bugged stringlengths 6 599k | fixed stringlengths 10 599k | __index_level_0__ int64 0 1.13M |
|---|---|---|
public void linkageToChrom(boolean[] markerResults, PedFile pedFile){ Vector indList = pedFile.getOrder(); int numMarkers = 0; Vector usedParents = new Vector(); Individual currentInd; Family currentFamily; Vector chrom = new Vector(); for(int x=0; x < indList.size()... | public void linkageToChrom(boolean[] markerResults, PedFile pedFile){ Vector indList = pedFile.getOrder(); int numMarkers = 0; Vector usedParents = new Vector(); Individual currentInd; Family currentFamily; Vector chrom = new Vector(); for(int x=0; x < indList.size()... | 1,110,676 |
void prepareHapsInput(File infile) throws IOException{ //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]; String ped, indiv;... | void prepareHapsInput(File infile) throws IOException{ //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]; String ped, indiv;... | 1,110,677 |
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 Vecto... | int prepareMarkerInput(File infile, long maxdist) 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 marke... | 1,110,678 |
public CreateRelationshipAction(PlayPen pp) { super("Create Relationship"); this.pp = pp; pp.addSelectionListener(this); } | public CreateRelationshipAction() { super("Create Relationship"); this.pp = pp; pp.addSelectionListener(this); } | 1,110,680 |
public CreateRelationshipAction(PlayPen pp) { super("Create Relationship"); this.pp = pp; pp.addSelectionListener(this); } | public CreateRelationshipAction(PlayPen pp) { super("Create Relationship"); this.pp = pp; pp.addSelectionListener(this); } | 1,110,681 |
EM(){ //an old-school speedup courtesy of mjdaly two_n[0]=1; for (int i=1; i<31; i++){ two_n[i]=2*two_n[i-1]; } } | EM(Vector chromosomes, int numTrios){ //an old-school speedup courtesy of mjdaly two_n[0]=1; for (int i=1; i<31; i++){ two_n[i]=2*two_n[i-1]; } } | 1,110,683 |
public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | private void full_em_breakup( byte[][] input_haplos, int[] block_size, int numTrios, Vector affStatus) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//, best, h1, h2; int... | 1,110,685 |
public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | 1,110,686 |
public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | 1,110,687 |
public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | 1,110,688 |
public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | 1,110,689 |
public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | 1,110,690 |
public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | 1,110,691 |
public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | 1,110,692 |
public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | 1,110,693 |
public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | 1,110,694 |
public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | 1,110,695 |
public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | 1,110,696 |
public float getFStop() { return FStop; } | public double getFStop() { return FStop; } | 1,110,698 |
public float getFocalLength() { return focalLength; } | public double getFocalLength() { return focalLength; } | 1,110,699 |
public static PhotoInfo retrievePhotoInfo( String strPhotoId ) throws PhotoNotFoundException { initDB(); String sql = "SELECT * from photos where photo_id=\"" + strPhotoId +"\""; PhotoInfo photo = new PhotoInfo(); try { Statement stmt = conn.createStatement(); ResultSet rs = stmt.executeQuery( sql ); if... | public static PhotoInfo retrievePhotoInfo( int photoId ) throws PhotoNotFoundException { initDB(); String sql = "SELECT * from photos where photo_id=\"" + strPhotoId +"\""; PhotoInfo photo = new PhotoInfo(); try { Statement stmt = conn.createStatement(); ResultSet rs = stmt.executeQuery( sql ); if ( !rs... | 1,110,700 |
public static PhotoInfo retrievePhotoInfo( String strPhotoId ) throws PhotoNotFoundException { initDB(); String sql = "SELECT * from photos where photo_id=\"" + strPhotoId +"\""; PhotoInfo photo = new PhotoInfo(); try { Statement stmt = conn.createStatement(); ResultSet rs = stmt.executeQuery( sql ); if... | public static PhotoInfo retrievePhotoInfo( String strPhotoId ) throws PhotoNotFoundException { initDB(); String sql = "SELECT * from photos where photo_id=\"" + photoId +"\""; PhotoInfo photo = new PhotoInfo(); try { Statement stmt = conn.createStatement(); ResultSet rs = stmt.executeQuery( sql ); if ( ... | 1,110,701 |
