageToChrom(File infile, int type) throws IllegalArgumentException, HaploViewException, PedFileException, IOException{ pedFile = new PedFile(); if (type == PED_FILE){ pedFile.parseLinkage(infile); }else{ pedFile.parseHapMap(infile); ...

1,110,803

public Vector linkageToChrom(File infile, int type) throws IllegalArgumentException, HaploViewException, PedFileException, IOException{ pedFile = new PedFile(); if (type == PED_FILE){ pedFile.parseLinkage(infile); }else{ pedFile.parseHapMap(infile); ...

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public Vector linkageToChrom(File infile, int type) throws IllegalArgumentException, HaploViewException, PedFileException, IOException{ pedFile = new PedFile(); if (type == PED_FILE){ pedFile.parseLinkage(infile); }else{ pedFile.parseHapMap(infile); ...

1,110,805

void prepareMarkerInput(File infile, String[][] hapmapGoodies) throws IOException, HaploViewException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position. the maxdist ...

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void prepareMarkerInput(File infile, String[][] hapmapGoodies) throws IOException, HaploViewException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position. the maxdist ...

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void prepareMarkerInput(File infile, String[][] hapmapGoodies) throws IOException, HaploViewException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position. the maxdist ...

1,110,808

public void doTag(final XMLOutput output) throws Exception { if ( xmlOutput == null ) { // lets default to system.out xmlOutput = XMLOutput.createXMLOutput( System.out ); } // lets create a child context final JellyContext newContext = new JellyContext(context); ...

public void doTag(final XMLOutput output) throws Exception { if ( xmlOutput == null ) { // lets default to system.out xmlOutput = XMLOutput.createXMLOutput( System.out ); } // lets create a child context final JellyContext newContext = context.newJellyContext(); ...

1,110,813

public void doTag(final XMLOutput output) throws Exception { if ( xmlOutput == null ) { // lets default to system.out xmlOutput = XMLOutput.createXMLOutput( System.out ); } // lets create a child context final JellyContext newContext = new JellyContext(context); ...

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public void run() { try { getBody().run(newContext, xmlOutput); xmlOutput.close(); } catch (Exception e) { e.printStackTrace(); } }

public void run() { try { getBody().run(newContext, xmlOutput); if (closeOutput) { xmlOutput.close(); } else { xmlOutput.flush(); } } catch (Exception e) { e.printStackTrace(); ...

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public void upgradeDatabase() { fireStatusChangeEvent( new SchemaUpdateEvent( PHASE_ALTERING_SCHEMA, 0 ) ); int oldVersion = db.getSchemaVersion(); // Find needed information fr DdlUtils ConnectionRepository cr = MetadataManager.getInstance().connectionRepository(); ...

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Haplotype[][] generateHaplotypes(Vector blocks, int hapthresh, boolean crossover) throws HaploViewException{ //TODO: output indiv hap estimates Haplotype[][] results = new Haplotype[blocks.size()][]; //String raw = new String(); //String currentLine; this.totalBlocks = blocks.size...

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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!"); } ...

public void doTag(XMLOutput output) throws MissingAttributeException, Exception { if (test != null) { try { while (test.evaluateAsBoolean(getContext())) { if (log.isDebugEnabled()) { log.debug("evaluated to true! gonna keep on chuggin!"); } invokeBody(output); } } catch (BreakException e) { ...

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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!"); } ...

public void doTag(XMLOutput output) throws MissingAttributeException, Exception { if (test != null) { while (test.evaluateAsBoolean(getContext())) { if (log.isDebugEnabled()) { log.debug("loop terminated by break: " + e, e); } inv...

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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!"); } ...

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public Relationship(PlayPen pp, SQLRelationship model) throws ArchitectException { this (pp, pp.findTablePane(model.getPkTable()), pp.findTablePane(model.getFkTable())); }

public Relationship(PlayPen pp, SQLRelationship model) throws ArchitectException { this.pp = pp; this.model = model; setPkTable(pp.findTablePane(model.getPkTable())); setFkTable(pp.findTablePane(model.getFkTable())); setup(); }

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public void stateChanged(ChangeEvent e) { viewMenuItems[tabs.getSelectedIndex()].setSelected(true); if (checkPanel != null && checkPanel.changed){ window.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); JTable table = checkPanel.getTable(); ...

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public void doEM(int[] theBlock) throws HaploViewException{ //break up large blocks if needed int[] block_size; if (theBlock.length < 9){ block_size = new int[1]; block_size[0] = theBlock.length; } else { //some base-8 arithmetic int ones = the...

