JoaoJunior/formatted-java-preprocessed-code-APR

public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ...

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public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ...

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public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ...

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public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ...

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public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ...

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public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ...

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public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ...

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void readMarkers(File inputFile, String[][] hminfo){ try { theData.prepareMarkerInput(inputFile, hminfo); if (theData.infoKnown){ analysisItem.setEnabled(true); gbrowseItem.setEnabled(true); spacingItem.setEnabled(true); }else{ ...

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public void doTag(XMLOutput output) throws Exception { TaskSource tag = (TaskSource) findAncestorWithClass( TaskSource.class ); if ( tag == null ) { throw new JellyException( "You should only use Ant DataType tags within an Ant Task" ); } Object task = tag.getT...

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public void doTag(XMLOutput output) throws Exception { TaskSource tag = (TaskSource) findAncestorWithClass( TaskSource.class ); if ( tag == null ) { throw new JellyException( "You should only use Ant DataType tags within an Ant Task" ); } Object task = tag.getT...

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public void doTag(XMLOutput output) throws Exception { TaskSource tag = (TaskSource) findAncestorWithClass( TaskSource.class ); if ( tag == null ) { throw new JellyException( "You should only use Ant DataType tags within an Ant Task" ); } Object task = tag.getT...

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public void doTag(XMLOutput output) throws Exception { TaskSource tag = (TaskSource) findAncestorWithClass( TaskSource.class ); if ( tag == null ) { throw new JellyException( "You should only use Ant DataType tags within an Ant Task" ); } Object task = tag.getT...

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public void doTag(XMLOutput output) throws Exception { TaskSource tag = (TaskSource) findAncestorWithClass( TaskSource.class ); if ( tag == null ) { throw new JellyException( "You should only use Ant DataType tags within an Ant Task" ); } Object task = tag.getT...

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public Object getDataType() { return dataType; }

public DataType getDataType() { return dataType; }

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public void setDataType(Object dataType) { this.dataType = dataType; setDynaBean( new ConvertingWrapDynaBean(dataType) ); }

public void setDataType(DataType dataType) { this.dataType = dataType; setDynaBean( new ConvertingWrapDynaBean(dataType) ); }

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public static Test suite() { TestSuite suite = new TestSuite("Test for regress"); //$JUnit-BEGIN$ suite.addTestSuite(TestSQLDatabase.class); suite.addTestSuite(ArchitectExceptionTest.class); suite.addTestSuite(SaveLoadTest.class); suite.addTestSuite(PLDotIniTest.class); suite.addTest(TestSQLColumn.suite()); su...

public static Test suite() { TestSuite suite = new TestSuite("Test for regress"); //$JUnit-BEGIN$ suite.addTestSuite(SQLObjectTest.class); suite.addTest(TestSQLDatabase.suite()); suite.addTest(TestSQLTable.suite()); suite.addTest(TestSQLColumn.suite()); suite.addTestSuite(TestSQLRelationship.class); suite.addTestS...

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public static Test suite() { TestSuite suite = new TestSuite("Test for regress"); //$JUnit-BEGIN$ suite.addTestSuite(TestSQLDatabase.class); suite.addTestSuite(ArchitectExceptionTest.class); suite.addTestSuite(SaveLoadTest.class); suite.addTestSuite(PLDotIniTest.class); suite.addTest(TestSQLColumn.suite()); su...

public static Test suite() { TestSuite suite = new TestSuite("Test for regress"); //$JUnit-BEGIN$ suite.addTestSuite(TestSQLDatabase.class); suite.addTestSuite(ArchitectExceptionTest.class); suite.addTestSuite(SaveLoadTest.class); suite.addTestSuite(PLDotIniTest.class); suite.addTestSuite(JDBCClassLoaderTest....

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public static Test suite() { TestSuite suite = new TestSuite("Test for regress"); //$JUnit-BEGIN$ suite.addTestSuite(TestSQLDatabase.class); suite.addTestSuite(ArchitectExceptionTest.class); suite.addTestSuite(SaveLoadTest.class); suite.addTestSuite(PLDotIniTest.class); suite.addTest(TestSQLColumn.suite()); su...