public static PhotoInfo retrievePhotoInfo( String strPhotoId ) throws PhotoNotFoundException { initDB(); String sql = "SELECT * from photos where photo_id=\"" + strPhotoId +"\""; PhotoInfo photo = new PhotoInfo(); try { Statement stmt = conn.createStatement(); ResultSet rs = stmt.executeQuery( sql ); if... | public static PhotoInfo retrievePhotoInfo( String strPhotoId ) throws PhotoNotFoundException { initDB(); String sql = "SELECT * from photos where photo_id=\"" + strPhotoId +"\""; PhotoInfo photo = new PhotoInfo(); try { Statement stmt = conn.createStatement(); ResultSet rs = stmt.executeQuery( sql ); if... | 1,110,702 |
public void setFStop(float v) { this.FStop = v; } | public void setFStop(double v) { this.FStop = v; } | 1,110,703 |
public void setFocalLength(float v) { this.focalLength = v; } | public void setFocalLength(double v) { this.focalLength = v; } | 1,110,704 |
public void showPreferencesDialog() { // XXX Can't easily use ArchitectPanelBuilder since this // contains a JTabbedPane which is not an ArchitectPanel. final JDialog d = new JDialog(af, "User Preferences"); JPanel cp = new JPanel(new BorderLayout(12,12)); JTabbedPane tp = new JTabbedPane(); cp.add(tp, BorderL... | public void showPreferencesDialog() { // XXX Can't easily use ArchitectPanelBuilder since this // contains a JTabbedPane which is not an ArchitectPanel. final JDialog d = new JDialog(af, "User Preferences"); JPanel cp = new JPanel(new BorderLayout(12,12)); JTabbedPane tp = new JTabbedPane(); cp.add(tp, BorderL... | 1,110,706 |
void prepareMarkerInput(File infile, long md, 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... | void prepareMarkerInput(File infile, long md, 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... | 1,110,710 |
public CheckDataPanel(File file) throws IOException{ //okay, for now we're going to assume the ped file has no header Vector pedFileStrings = new Vector(); BufferedReader reader = new BufferedReader(new FileReader(file)); String line; while((line = reader.readLine())!=null){ ... | public CheckDataPanel(File file) throws IOException{ //okay, for now we're going to assume the ped file has no header Vector pedFileStrings = new Vector(); BufferedReader reader = new BufferedReader(new FileReader(file)); String line; while((line = reader.readLine())!=null){ ... | 1,110,711 |
public void dbObjectChanged(SQLObjectEvent e) { if (e.getSource() == table) { int[] changedIndices = e.getChangedIndices(); for (int i = 0; i < changedIndices.length; i++) { // XXX: should group contiguous regions into one event! logger.debug("Firing contentsChanged event for index "+i); fireContentsChan... | public void dbObjectChanged(SQLObjectEvent e) { if (e.getSource() == table.getColumnsFolder()) { int[] changedIndices = e.getChangedIndices(); for (int i = 0; i < changedIndices.length; i++) { // XXX: should group contiguous regions into one event! logger.debug("Firing contentsChanged event for index "+i); ... | 1,110,712 |
public Object getElementAt(int index) { try { return table.getChildren().get(index); } catch (ArchitectException ex) { throw new RuntimeException("Couldn't get child "+index, ex); } } | public Object getElementAt(int index) { try { return table.getColumnsFolder().getChild(index); } catch (ArchitectException ex) { throw new RuntimeException("Couldn't get child "+index, ex); } } | 1,110,713 |
public int getSize() { try { return table.getChildCount(); } catch (ArchitectException ex) { throw new RuntimeException("Couldn't get child count", ex); } } | public int getSize() { try { return table.getColumnsFolder().getChildCount(); } catch (ArchitectException ex) { throw new RuntimeException("Couldn't get child count", ex); } } | 1,110,714 |
public void dbChildrenRemoved(SQLObjectEvent e) { if (e.getSource() == this.model.getColumnsFolder()) { int ci[] = e.getChangedIndices(); logger.debug("Columns removed. Syncing select/highlight lists. Removed indices="+Arrays.asList(ci)); for (int i = 0; i < ci.length; i++) { columnSelection.remove(ci[i])... | public void dbChildrenRemoved(SQLObjectEvent e) { if (e.getSource() == this.model.getColumnsFolder()) { int ci[] = e.getChangedIndices(); logger.debug("Columns removed. Syncing select/highlight lists. Removed indices="+Arrays.asList(ci)); for (int i = 0; i < ci.length; i++) { columnSelection.remove(ci[i])... | 1,110,715 |