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public void doEM(int[] theBlock) throws HaploViewException{ //break up large blocks if needed int[] block_size; if (theBlock.length < 9){ block_size = new int[1]; block_size[0] = theBlock.length; } else { //some base-8 arithmetic int ones = the...

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public void doEM(int[] theBlock) throws HaploViewException{ //break up large blocks if needed int[] block_size; if (theBlock.length < 9){ block_size = new int[1]; block_size[0] = theBlock.length; } else { //some base-8 arithmetic int ones = the...

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boolean kid_consistent(int chap1, int chap2, int num_blocks, int[] block_size, int[][] hlist, int[] num_hlist, int this_trio, int num_loci) { int i, val; boolean retval; int[] temp1 = decode_haplo_str(chap1,num_blocks,block_size,hlist,num_hlist); int[] temp2 = decode_haplo_str(chap2,n...

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boolean kid_consistent(int chap1, int chap2, int num_blocks, int[] block_size, int[][] hlist, int[] num_hlist, int this_trio, int num_loci) { int i, val; boolean retval; int[] temp1 = decode_haplo_str(chap1,num_blocks,block_size,hlist,num_hlist); int[] temp2 = decode_haplo_str(chap2,n...

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boolean kid_consistent(int chap1, int chap2, int num_blocks, int[] block_size, int[][] hlist, int[] num_hlist, int this_trio, int num_loci) { int i, val; boolean retval; int[] temp1 = decode_haplo_str(chap1,num_blocks,block_size,hlist,num_hlist); int[] temp2 = decode_haplo_str(chap2,n...

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public void runFileTests(HaploData theData, Vector inputSNPResults) throws HaploViewException { Vector res = new Vector(); if(tests == null || theData == null) { return; } Vector blocks = new Vector(); Vector names = new Vector(); for(int i=0;i<tests.size();i++) ...

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public void runFileTests(HaploData theData, Vector inputSNPResults) throws HaploViewException { Vector res = new Vector(); if(tests == null || theData == null) { return; } Vector blocks = new Vector(); Vector names = new Vector(); for(int i=0;i<tests.size();i++) ...

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public void doTag(XMLOutput output) throws Exception { }

public void doTag(XMLOutput output) { }

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public void refreshTable(){ this.removeAll(); Vector tableData = new Vector(); int numRes = Chromosome.getFilteredSize(); for (int i = 0; i < numRes; i++){ Vector tempVect = new Vector(); TDTResult currentResult = (TDTResult)result.get(Chromosome.realIndex[i]); ...

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public void setJellyContext(JellyContext context) throws EvalError { this.context = context; // now pass in all the variables for ( Iterator iter = context.getVariableNames(); iter.hasNext(); ) { String name = (String) iter.next(); Object value = context.getVariabl...

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public void setJellyContext(JellyContext context) throws EvalError { this.context = context; // now pass in all the variables for ( Iterator iter = context.getVariableNames(); iter.hasNext(); ) { String name = (String) iter.next(); Object value = context.getVariabl...

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private void prepareUserForm(ActionForm form, User user){ UserForm userForm = (UserForm)form; userForm.setUsername(user.getUsername()); userForm.setPassword(UserForm.FORM_PASSWORD); userForm.setConfirmPassword(UserForm.FORM_PASSWORD); //TODO Need to handle multiple role scenario ...

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void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files re...

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public AntTagLibrary() { this.project = new Project(); BuildLogger logger = new NoBannerLogger(); logger.setMessageOutputLevel( org.apache.tools.ant.Project.MSG_INFO ); logger.setOutputPrintStream( System.out ); logger.setErrorPrintStream( System.err); project.addBuildListe...

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protected Tag createTag() throws Exception { if ( tagFactory != null) { return tagFactory.createTag(); } return null; }

protected Tag createTag() throws Exception { if ( tagFactory != null) { return tagFactory.createTag(localName, getSaxAttributes()); } return null; }

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public void setPrimaryKeySeq(Integer argPrimaryKeySeq) { // do nothing if there's no change if ( (primaryKeySeq == null && argPrimaryKeySeq == null) || (primaryKeySeq != null && primaryKeySeq.equals(argPrimaryKeySeq)) ) { return; } try { startCompoundEdit("Starting Pri...

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public void setPrimaryKeySeq(Integer argPrimaryKeySeq) { // do nothing if there's no change if ( (primaryKeySeq == null && argPrimaryKeySeq == null) || (primaryKeySeq != null && primaryKeySeq.equals(argPrimaryKeySeq)) ) { return; } try { startCompoundEdit("Starting Pri...