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private File getNewFname( java.util.Date date, String strExtension ) { SimpleDateFormat fmt = new SimpleDateFormat( "yyyy" ); String strYear = fmt.format( date ); fmt.applyPattern( "yyyyMM" ); String strMonth = fmt.format( date ); fmt.applyPattern( "yyyyMMdd" ); String strDate = fmt.format( date ); File yearDir = n...

private File getNewFname( java.util.Date date, String strExtension ) { System.err.println( "getNewFname " + date + " " + strExtension ); SimpleDateFormat fmt = new SimpleDateFormat( "yyyy" ); String strYear = fmt.format( date ); fmt.applyPattern( "yyyyMM" ); String strMonth = fmt.format( date ); fmt.applyPattern( "...

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private File getNewFname( java.util.Date date, String strExtension ) { SimpleDateFormat fmt = new SimpleDateFormat( "yyyy" ); String strYear = fmt.format( date ); fmt.applyPattern( "yyyyMM" ); String strMonth = fmt.format( date ); fmt.applyPattern( "yyyyMMdd" ); String strDate = fmt.format( date ); File yearDir = n...

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private File getNewFname( java.util.Date date, String strExtension ) { SimpleDateFormat fmt = new SimpleDateFormat( "yyyy" ); String strYear = fmt.format( date ); fmt.applyPattern( "yyyyMM" ); String strMonth = fmt.format( date ); fmt.applyPattern( "yyyyMMdd" ); String strDate = fmt.format( date ); File yearDir = n...

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static Vector do4Gamete(DPrimeTable dPrime){ Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first make a list of marker pairs with < 4 gametes, sorted by distance apart for (int x = 0; x < Chromosome.getSize()-1; x++){ for (int y = x+1; y < Chromosome.getSi...

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static Vector do4Gamete(DPrimeTable dPrime){ Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first make a list of marker pairs with < 4 gametes, sorted by distance apart for (int x = 0; x < Chromosome.getSize()-1; x++){ for (int y = x+1; y < Chromosome.getSi...

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static Vector do4Gamete(DPrimeTable dPrime){ Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first make a list of marker pairs with < 4 gametes, sorted by distance apart for (int x = 0; x < Chromosome.getSize()-1; x++){ for (int y = x+1; y < Chromosome.getSi...

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static Vector do4Gamete(DPrimeTable dPrime){ Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first make a list of marker pairs with < 4 gametes, sorted by distance apart for (int x = 0; x < Chromosome.getSize()-1; x++){ for (int y = x+1; y < Chromosome.getSi...

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static Vector doGabriel(DPrimeTable 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[Chromosome.getSi...

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static Vector doGabriel(DPrimeTable 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[Chromosome.getSi...

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static Vector doGabriel(DPrimeTable 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[Chromosome.getSi...

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public static PhotoFolder create( String name, PhotoFolder parent ) { ODMGXAWrapper txw = new ODMGXAWrapper(); PhotoFolder folder = new PhotoFolder(); folder.setName( name ); folder.setParentFolder( parent ); txw.lock( folder, Transaction.WRITE ); txw.commit(); return folder; }

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public void setName(String v) { ODMGXAWrapper txw = new ODMGXAWrapper(); txw.lock( this, Transaction.WRITE ); this.name = v; modified(); txw.commit(); }

public void setName(String v) { checkStringProperty( "Name", v, NAME_LENGTH ); ODMGXAWrapper txw = new ODMGXAWrapper(); txw.lock( this, Transaction.WRITE ); this.name = v; modified(); txw.commit(); }

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private double hwCalculate(int obsAA, int obsAB, int obsBB) throws PedFileException{ //Calculates exact two-sided hardy-weinberg p-value. Parameters //are number of genotypes, number of rare alleles observed and //number of heterozygotes observed. // // (c) 2003 Jan Wigginton, Goncal...

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public void addChild(Component component) { Object parent = getBean(); if ( parent instanceof JFrame && component instanceof JMenuBar ) { JFrame frame = (JFrame) parent; frame.setJMenuBar( (JMenuBar) component ); } else if ( parent instanceof RootPaneContainer ) { ...

public void addChild(Component component, Object constraints) { Object parent = getBean(); if ( parent instanceof JFrame && component instanceof JMenuBar ) { JFrame frame = (JFrame) parent; frame.setJMenuBar( (JMenuBar) component ); } else if ( parent instanceof Roo...