public void dbChildrenRemoved(SQLObjectEvent e) { if (e.getSource() == this.model.getColumnsFolder()) { int ci[] = e.getChangedIndices(); logger.debug("Columns removed. Syncing select/highlight lists. Removed indices="+Arrays.asList(ci)); for (int i = 0; i < ci.length; i++) { columnSelection.remove(ci[i])... | public void dbChildrenRemoved(SQLObjectEvent e) { if (e.getSource() == this.model.getColumnsFolder()) { int ci[] = e.getChangedIndices(); logger.debug("Columns removed. Syncing select/highlight lists. Removed indices="+Arrays.asList(ci)); for (int i = 0; i < ci.length; i++) { columnSelection.remove(ci[i])... | 1,110,716 |
public void doTag(XMLOutput output) throws Exception { if (getVar() == null) { throw new IllegalArgumentException("The var attribute cannot be null"); } Document document = null; if (html == null) { document = parseBody(output); } else { doc... | public void doTag(XMLOutput output) throws Exception { if (getVar() == null) { throw new IllegalArgumentException("The var attribute cannot be null"); } Document document = null; if (html == null) { String text = getText(); if (text != null) { document = parseText(t... | 1,110,717 |
protected Transferable createTransferable(JComponent c) { log.warn( "createTransferable" ); Collection selection = view.getSelection(); sourcePhotos = new PhotoInfo[selection.size()]; Iterator iter = selection.iterator(); int i = 0; while ( iter.hasNext() ) { sourcePhotos[i] = (PhotoInfo) iter.next(); i++; ... | protected Transferable createTransferable(JComponent c) { log.warn( "createTransferable" ); Collection selection = view.getSelection(); sourcePhotos = new PhotoInfo[selection.size()]; Iterator iter = selection.iterator(); int i = 0; while ( iter.hasNext() ) { sourcePhotos[i] = (PhotoInfo) iter.next(); i++; ... | 1,110,718 |
protected void exportDone(JComponent c, Transferable data, int action) { PhotoCollection coll = view.getCollection(); if (/*shouldRemove && */ (action == MOVE) && coll instanceof PhotoFolder ) { PhotoFolder folder = (PhotoFolder) coll; for ( int i = 0; i < sourcePhotos.length; i++ ) { folder.removeP... | protected void exportDone(JComponent c, Transferable data, int action) { PhotoCollection coll = view.getCollection(); if (/*shouldRemove && */ (action == MOVE) && coll instanceof PhotoFolder ) { PhotoFolder folder = (PhotoFolder) coll; for ( int i = 0; i < sourcePhotos.length; i++ ) { folder.removeP... | 1,110,719 |
void generateDPrimeTable(long maxdist){ //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset dPrimeTable = new PairwiseLinkage[((Chromosome) chromosomes.firstElement()).size()][((Chromosome) chromosomes.firstElement()).size()]; int doublehet; ... | void generateDPrimeTable(long maxdist){ //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset dPrimeTable = new PairwiseLinkage[Chromosome.size()][Chromosome.size()]; int doublehet; long negMaxdist = -1*maxdist; int[][] twoMarkerHapl... | 1,110,722 |
void generateDPrimeTable(long maxdist){ //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset dPrimeTable = new PairwiseLinkage[((Chromosome) chromosomes.firstElement()).size()][((Chromosome) chromosomes.firstElement()).size()]; int doublehet; ... | void generateDPrimeTable(long maxdist){ //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset dPrimeTable = new PairwiseLinkage[((Chromosome) chromosomes.firstElement()).size()][((Chromosome) chromosomes.firstElement()).size()]; int doublehet; ... | 1,110,723 |
void guessBlocks(int method){ Vector returnVec = new Vector(); switch(method){ case 0: returnVec = new FindBlocks(dPrimeTable, markerInfo).doSFS(); break; case 1: returnVec = new FindBlocks(dPrimeTable).do4Gamete(); break; case 2: returnVec = new FindBlocks(dPrimeTable... | void guessBlocks(int method){ Vector returnVec = new Vector(); switch(method){ case 0: returnVec = new FindBlocks(dPrimeTable).doSFS(); break; case 1: returnVec = new FindBlocks(dPrimeTable).do4Gamete(); break; case 2: returnVec = new FindBlocks(dPrimeTable).doMJD(); b... | 1,110,724 |
public void linkageToChrom(boolean[] markerResults, PedFile pedFile){ Vector indList = pedFile.getOrder(); int numMarkers = 0; Vector usedParents = new Vector(); Individual currentInd; Family currentFamily; Vector chrom = new Vector(); for(int x=0; x < indList.size()... | public void linkageToChrom(boolean[] markerResults, PedFile pedFile){ Vector indList = pedFile.getOrder(); int numMarkers = 0; Vector usedParents = new Vector(); Individual currentInd; Family currentFamily; Vector chrom = new Vector(); for(int x=0; x < indList.size()... | 1,110,725 |