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public void setPrimaryKeySeq(Integer argPrimaryKeySeq) { // do nothing if there's no change if ( (primaryKeySeq == null && argPrimaryKeySeq == null) || (primaryKeySeq != null && primaryKeySeq.equals(argPrimaryKeySeq)) ) { return; } try { startCompoundEdit("Starting Pri...

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public FontRenderContext getFontRenderContext() { Graphics2D g2 = (Graphics2D) getGraphics(); g2.scale(zoom, zoom); FontRenderContext frc = g2.getFontRenderContext(); if (logger.isDebugEnabled()) logger.debug("Returning frc="+frc); return frc; }

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static Vector doSFS(PairwiseLinkage[][] dPrime){ int numStrong = 0; int numRec = 0; int numInGroup = 0; Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first set up a filter of markers which fail the MAF threshhold boolean[] skipMarker = new boolean[dPrime.lengt...

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static Vector doSFS(PairwiseLinkage[][] dPrime){ int numStrong = 0; int numRec = 0; int numInGroup = 0; Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first set up a filter of markers which fail the MAF threshhold boolean[] skipMarker = new boolean[dPrime.lengt...

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public TagScript createTagScript(String name, Attributes attributes) throws Exception { Project project = getProject(); // custom Ant tags if ( name.equals("fileScanner") ) { Tag tag = new FileScannerTag(new FileScanner(project)); return TagScript.newIn...

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public void doTag(XMLOutput output) throws Exception { Stylesheet stylesheet = getStylesheet(); if ( stylesheet == null ) { throw new JellyException( "<applyTemplates> tag must be inside a <stylesheet> tag" ); } Object context = getXPathConte...

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public void doTag(XMLOutput output) throws Exception { Stylesheet stylesheet = getStylesheet(); if ( stylesheet == null ) { throw new JellyException( "<applyTemplates> tag must be inside a <stylesheet> tag" ); } Object context = getXPathConte...

public void doTag(XMLOutput output) throws Exception { Stylesheet stylesheet = getStylesheet(); if ( stylesheet == null ) { throw new JellyException( "<applyTemplates> tag must be inside a <stylesheet> tag" ); } Stylesheet stylesheet = tag.ge...

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public void doTag(XMLOutput output) throws Exception { Stylesheet stylesheet = getStylesheet(); if ( stylesheet == null ) { throw new JellyException( "<applyTemplates> tag must be inside a <stylesheet> tag" ); } Object context = getXPathConte...

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public void doTag(XMLOutput output) throws Exception { Stylesheet stylesheet = getStylesheet(); if ( stylesheet == null ) { throw new JellyException( "<applyTemplates> tag must be inside a <stylesheet> tag" ); } Object context = getXPathConte...

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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...

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public ApplicationEvent(ApplicationConfig config){ super(config); time = System.currentTimeMillis(); }

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public ViewerTag(Class widgetClass) { super(widgetClass); }

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public List keysOfColumn(SQLColumn col) throws ArchitectException { LinkedList keys = new LinkedList(); Iterator it = getExportedKeys().iterator(); while (it.hasNext()) { SQLRelationship r = (SQLRelationship) it.next(); if (r.containsPkColumn(col)) { keys.add(r); } } it = getExportedKeys().iterator(); w...

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private void processFile(String fileName, int fileType, String infoFileName){ try { HaploData textData; File outputFile; File inputFile; AssociationTestSet customAssocSet; if(!quietMode && fileName != null){ System.out.println("Using data ...

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public HaplotypeAssociationResult(Haplotype[] locusHaplos, int freqCutoff, String n) { nf.setGroupingUsed(false); for (int i = 0; i < locusHaplos.length; i++){ alleles.add(locusHaplos[i]); } setFrequencyCutoff(((double)freqCutoff)/100); name = n; haps = locusHapl...

public HaplotypeAssociationResult(Haplotype[] locusHaplos, int freqCutoff, String n) { nf.setGroupingUsed(false); for (int i = 0; i < locusHaplos.length; i++){ alleles.add(locusHaplos[i]); } filterByFrequency(((double)freqCutoff)/100); name = n; haps = locusHaplo...

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public String getCountString(int i){ nf.setMinimumFractionDigits(1); nf.setMaximumFractionDigits(1); Haplotype h = (Haplotype) filteredAlleles.get(i); StringBuffer countSB = new StringBuffer(); if(Options.getAssocTest() == ASSOC_TRIO) { countSB.append(nf.format(h.getTra...