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public void addChild(Component component) { Object parent = getBean(); if ( parent instanceof JFrame && component instanceof JMenuBar ) { JFrame frame = (JFrame) parent; frame.setJMenuBar( (JMenuBar) component ); } else if ( parent instanceof RootPaneContainer ) { ...

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protected void processBean(String var, Object bean) throws Exception { if (var != null) { context.setVariable(var, bean); } else { Component component = getComponent(); if ( component != null ) { ComponentTag parentTag = (ComponentTag) findAncesto...

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protected void setBeanProperties(Object bean, Map attributes) throws Exception { for (Iterator iter = attributes.entrySet().iterator(); iter.hasNext(); ) { Map.Entry entry = (Map.Entry) iter.next(); String name = (String) entry.getKey(); Object value = entry.getValue(); ...

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protected abstract void init(Map<String, String> properties);

public void init(Element qualifyingCriteria) { properties = new Properties(qualifyingCriteria); init(properties); }

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public boolean canAccess(String acl){ String authorizedList = ACLStore.getInstance().getProperty(acl); if(authorizedList == null) return false; StringTokenizer tokenizer = new StringTokenizer(authorizedList, ","); while(tokenizer.hasMoreTokens()){ if(getUsername().e...

public boolean canAccess(String acl){ String authorizedList = ACLStore.getInstance().getProperty(acl); if(authorizedList == null) return true; StringTokenizer tokenizer = new StringTokenizer(authorizedList, ","); while(tokenizer.hasMoreTokens()){ if(getUsername().eq...

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public String computeDPrime(int a, int b, int c, int d, int e, double f){ int i,j,k,count,itmp; int low_i = 0; int high_i = 0; double[] nAA = new double[1]; double[] nBB = new double[1]; double[] nAB = new double[1]; double[] nBA = new double[1]; double[] pAA = new double[1]; double[] pBB = new double[1]; double[...

public PairwiseLinkage computeDPrime(int a, int b, int c, int d, int e, double f){ int i,j,k,count,itmp; int low_i = 0; int high_i = 0; double[] nAA = new double[1]; double[] nBB = new double[1]; double[] nAB = new double[1]; double[] nBA = new double[1]; double[] pAA = new double[1]; double[] pBB = new double[1]...

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public String computeDPrime(int a, int b, int c, int d, int e, double f){ int i,j,k,count,itmp; int low_i = 0; int high_i = 0; double[] nAA = new double[1]; double[] nBB = new double[1]; double[] nAB = new double[1]; double[] nBA = new double[1]; double[] pAA = new double[1]; double[] pBB = new double[1]; double[...

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public String computeDPrime(int a, int b, int c, int d, int e, double f){ int i,j,k,count,itmp; int low_i = 0; int high_i = 0; double[] nAA = new double[1]; double[] nBB = new double[1]; double[] nAB = new double[1]; double[] nBA = new double[1]; double[] pAA = new double[1]; double[] pBB = new double[1]; double[...

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String[][] generateDPrimeTable(final Vector chromosomes){ numCompleted = 0; //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset String [][] dPrimeTable = new String[((Chromosome) chromosomes.firstElement()).size()][((Chromosome) chromosomes.firstElement()).size()]; int dou...

PairwiseLinkage[][] generateDPrimeTable(final Vector chromosomes){ numCompleted = 0; //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset String [][] dPrimeTable = new String[((Chromosome) chromosomes.firstElement()).size()][((Chromosome) chromosomes.firstElement()).size()]...

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String[][] generateDPrimeTable(final Vector chromosomes){ numCompleted = 0; //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset String [][] dPrimeTable = new String[((Chromosome) chromosomes.firstElement()).size()][((Chromosome) chromosomes.firstElement()).size()]; int dou...

String[][] generateDPrimeTable(final Vector chromosomes){ numCompleted = 0; //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset PairwiseLinkage[][] dPrimeTable = new PairwiseLinkage[((Chromosome) chromosomes.firstElement()).size()][((Chromosome) chromosomes.firstElement())...

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String[][] generateDPrimeTable(final Vector chromosomes){ numCompleted = 0; //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset String [][] dPrimeTable = new String[((Chromosome) chromosomes.firstElement()).size()][((Chromosome) chromosomes.firstElement()).size()]; int dou...