public void linkageToChrom(boolean[] markerResults, PedFile pedFile){ Vector indList = pedFile.getOrder(); int numMarkers = 0; Vector usedParents = new Vector(); Individual currentInd; Family currentFamily; Vector chrom = new Vector(); for(int x=0; x < indList.size()... | public void linkageToChrom(boolean[] markerResults, PedFile pedFile){ Vector indList = pedFile.getOrder(); int numMarkers = 0; Vector usedParents = new Vector(); Individual currentInd; Family currentFamily; Vector chrom = new Vector(); for(int x=0; x < indList.size()... | 1,110,726 |
public void linkageToChrom(boolean[] markerResults, PedFile pedFile){ Vector indList = pedFile.getOrder(); int numMarkers = 0; Vector usedParents = new Vector(); Individual currentInd; Family currentFamily; Vector chrom = new Vector(); for(int x=0; x < indList.size()... | public void linkageToChrom(boolean[] markerResults, PedFile pedFile){ Vector indList = pedFile.getOrder(); int numMarkers = 0; Vector usedParents = new Vector(); Individual currentInd; Family currentFamily; Vector chrom = new Vector(); for(int x=0; x < indList.size()... | 1,110,727 |
public void linkageToChrom(boolean[] markerResults, PedFile pedFile){ Vector indList = pedFile.getOrder(); int numMarkers = 0; Vector usedParents = new Vector(); Individual currentInd; Family currentFamily; Vector chrom = new Vector(); for(int x=0; x < indList.size()... | public void linkageToChrom(boolean[] markerResults, PedFile pedFile){ Vector indList = pedFile.getOrder(); int numMarkers = 0; Vector usedParents = new Vector(); Individual currentInd; Family currentFamily; Vector chrom = new Vector(); for(int x=0; x < indList.size()... | 1,110,728 |
void prepareGenotypeInput(File infile) throws IOException{ //this method is called to suck in data from a file (its only argument) //of genotypes and return a vector of Chromosome objects. String currentLine; Vector chroms = new Vector(); byte[] genos = new byte[0]; String ... | void prepareGenotypeInput(File infile) throws IOException{ //this method is called to suck in data from a file (its only argument) //of genotypes and return a vector of Chromosome objects. String currentLine; Vector chroms = new Vector(); byte[] genos = new byte[0]; String ... | 1,110,730 |
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 Vecto... | 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 Vecto... | 1,110,732 |
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 Vecto... | 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 Vecto... | 1,110,733 |
public Object javaToSql( Object src ) { log.debug( "javaToSql: " + src.getClass().getName() + " " + src ); if ( src instanceof Date ) { return new Timestamp( ((Date)src).getTime() ); } return src; } | public Object javaToSql( Object src ) { log.debug( "javaToSql: " + src ); if ( src instanceof Date ) { return new Timestamp( ((Date)src).getTime() ); } return src; } | 1,110,734 |
public Object sqlToJava( Object src ) { log.debug( "sqlToJava: " + src.getClass().getName() + " " + src ); if ( src instanceof Timestamp ) { return new Date( ((Timestamp)src).getTime() ); } return src; } | public Object sqlToJava( Object src ) { log.debug( "sqlToJava: " + src ); if ( src instanceof Timestamp ) { return new Date( ((Timestamp)src).getTime() ); } return src; } | 1,110,735 |
public void dragDropEnd(DragSourceDropEvent dsde) { System.out.println("DBTree: got dragDropEnd event"); } | public void dragDropEnd(DragSourceDropEvent dsde) { } | 1,110,736 |
public void dragEnter(DragSourceDragEvent dsde) { System.out.println("DBTree: got dragEnter event"); } | public void dragEnter(DragSourceDragEvent dsde) { } | 1,110,737 |
public void dragExit(DragSourceEvent dse) { System.out.println("DBTree: got dragExit event"); } | public void dragExit(DragSourceEvent dse) { } | 1,110,738 |
public void dragOver(DragSourceDragEvent dsde) { System.out.println("DBTree: got dragOver event"); } | public void dragOver(DragSourceDragEvent dsde) { } | 1,110,739 |
public void dropActionChanged(DragSourceDragEvent dsde) { System.out.println("DBTree: got dropActionChanged event"); } | public void dropActionChanged(DragSourceDragEvent dsde) { } | 1,110,740 |
public void run(Context context, XMLOutput output) throws Exception { output.write( text ); } | public void run(JellyContext context, XMLOutput output) throws Exception { output.write( text ); } | 1,110,741 |
void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //type is either 3 or 4 for ped and hapmap files respectively final File inFile = new File(inputOptions[0]); try ... | void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //type is either 3 or 4 for ped and hapmap files respectively final File inFile = new File(inputOptions[0]); try ... | 1,110,742 |