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public Context getContext() { return context; }

public JellyContext getContext() { return context; }

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private void argHandler(String[] args){ //TODO: -specify values from HaplotypeDisplayController (min hap percentage etc) //TODO: -want to be able to output haps file from pedfile /* boolean nogui = false; String batchMode = ""; String hapsFileName = ""; String pedFileNa...

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protected String getBodyText( Context context ) throws Exception { // XXX: could maybe optimise this later on by having a pool of buffers StringWriter writer = new StringWriter(); body.run( context, XMLOutput.createXMLOutput( writer ) ); return writer.toString(); }

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public void run(Context context, XMLOutput output) throws Exception { getBody().run(context, output); }

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public void clear() { getThreadScriptDataMap().clear(); variables.clear(); }

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public void clearScriptData() { threadLocalScriptData = new ThreadLocal(); }

public void clearScriptData() { threadLocalScriptData.clear(); }

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public Map getThreadScriptDataMap() { Map rv; Map data = (Map) threadLocalScriptData.get(); if (data == null) { rv = new HashMap(); threadLocalScriptData.set(rv); } else { rv = data; } return rv; }

public Map getThreadScriptDataMap() { Map rv; Thread t = Thread.currentThread(); Map data = (Map) threadLocalScriptData.get(t); if (data == null) { rv = new HashMap(); threadLocalScriptData.set(rv); } else { rv = data; } return rv; }

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public Map getThreadScriptDataMap() { Map rv; Map data = (Map) threadLocalScriptData.get(); if (data == null) { rv = new HashMap(); threadLocalScriptData.set(rv); } else { rv = data; } return rv; }

public Map getThreadScriptDataMap() { Map rv; Map data = (Map) threadLocalScriptData.get(); if (data == null) { rv = new HashMap(); threadLocalScriptData.put(t, rv); } else { rv = data; } return rv; }

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public void setNullable(int argNullable) { int oldNullable = this.nullable; logger.debug("Changing nullable "+oldNullable+" -> "+argNullable); if (this.nullable != argNullable) { this.nullable = argNullable; fireDbObjectChanged("nullable",oldNullable,argNullable); } }

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public void setPrimaryKeySeq(Integer argPrimaryKeySeq) { // do nothing if there's no change if ( (primaryKeySeq == null && argPrimaryKeySeq == null) || (primaryKeySeq != null && primaryKeySeq.equals(argPrimaryKeySeq)) ) { return; } try { startCompoundEdit("Starting Pri...

public void setPrimaryKeySeq(Integer argPrimaryKeySeq) { // do nothing if there's no change if ( (primaryKeySeq == null && argPrimaryKeySeq == null) || (primaryKeySeq != null && primaryKeySeq.equals(argPrimaryKeySeq)) ) { return; } Integer oldPrimaryKeySeq = primaryKeySeq; if (!i...

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public void setPrimaryKeySeq(Integer argPrimaryKeySeq) { // do nothing if there's no change if ( (primaryKeySeq == null && argPrimaryKeySeq == null) || (primaryKeySeq != null && primaryKeySeq.equals(argPrimaryKeySeq)) ) { return; } try { startCompoundEdit("Starting Pri...

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public void setType(int argType) { int oldType = type; if (type != argType) { setSourceDataTypeName(null); this.type = argType; fireDbObjectChanged("type",oldType,argType); } }

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public void mouseClicked(MouseEvent evt) { Point p = evt.getPoint(); unzoomPoint(p); PlayPenComponent c = contentPane.getComponentAt(p); if (c != null) p.translate(-c.getX(), -c.getY()); if ( c instanceof Relationship) { if (evt.getClickCount() == 2) { ArchitectFrame.getMainInstance().editRelationshi...

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private void addDependantsFromKeys(ResultSet rs) throws SQLException { Conflict prev = null; while (rs.next()) { Conflict c = new Conflict("FOREIGN KEY", rs.getString("FKTABLE_CAT"), rs.getString("FKTABLE_SCHEM"), ...

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public void findConflicting() throws SQLException, ArchitectException { doingFindConflicting = true; Connection con = null; try { conflicts = new ArrayList(); monitorableProgress = 0; if (logger.isDebugEnabled()) { logger.debug("About to find conflicting objects for DDL Script...