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Vector guessBlocks(String[][] dPrime, int method){ Vector returnVec = new Vector(); switch(method){ case 0: returnVec = new FindBlocks(dPrime).doSFS(); break; case 1: returnVec = new FindBlocks(dPrime).doMJD(); break; } return returnVec; }

Vector guessBlocks(PairwiseLinkage[][] dPrime, int method){ Vector returnVec = new Vector(); switch(method){ case 0: returnVec = new FindBlocks(dPrime).doSFS(); break; case 1: returnVec = new FindBlocks(dPrime).doMJD(); break; } return returnVec; }

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Vector guessBlocks(String[][] dPrime, int method){ Vector returnVec = new Vector(); switch(method){ case 0: returnVec = new FindBlocks(dPrime).doSFS(); break; case 1: returnVec = new FindBlocks(dPrime).doMJD(); break; } return returnVec; }

Vector guessBlocks(String[][] dPrime, int method){ Vector returnVec = new Vector(); switch(method){ case 0: returnVec = new FindBlocks(dPrime).doSFS(); break; case 1: returnVec = new FindBlocks(dPrime).do4Gamete(); break; case 2: returnVec = new FindBlocks(dPrime).doMJD(); break; } return returnVec; }

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int prepareMarkerInput(File infile) throws IOException{ //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 String currentLine; Vector markers = new Vector(); //read the file: BufferedRead...

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public TaggerController(HaploData hd, Vector included, Vector excluded, Vector sitesToCapture, int aggressionLevel) { theData = hd; taggerSNPs = new Vector(); snpHash = new Hashtable(); for(int i=0;i<sitesToCapture.size();i++) { SNP tempSNP = (SNP) s...

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public TaggerController(HaploData hd, Vector included, Vector excluded, Vector sitesToCapture, int aggressionLevel) { theData = hd; taggerSNPs = new Vector(); snpHash = new Hashtable(); for(int i=0;i<sitesToCapture.size();i++) { SNP tempSNP = (SNP) s...

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public Vector findTags() { tags = new Vector(); untagged = new Vector(); taggedSoFar = 0; //potentialTagsHash stores the PotentialTag objects keyed on the corresponding sequences Hashtable potentialTagByVarSeq = new Hashtable(); PotentialTagComparator ptcomp = new Potential...

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public Vector findTags() { tags = new Vector(); untagged = new Vector(); taggedSoFar = 0; //potentialTagsHash stores the PotentialTag objects keyed on the corresponding sequences Hashtable potentialTagByVarSeq = new Hashtable(); PotentialTagComparator ptcomp = new Potential...

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protected void calculateChiSquares() { chiSquares = new Vector(); pValues = new Vector(); if (Options.getAssocTest() == ASSOC_TRIO) { Iterator faitr = filteredAlleles.iterator(); while(faitr.hasNext()) { if(Options.getTdtType() == TDT_STD) { ...

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protected void calculateChiSquares() { chiSquares = new Vector(); pValues = new Vector(); if (Options.getAssocTest() == ASSOC_TRIO) { Iterator faitr = filteredAlleles.iterator(); while(faitr.hasNext()) { if(Options.getTdtType() == TDT_STD) { ...

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public void parseLinkage(Vector pedigrees) throws PedFileException { int colNum = -1; boolean withOptionalColumn = false; int numMarkers = 0; boolean genoError = false; int numLines = pedigrees.size(); if (numLines == 0){ throw new PedFileException("Data format e...

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public void parseLinkage(Vector pedigrees) throws PedFileException { int colNum = -1; boolean withOptionalColumn = false; int numMarkers = 0; boolean genoError = false; int numLines = pedigrees.size(); if (numLines == 0){ throw new PedFileException("Data format e...

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public void parseLinkage(Vector pedigrees) throws PedFileException { int colNum = -1; boolean withOptionalColumn = false; int numMarkers = 0; boolean genoError = false; int numLines = pedigrees.size(); if (numLines == 0){ throw new PedFileException("Data format e...

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public void parseLinkage(Vector pedigrees) throws PedFileException { int colNum = -1; boolean withOptionalColumn = false; int numMarkers = 0; boolean genoError = false; int numLines = pedigrees.size(); if (numLines == 0){ throw new PedFileException("Data format e...