void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //type is either 3 or 4 for ped and hapmap files respectively final File inFile = new File(inputOptions[0]); try ... | void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //type is either 3 or 4 for ped and hapmap files respectively final File inFile = new File(inputOptions[0]); try ... | 1,110,743 |
public PairwiseLinkage computeDPrime(int pos1, int pos2){ int doublehet = 0; int[][] twoMarkerHaplos = new int[3][3]; for (int i = 0; i < twoMarkerHaplos.length; i++){ for (int j = 0; j < twoMarkerHaplos[i].length; j++){ twoMarkerHaplos[i][j] = 0; } }... | public PairwiseLinkage computeDPrime(int pos1, int pos2){ int doublehet = 0; int[][] twoMarkerHaplos = new int[3][3]; for (int i = 0; i < twoMarkerHaplos.length; i++){ for (int j = 0; j < twoMarkerHaplos[i].length; j++){ twoMarkerHaplos[i][j] = 0; } }... | 1,110,745 |
public PairwiseLinkage computeDPrime(int pos1, int pos2){ int doublehet = 0; int[][] twoMarkerHaplos = new int[3][3]; for (int i = 0; i < twoMarkerHaplos.length; i++){ for (int j = 0; j < twoMarkerHaplos[i].length; j++){ twoMarkerHaplos[i][j] = 0; } }... | public PairwiseLinkage computeDPrime(int pos1, int pos2){ int doublehet = 0; int[][] twoMarkerHaplos = new int[3][3]; for (int i = 0; i < twoMarkerHaplos.length; i++){ for (int j = 0; j < twoMarkerHaplos[i].length; j++){ twoMarkerHaplos[i][j] = 0; } }... | 1,110,746 |
public void init() { setAttribute("enabled", true); addChild(getValuedConfiguration("port", "" + m_smtpListenerPort)); DefaultConfiguration handlerConfig = new DefaultConfiguration("handler"); handlerConfig.addChild(getValuedConfiguration("helloName", "myMailServer")); handlerConf... | public void init() { setAttribute("enabled", true); addChild(getValuedConfiguration("port", "" + m_smtpListenerPort)); DefaultConfiguration handlerConfig = new DefaultConfiguration("handler"); handlerConfig.addChild(getValuedConfiguration("helloName", "myMailServer")); handlerConf... | 1,110,747 |
public Tag getTag(JellyContext context) throws JellyException { Tag tag = context.getTagOfTagScript(this); if ( tag == null ) { tag = createTag(); if ( tag != null ) { context.setTagForScript(this,tag); } } configureTag(tag,context); ... | public Tag getTag(JellyContext context) throws JellyException { Tag tag = context.getTagOfTagScript(this); if ( tag == null ) { tag = createTag(); if ( tag != null ) { context.setTagForScript(this,tag); } } return tag; } | 1,110,749 |
void prepareMarkerInput(File infile, long maxdist) 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 is //... | void prepareMarkerInput(File infile, long maxdist) 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 is //... | 1,110,751 |
void prepareMarkerInput(File infile, long maxdist) 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 is //... | void prepareMarkerInput(File infile, long maxdist) 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 is //... | 1,110,752 |
public void saveHapsToText(Haplotype[][] finishedHaplos, double[] multidprime, File saveHapsFile) throws IOException{ if (finishedHaplos == null) return; NumberFormat nf = NumberFormat.getInstance(); nf.setMinimumFractionDigits(3); nf.setMaximumFractionDigit... | public void saveHapsToText(Haplotype[][] finishedHaplos, double[] multidprime, File saveHapsFile) throws IOException{ if (finishedHaplos == null) return; NumberFormat nf = NumberFormat.getInstance(Locale.US); nf.setMinimumFractionDigits(3); nf.setMaximumFrac... | 1,110,753 |
public CheckDataPanel(HaploData hd, boolean disp) throws IOException, PedFileException{ STATUS_COL = 8; setLayout(new BoxLayout(this,BoxLayout.Y_AXIS)); pedfile = hd.getPedFile(); theData = hd; Vector result = pedfile.getResults(); int numResults = result.size(); Vec... | public CheckDataPanel(HaploData hd, boolean disp) throws IOException, PedFileException{ STATUS_COL = 8; setLayout(new BoxLayout(this,BoxLayout.Y_AXIS)); pedfile = hd.getPedFile(); theData = hd; Vector result = pedfile.getResults(); int numResults = result.size(); Vec... | 1,110,754 |
public void registerTagLibrary(String namespaceURI, TagLibrary taglib) { log.info("Registering tag library to: " + namespaceURI + " taglib: " + taglib); taglibs.put(namespaceURI, taglib); } | public void registerTagLibrary(String namespaceURI, TagLibrary taglib) { log.info("Registering tag library to: " + namespaceURI + " taglib: " + taglib); taglibs.put(namespaceURI, taglib); } | 1,110,756 |