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public Tag getTagOfTagScript(TagScript script) { if( script == null ) return null; return (Tag) tagHolderMap.get(script); }

public Tag getTagOfTagScript(TagScript script) { if( script == null ) return null; Tag tag = (Tag) tagHolderMap.get(script); if( tag == null && getParent() != null) { return getParent().getTagOfTagScript(script); } else { return tag; } }

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public void run(Context context, XMLOutput output) throws Exception { tagLibrary = new DynamicTagLibrary( getUri() ); context.registerTagLibrary( getUri(), tagLibrary ); getBody().run(context, output); tagLibrary = null; }

public void run(JellyContext context, XMLOutput output) throws Exception { tagLibrary = new DynamicTagLibrary( getUri() ); context.registerTagLibrary( getUri(), tagLibrary ); getBody().run(context, output); tagLibrary = null; }

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public DynamicTagLibrary(String uri) { this.uri = uri; }

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public Vector calcTDT(Vector chromosomes) { int numChroms; Chromosome chromT, chromU,chromTemp; String ped,ind; Vector temp; numChroms = chromosomes.size(); temp = (Vector)chromosomes.clone(); chromosomes = temp; int numMarkers = Chromosome.getSize(); f...

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public Vector calcTDT(Vector chromosomes) { int numChroms; Chromosome chromT, chromU,chromTemp; String ped,ind; Vector temp; numChroms = chromosomes.size(); temp = (Vector)chromosomes.clone(); chromosomes = temp; int numMarkers = Chromosome.getSize(); f...

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public Vector calcTDT(Vector chromosomes) { int numChroms; Chromosome chromT, chromU,chromTemp; String ped,ind; Vector temp; numChroms = chromosomes.size(); temp = (Vector)chromosomes.clone(); chromosomes = temp; int numMarkers = Chromosome.getSize(); f...

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public Vector calcTDT(Vector chromosomes) { int numChroms; Chromosome chromT, chromU,chromTemp; String ped,ind; Vector temp; numChroms = chromosomes.size(); temp = (Vector)chromosomes.clone(); chromosomes = temp; int numMarkers = Chromosome.getSize(); f...

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public void doTag(XMLOutput output) throws Exception { Object obj = getObject(); if ( this.task != null ) { Method method = MethodUtils.getAccessibleMethod( this.task.getClass(), "addText", ...

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public void actionPerformed( ActionEvent evt ) { if ( evt.getActionCommand().equals( "save" ) ) { try { ctrl.save(); } catch ( Exception e ) { log.warn( "exception while saving" + e.getMessage() ); e.printStackTrace(); } } else if ( evt.getActionCommand().equals( "discard" ) ) { log.debug( "Disca...

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public String getPhotographer( ) { return photographerField.getText( ); }

public String getPhotographer( ) { String str = photographerField.getText( ); return str; }

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public Number getQuality() { return new Integer( qualityField.getSelectedIndex() ); }

public Number getQuality() { int q = qualityField.getSelectedIndex(); Integer retval = null; if ( q >= 0 ) { retval = new Integer( q ); } return retval; }

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public void insertUpdate( DocumentEvent ev ) { Document changedDoc = ev.getDocument(); String changedField = (String) changedDoc.getProperty( FIELD_NAME ); ctrl.viewChanged( this, changedField );// // Handle fuzzy time// if ( changedDoc == fuzzyDateDoc ) {// log.warn( "Fuzzy date entered" );// String fd...

public void insertUpdate( DocumentEvent ev ) { Document changedDoc = ev.getDocument(); String changedField = (String) changedDoc.getProperty( FIELD_NAME ); Object fieldValue = ctrl.getField( changedField ); if ( fieldValue != null || changedDoc.getLength() > 0 ) { ctrl.viewChanged( this, changedField ); }// // Ha...

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public void propertyChange( PropertyChangeEvent ev ) { if ( ev.getPropertyName().equals( "value" ) ) { Object src = ev.getSource(); if ( src.getClass() == JFormattedTextField.class ) { Object field = ((JFormattedTextField) src).getClientProperty( FIELD_NAME ); Object value = ((JFormattedTextField) src).ge...

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public void setQuality( Number quality ) { if ( quality != null ) { qualityField.setSelectedIndex( quality.intValue() ); } else { qualityField.setSelectedIndex( 0 ); } }

public void setQuality( Number quality ) { if ( quality != null ) { qualityField.setSelectedIndex( quality.intValue() ); } else { qualityField.setSelectedIndex( -1 ); } }

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public void addSQLObjectListener(SQLObjectListener l) { if (l == null) throw new NullPointerException("You can't add a null listener"); if (getSQLObjectListeners().contains(l)) { if (logger.isDebugEnabled()) { logger.debug("NOT Adding duplicate listener "+l+" to SQLObject "+this); } return; } getSQLObject...