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public Expression createExpression(String text) throws JellyException {/* org.apache.commons.jexl.Expression expr = org.apache.commons.jexl.ExpressionFactory.createExpression(text); if ( isSupportAntVariables() ) { expr.addPostResolver(new FlatResolve...

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public void run() { int ch; try { while ( (ch = is.read()) >= 0) { output.append(String.valueOf((char) ch)); } } catch (IOException ex) { ex.printStackTrace(); } }

public void run() { int ch; try { while ( (ch = is.read()) >= 0) { msg.append(String.valueOf((char) ch)); if ( ch == '\n' ) { output.append(msg.toString()); output.setCaretPosition(output.getText().length()); msg.delete(0,msg.length()); } } if ( msg.length() > 0 ) { output.append(msg.toString()); output.se...

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public EngineExecPanel(String header, Process pr) { super(new BorderLayout()); proc = pr; abortButton = new JButton("Abort"); abortButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { proc.destroy(); } }); JPanel p = new JPanel(new FlowLayout(FlowLayout.CENTER))...

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public EngineExecPanel(String header, Process pr) { super(new BorderLayout()); proc = pr; abortButton = new JButton("Abort"); abortButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { proc.destroy(); } }); JPanel p = new JPanel(new FlowLayout(FlowLayout.CENTER))...

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public EngineExecPanel(String header, Process pr) { super(new BorderLayout()); proc = pr; abortButton = new JButton("Abort"); abortButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { proc.destroy(); } }); JPanel p = new JPanel(new FlowLayout(FlowLayout.CENTER))...

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public void actionPerformed(ActionEvent e) { proc.destroy(); }

public void actionPerformed(ActionEvent e) { proc.destroy(); if ( output != null && output.isEnabled() ) { output.append("Aborted ..."); output.setEnabled(false); }

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public void waitForProcessCompletion() { try { iss.join(); ess.join(); } catch (InterruptedException ex) { System.out.println("Interrupted while waiting for engine"); } abortButton.setEnabled(false); output.append("Execution halted"); }

public void waitForProcessCompletion() { try { iss.join(); ess.join(); } catch (InterruptedException ex) { System.out.println("Interrupted while waiting for engine"); } output.append("Execution halted"); }

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public CreateTableAction() { super("Create Table", ASUtils.createIcon("NewTable", "Create Table", ArchitectFrame.getMainInstance().sprefs.getInt(SwingUserSettings.ICON_SIZE, 24))); }

public CreateTableAction() { super("New Table", ASUtils.createIcon("NewTable", "Create Table", ArchitectFrame.getMainInstance().sprefs.getInt(SwingUserSettings.ICON_SIZE, 24))); }

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public CreateTableAction() { super("Create Table", ASUtils.createIcon("NewTable", "Create Table", ArchitectFrame.getMainInstance().sprefs.getInt(SwingUserSettings.ICON_SIZE, 24))); }

public CreateTableAction() { super("New Table", ASUtils.createIcon("NewTable", "New Table", ArchitectFrame.getMainInstance().sprefs.getInt(SwingUserSettings.ICON_SIZE, 24))); }

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public static void main(String[] args) { //set defaults Options.setMissingThreshold(0.5); Options.setSpacingThreshold(0.0); Options.setAssocTest(ASSOC_NONE); Options.setHaplotypeDisplayThreshold(1); Options.setMaxDistance(500); Options.setLDColorScheme(STD_SCHEME); ...

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public void finished() { if(uc != null) { if(uc.isNewVersionAvailable()) { //theres an update available so lets pop some crap up final JLayeredPane jlp = window.getLayeredPane(); fi...

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private void connectionClosed(){ try { this.unregisterInternal(); } catch (Exception e) { logger.severe("Error unregistering for monitoring. error=" + e.getMessage()); } /* close the connection */ try { connection.close(); ...

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private void connectionOpen(){ try { /* start monitoring */ registerInternal(); logger.info("Registered for alert: " + alertName + ", application: " + sourceConfig.getApplicationConfig().getName()); } catch (Exception e) { ...

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public void paintComponent(Graphics graphics) { if (filteredHaplos == null){ super.paintComponent(graphics); return; } Graphics2D g = (Graphics2D) graphics; g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); ...