public void addBlock(int firstMarker, int lastMarker) { if (firstMarker < 0){ firstMarker = 0; } if (lastMarker >= Chromosome.realIndex.length){ lastMarker = Chromosome.realIndex.length-1; } if (lastMarker - firstMarker < 1){ return; } ... | public void addBlock(int firstMarker, int lastMarker) { if (firstMarker < 0){ firstMarker = 0; } if (lastMarker >= Chromosome.realIndex.length){ lastMarker = Chromosome.realIndex.length-1; } if (lastMarker - firstMarker < 1){ return; } ... | 1,110,757 |
public Vector check() throws PedFileException{ Vector results = new Vector(); //_size = _pedFile.getNumIndividuals(); int numOfMarkers = _pedFile.getNumMarkers(); //not worrying about names right now //TODO: store and use marker names //Vector names = this._pedFile.getMarkerNames(); Vector names = null; boolea... | public Vector check() throws PedFileException{ Vector results = new Vector(); //_size = _pedFile.getNumIndividuals(); int numOfMarkers = _pedFile.getNumMarkers(); //not worrying about names right now //TODO: store and use marker names //Vector names = this._pedFile.getMarkerNames(); Vector names = null; boolea... | 1,110,760 |
public Vector check() throws PedFileException{ Vector results = new Vector(); //_size = _pedFile.getNumIndividuals(); int numOfMarkers = _pedFile.getNumMarkers(); //not worrying about names right now //TODO: store and use marker names //Vector names = this._pedFile.getMarkerNames(); Vector names = null; boolea... | public Vector check() throws PedFileException{ Vector results = new Vector(); //_size = _pedFile.getNumIndividuals(); int numOfMarkers = _pedFile.getNumMarkers(); //not worrying about names right now //TODO: store and use marker names //Vector names = this._pedFile.getMarkerNames(); Vector names = null; boolea... | 1,110,761 |
private MarkerResult checkMarker(int loc, String name)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, parenthet=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable(); Hashtable numindivs=n... | private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, parenthet=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable(); Hashtable numindivs=new Hashtable(... | 1,110,762 |
private MarkerResult checkMarker(int loc, String name)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, parenthet=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable(); Hashtable numindivs=n... | private MarkerResult checkMarker(int loc, String name)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, parenthet=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable(); Hashtable numindivs=n... | 1,110,763 |
public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == "Open"){ int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { try{ theData = new HaploData(fc.getSelectedFile()); infileName = fc.getSelectedFile().getName(); ... | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == "Open"){ int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { try{ theData = new HaploData(fc.getSelectedFile()); infileName = fc.getSelectedFile().getName(); ... | 1,110,767 |
public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == "Open"){ int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { try{ theData = new HaploData(fc.getSelectedFile()); infileName = fc.getSelectedFile().getName(); ... | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == "Open"){ int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { try{ theData = new HaploData(fc.getSelectedFile()); infileName = fc.getSelectedFile().getName(); ... | 1,110,768 |
public void actionPerformed(ActionEvent evt){ progressMonitor.setProgress(theData.getComplete()); if (theData.getComplete() == theData.getToBeCompleted()){ timer.stop(); progressMonitor.close(); infoKnown=false; drawPicture(theData); loadInfoMenuItem.setEnabled(true); ... | public void actionPerformed(ActionEvent evt){ progressMonitor.setProgress(theData.getComplete()); if (theData.finished){ timer.stop(); progressMonitor.close(); infoKnown=false; drawPicture(theData); loadInfoMenuItem.setEnabled(true); hapMenuItem.setEnabled(true); ... | 1,110,769 |
public String draw(DashboardContext context) { StringBuffer output = new StringBuffer(); output.append(component.draw(context)); // append script final String dashboardId = context.getDashboardConfig().getDashboardId(); String appId = context.getWebContext().getApplicationConfig()... | public String draw(DashboardContext context) { StringBuffer output = new StringBuffer(); output.append(component.draw(context)); // append script final String dashboardId = context.getDashboardConfig().getDashboardId(); String appId = context.getWebContext().getApplicationConfig()... | 1,110,770 |