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public void addSQLObjectListener(SQLObjectListener l) { if (l == null) throw new NullPointerException("You can't add a null listener"); if (getSQLObjectListeners().contains(l)) { if (logger.isDebugEnabled()) { logger.debug("NOT Adding duplicate listener "+l+" to SQLObject "+this); } return; } getSQLObject...

public void addSQLObjectListener(SQLObjectListener l) { if (l == null) throw new NullPointerException("You can't add a null listener"); if (getSQLObjectListeners().contains(l)) { if (logger.isDebugEnabled()) { logger.debug("NOT Adding duplicate listener "+l+" to SQLObject "+this); } return; } }

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protected void fireDbChildrenInserted(int[] newIndices, List newChildren) { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbChildrenInserted event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent (this, newIndic...

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protected void fireDbChildrenInserted(int[] newIndices, List newChildren) { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbChildrenInserted event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent (this, newIndic...

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protected void fireDbChildrenRemoved(int[] oldIndices, List oldChildren) { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbChildrenRemoved event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent (this, oldIndices...

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protected void fireDbObjectChanged(String propertyName, Object oldValue, Object newValue) { SQLObjectEvent e = new SQLObjectEvent( this, propertyName, oldValue, newValue, isSecondaryChangeMode()); boolean same = (oldValue == null ? oldValue == newValue : oldValue.equals(newValue)); if (same) { logg...

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protected void fireDbStructureChanged(String propertyName) { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbStructureChanged event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent( this, propertyName, isSec...

public void fireDbStructureChanged() { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbStructureChanged event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent( this, propertyName, isSecondaryChangeMode()); ...

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protected void fireDbStructureChanged(String propertyName) { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbStructureChanged event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent( this, propertyName, isSec...

protected void fireDbStructureChanged(String propertyName) { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbStructureChanged event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent( this, null, isSecondaryCh...

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protected void fireDbStructureChanged(String propertyName) { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbStructureChanged event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent( this, propertyName, isSec...

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public List getSQLObjectListeners() { if (sqlObjectListeners == null) { sqlObjectListeners = new LinkedList(); } return sqlObjectListeners; }

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public void removeSQLObjectListener(SQLObjectListener l) { getSQLObjectListeners().remove(l); }

public void removeSQLObjectListener(SQLObjectListener l) { synchronized(sqlObjectListeners) { sqlObjectListeners.remove(l); } }

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public void invokeBody(XMLOutput output) throws Exception { if ( isTrim() && ! hasTrimmed ) { trimBody(); } getBody().run(context, output); }

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

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public boolean containsMBean(String objectName) { for(Iterator it=mbeanList.iterator(); it.hasNext();){ MBeanConfig mbeanConfig = (MBeanConfig)it.next(); if(mbeanConfig.getObjectName().equals(objectName)){ return true; } } return false; }

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public BaseObject getFirstObject(String fieldname, XWikiContext context) { Collection objectscoll = getxWikiObjects().values(); if (objectscoll == null) return null; for (Iterator itobjs = objectscoll.iterator(); itobjs.hasNext();) { Vector objects = (Vector) itobjs.next()...

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public boolean equals(Object o) { if (this == o) return true; if (!(o instanceof DashboardConfig)) return false; final DashboardConfig dashboardConfig = (DashboardConfig) o; if (!dashboardId.equals(dashboardConfig.dashboardId)) return false; return true; }

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public static boolean isKnownDataType(Class clazz){ if(clazz.isPrimitive() || clazz.isAssignableFrom(Boolean.class) || clazz.isAssignableFrom(Character.class) || clazz.isAssignableFrom(Byte.class) || clazz.isAssignableFrom(Short.class) || clazz.isAssigna...

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public void run(JellyContext context, XMLOutput output) throws Exception { if ( ! context.isCacheTags() ) { clearTag(); } try { Tag tag = getTag(); if ( tag == null ) { return; } tag.setContext(context); if ( t...

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private void makeDialog(SQLTable st, int colIdx) throws ArchitectException { if (editDialog != null) { columnEditPanel.setModel(st); columnEditPanel.selectColumn(colIdx); editDialog.setTitle("Column Properties of "+st.getName()); editDialog.setVisible(true); //editDialog.requestFocus(); } else { ...

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

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