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public void paintComponent(Graphics graphics) { if (filteredHaplos == null){ super.paintComponent(graphics); return; } Graphics2D g = (Graphics2D) graphics; g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); ...

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public static ImageInstance create ( VolumeBase vol, File imgFile ) { ODMGXAWrapper txw = new ODMGXAWrapper(); ImageInstance i = new ImageInstance(); i.volume = vol; i.volumeId = vol.getName(); i.imageFile = imgFile; i.fileSize = imgFile.length(); i.mtime = imgFile.lastModified(); i.fnam...

public static ImageInstance create ( VolumeBase vol, File imgFile ) { log.debug( "Creating instance " + imgFile.getAbsolutePath() ); ODMGXAWrapper txw = new ODMGXAWrapper(); ImageInstance i = new ImageInstance(); i.volume = vol; i.volumeId = vol.getName(); i.imageFile = imgFile; i.fileSize = imgFile.l...

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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 = null; try { iis = Image...

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private void processFile(String fileName,boolean fileType,String infoFileName){ try { int outputType; long maxDistance; HaploData textData; File OutputFile; File inputFile; inputFile = new File(fileName); if(!inputFile.exists()){ ...

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

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

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

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void export(int tabNum, int format, int start, int stop){ fc.setSelectedFile(new File("")); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION){ File outfile = fc.getSelectedFile(); if (format == PNG_MODE || format == COMPRESSED_PNG_MODE){ BufferedImage ima...

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public void stateChanged(ChangeEvent e) { int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ exportMenuItems[0].setEnabled(true); exportMenuItems[1].setEnabled(true); }else if (tabNum == VIEW_TDT_NUM || tabNum...

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void prepareHapsInput(File infile) throws IOException, HaploViewException{ //this method is called to suck in data from a file (its only argument) //of genotypes and sets up the Chromosome objects. String currentLine; Vector chroms = new Vector(); byte[] genos = new byte[0]; ...

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public Dimension getPreferredSize() { int count = dPrimeTable.length; int high = V_BORDER+2 + count*BOX_SIZE/2; if (markersLoaded){ high += TICK_BOTTOM + widestMarkerName + TEXT_NUMBER_GAP; } return new Dimension(H_BORDER+2 + BOX_SIZE*(count-1), high); }

public Dimension getPreferredSize() { int count = dPrimeTable.length; int high = 2*V_BORDER + count*BOX_SIZE/2; if (markersLoaded){ high += TICK_BOTTOM + widestMarkerName + TEXT_NUMBER_GAP; } return new Dimension(H_BORDER+2 + BOX_SIZE*(count-1), high); }

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public Dimension getPreferredSize() { int count = dPrimeTable.length; int high = V_BORDER+2 + count*BOX_SIZE/2; if (markersLoaded){ high += TICK_BOTTOM + widestMarkerName + TEXT_NUMBER_GAP; } return new Dimension(H_BORDER+2 + BOX_SIZE*(count-1), high); }

public Dimension getPreferredSize() { int count = dPrimeTable.length; int high = V_BORDER+2 + count*BOX_SIZE/2; if (markersLoaded){ high += TICK_BOTTOM + widestMarkerName + TEXT_NUMBER_GAP; } return new Dimension(2*H_BORDER + BOX_SIZE*(count-1), high); }

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public void paintComponent(Graphics gComponent){ Dimension size = getSize(); Dimension pref = getPreferredSize(); if (!(alreadyPainted)){ buffIm = new BufferedImage(pref.width, pref.height, BufferedImage.TYPE_3BYTE_BGR); Graphics g = buffIm.getGraphics(); FontMe...

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public void populate() throws ArchitectException { return; }

public void populate() throws ArchitectException { logger.debug("SQLRelationship: populate is a no-op"); }

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public void doTag(XMLOutput output) throws Exception { if (test == null && xpath == null) { throw new MissingAttributeException( "test" ); } if (test != null) { if (! test.evaluateAsBoolean(context)) { fail( getBodyText(), "evaluating test: "+ test ); ...

public void doTag(XMLOutput output) throws Exception { if (test == null && xpath == null) { throw new MissingAttributeException( "test" ); } if (test != null) { if (! test.evaluateAsBoolean(context)) { fail( getBodyText(), "evaluating test: "+ test.getExpres...