public void colorDPrime(int scheme){ PairwiseLinkage dPrime[][] = theData.filteredDPrimeTable; if (scheme == STD_SCHEME){ // set coloring based on LOD and D' for (int i = 0; i < dPrime.length; i++){ for (int j = i+1; j < dPrime[i].length; j++){ P... | public void colorDPrime(int scheme){ PairwiseLinkage dPrime[][] = theData.filteredDPrimeTable; if (scheme == STD_SCHEME){ // set coloring based on LOD and D' for (int i = 0; i < dPrime.length; i++){ for (int j = i+1; j < dPrime[i].length; j++){ P... | 1,110,772 |
public void mouseClicked(MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON1_MASK) == InputEvent.BUTTON1_MASK) { int clickX = e.getX(); int clickY = e.getY(); if (showWM && wmInteriorRect.contains(clickX,clickY)){ //convert a click on the ... | public void mouseClicked(MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON1_MASK) == InputEvent.BUTTON1_MASK) { int clickX = e.getX(); int clickY = e.getY(); if (showWM && wmInteriorRect.contains(clickX,clickY)){ //convert a click on the ... | 1,110,773 |
public void mouseReleased(MouseEvent e) { //remove popped up window if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK){ popupExists = false; repaint(); //resize window once user has ceased dragging } else if ((e.getModifiers(... | public void mouseReleased(MouseEvent e) { //remove popped up window if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK){ popupExists = false; repaint(); //resize window once user has ceased dragging } else if ((e.getModifiers(... | 1,110,774 |
public void refresh(int scheme){ if (scheme != 0){ colorDPrime(scheme); } noImage = true; repaint(); } | public void refresh(int scheme){ if (scheme != 0){ colorDPrime(scheme); } noImage = true; repaint(); } | 1,110,775 |
Haplotype[][] generateCrossovers(Haplotype[][] haplos) throws HaploViewException{ Vector crossBlock = new Vector(); double CROSSOVER_THRESHOLD = 0.001; //to what percentage do we want to consider crossings? if (haplos.length == 0) return null; //seed first block with ordering numbers ... | Haplotype[][] generateCrossovers(Haplotype[][] haplos) throws HaploViewException{ Vector crossBlock = new Vector(); double CROSSOVER_THRESHOLD = 0.001; //to what percentage do we want to consider crossings? if (haplos.length == 0) return null; //seed first block with ordering numbers ... | 1,110,776 |
Haplotype[][] generateCrossovers(Haplotype[][] haplos) throws HaploViewException{ Vector crossBlock = new Vector(); double CROSSOVER_THRESHOLD = 0.001; //to what percentage do we want to consider crossings? if (haplos.length == 0) return null; //seed first block with ordering numbers ... | Haplotype[][] generateCrossovers(Haplotype[][] haplos) throws HaploViewException{ Vector crossBlock = new Vector(); double CROSSOVER_THRESHOLD = 0.001; //to what percentage do we want to consider crossings? if (haplos.length == 0) return null; //seed first block with ordering numbers ... | 1,110,777 |
Haplotype[][] generateCrossovers(Haplotype[][] haplos) throws HaploViewException{ Vector crossBlock = new Vector(); double CROSSOVER_THRESHOLD = 0.001; //to what percentage do we want to consider crossings? if (haplos.length == 0) return null; //seed first block with ordering numbers ... | Haplotype[][] generateCrossovers(Haplotype[][] haplos) throws HaploViewException{ Vector crossBlock = new Vector(); double CROSSOVER_THRESHOLD = 0.001; //to what percentage do we want to consider crossings? if (haplos.length == 0) return null; //seed first block with ordering numbers ... | 1,110,778 |
Haplotype[][] generateCrossovers(Haplotype[][] haplos) throws HaploViewException{ Vector crossBlock = new Vector(); double CROSSOVER_THRESHOLD = 0.001; //to what percentage do we want to consider crossings? if (haplos.length == 0) return null; //seed first block with ordering numbers ... | Haplotype[][] generateCrossovers(Haplotype[][] haplos) throws HaploViewException{ Vector crossBlock = new Vector(); double CROSSOVER_THRESHOLD = 0.001; //to what percentage do we want to consider crossings? if (haplos.length == 0) return null; //seed first block with ordering numbers ... | 1,110,779 |
Haplotype[][] generateCrossovers(Haplotype[][] haplos) throws HaploViewException{ Vector crossBlock = new Vector(); double CROSSOVER_THRESHOLD = 0.001; //to what percentage do we want to consider crossings? if (haplos.length == 0) return null; //seed first block with ordering numbers ... | Haplotype[][] generateCrossovers(Haplotype[][] haplos) throws HaploViewException{ Vector crossBlock = new Vector(); double CROSSOVER_THRESHOLD = 0.001; //to what percentage do we want to consider crossings? if (haplos.length == 0) return null; //seed first block with ordering numbers ... | 1,110,780 |