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public void testNoCrossingLinesEasy() throws ArchitectException { PlayPen pp = layoutAction.getPlayPen(); SQLDatabase ppdb = pp.getDatabase(); SQLTable tables[] = new SQLTable[4]; TablePane tablePanes[] = new TablePane[tables.length]; for (int i = 0; i < tables.length; i++) { tables[i] = new SQLTable(ppdb, ...

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public void testNoCrossingLinesEasy() throws ArchitectException { PlayPen pp = layoutAction.getPlayPen(); SQLDatabase ppdb = pp.getDatabase(); SQLTable tables[] = new SQLTable[4]; TablePane tablePanes[] = new TablePane[tables.length]; for (int i = 0; i < tables.length; i++) { tables[i] = new SQLTable(ppdb, ...

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

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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 parsePhasedData(String[] info) throws IOException, PedFileException{ if (info[4].equals("")){ Chromosome.setDataChrom("none"); }else{ Chromosome.setDataChrom("chr" + info[4]); } Chromosome.setDataBuild("ncbi_b35"); Vector sampleData = new Vector()...

public void parsePhasedData(String[] info) throws IOException, PedFileException{ if (info[3].equals("")){ Chromosome.setDataChrom("none"); }else{ Chromosome.setDataChrom("chr" + info[4]); } Chromosome.setDataBuild("ncbi_b35"); Vector sampleData = new Vector()...

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public void parsePhasedData(String[] info) throws IOException, PedFileException{ if (info[4].equals("")){ Chromosome.setDataChrom("none"); }else{ Chromosome.setDataChrom("chr" + info[4]); } Chromosome.setDataBuild("ncbi_b35"); Vector sampleData = new Vector()...

public void parsePhasedData(String[] info) throws IOException, PedFileException{ if (info[4].equals("")){ Chromosome.setDataChrom("none"); }else{ Chromosome.setDataChrom("chr" + info[3]); } Chromosome.setDataBuild("ncbi_b35"); Vector sampleData = new Vector()...

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public static void main( String [] args ) { URL log4jPropertyURL = Photovault.class.getClassLoader().getResource( "log4j.properties"); PropertyConfigurator.configure( log4jPropertyURL ); Photovault app = new Photovault(); app.run(); }

public static void main( String [] args ) { URL log4jPropertyURL = Photovault.class.getClassLoader().getResource( "photovault_log4j.properties"); PropertyConfigurator.configure( log4jPropertyURL ); Photovault app = new Photovault(); app.run(); }

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public Destination getDestination() { return destination; }

public Destination getDestination() throws JellyException, JMSException { if (destination == null) { if (subject != null) { destination = findDestination(subject); } } return destination; }

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protected void appendIdentifier(StringBuffer sb, String text) { sb.append(text.replace(' ', '_')); }

protected void appendIdentifier(StringBuffer sb, String text) { sb.append(toIdentifier(text)); }

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public static void main(String[] args) { int exitValue = 0; String dir = System.getProperty("user.dir"); String sep = System.getProperty("file.separator"); String ver = System.getProperty("java.version"); System.out.println(ver); String jarfile = System.getProperty("java.cl...

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public static void main(String[] args) { int exitValue = 0; String dir = System.getProperty("user.dir"); String sep = System.getProperty("file.separator"); String ver = System.getProperty("java.version"); System.out.println(ver); String jarfile = System.getProperty("java.cl...

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public static void main(String[] args) { int exitValue = 0; String dir = System.getProperty("user.dir"); String sep = System.getProperty("file.separator"); String ver = System.getProperty("java.version"); System.out.println(ver); String jarfile = System.getProperty("java.cl...

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public void testMovement() { component.addPlayPenComponentListener( eventCounter); assertEquals("" + "We started out with the wrong number of events", 0,eventCounter.getEvents() ); //component.setMoving(true); //assertEquals("We did not generate a move start event",1,eventCounter.getStarts()); pp.startCompound...

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public void testMovement() { component.addPlayPenComponentListener( eventCounter); assertEquals("" + "We started out with the wrong number of events", 0,eventCounter.getEvents() ); //component.setMoving(true); //assertEquals("We did not generate a move start event",1,eventCounter.getStarts()); pp.startCompound...

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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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