Haplotype[][] generateHaplotypes(Vector blocks, 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(); this... | Haplotype[][] generateHaplotypes(Vector blocks, boolean crossover) throws HaploViewException{ //TODO: output indiv hap estimates Haplotype[][] rawHaplotypes = new Haplotype[blocks.size()][]; //String raw = new String(); //String currentLine; this.totalBlocks = blocks.size(); ... | 1,110,781 |
Haplotype[][] generateHaplotypes(Vector blocks, 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(); this... | Haplotype[][] generateHaplotypes(Vector blocks, 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(); this... | 1,110,782 |
Haplotype[][] generateHaplotypes(Vector blocks, 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(); this... | Haplotype[][] generateHaplotypes(Vector blocks, 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(); this... | 1,110,783 |
Haplotype[][] generateHaplotypes(Vector blocks, 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(); this... | Haplotype[][] generateHaplotypes(Vector blocks, 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(); this... | 1,110,784 |
Haplotype[][] generateHaplotypes(Vector blocks, 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(); this... | Haplotype[][] generateHaplotypes(Vector blocks, 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(); this... | 1,110,785 |
public Tag createTag(String name, Attributes attributes) throws JellyException { return new MenuManagerTag(); } | public Tag createTag(String name, Attributes attributes) throws JellyException { return new MenuManagerTag(); } | 1,110,787 |
public Tag createTag(String name, Attributes attributes) throws JellyException { return new ViewerTag(theclass, style); } | public Tag createTag(String name, Attributes attributes) throws JellyException { return new ViewerTag(theclass, style); } | 1,110,788 |
public void mouseMoved(MouseEvent evt) { if (rubberBand != null) { // repaint old region in case of shrinkage Rectangle dirtyRegion = zoomRect(new Rectangle(rubberBand)); Point p = unzoomPoint(new Point(evt.getPoint())); rubberBand.setBounds(rubberBandOrigin.x, rubberBandOrigin.y, 0, 0); rubberBand.a... | public void mouseMoved(MouseEvent evt) { if (rubberBand != null) { // repaint old region in case of shrinkage Rectangle dirtyRegion = zoomRect(new Rectangle(rubberBand)); Point p = unzoomPoint(new Point(evt.getPoint())); rubberBand.setBounds(rubberBandOrigin.x, rubberBandOrigin.y, 0, 0); rubberBand.a... | 1,110,789 |
public void mouseReleased(MouseEvent evt) { if (rubberBand != null) { if (evt.getButton() == MouseEvent.BUTTON1) { Rectangle dirtyRegion = rubberBand; rubberBandOrigin = null; rubberBand = null; repaint(zoomRect(new Rectangle(dirtyRegion))); } } else if (!retargetToContentPane(evt)) { //(... | public void mouseReleased(MouseEvent evt) { if (rubberBand != null) { if (evt.getButton() == MouseEvent.BUTTON1) { Rectangle dirtyRegion = new Rectangle(rubberBand); dirtyRegion.width += (int) (dirtyRegion.width * 0.1); dirtyRegion.height += (int) (dirtyRegion.height * 0.1); rubberBandOrigin = null; ... | 1,110,790 |
public void mouseReleased(MouseEvent evt) { if (rubberBand != null) { if (evt.getButton() == MouseEvent.BUTTON1) { Rectangle dirtyRegion = rubberBand; rubberBandOrigin = null; rubberBand = null; repaint(zoomRect(new Rectangle(dirtyRegion))); } } else if (!retargetToContentPane(evt)) { //(... | public void mouseReleased(MouseEvent evt) { if (rubberBand != null) { if (evt.getButton() == MouseEvent.BUTTON1) { Rectangle dirtyRegion = rubberBand; rubberBandOrigin = null; rubberBand = null; repaint(zoomRect(dirtyRegion)); } } else if (!retargetToContentPane(evt)) { //((PlayPen) evt.g... | 1,110,791 |
public Object convert(Class type, Object value) { if ( value != null ) { String text = value.toString(); StringTokenizer enum = new StringTokenizer( text, "," ); int x = 0; int y = 0; if ( enum.hasMoreTokens() ) { x = parseNumber( enum.nex... | public Object convert(Class type, Object value) { if ( value != null ) { String text = value.toString(); StringTokenizer pointEnum = new StringTokenizer( text, "," ); int x = 0; int y = 0; if ( enum.hasMoreTokens() ) { x = parseNumber( enu... | 1,110,794 |
public Object convert(Class type, Object value) { if ( value != null ) { String text = value.toString(); StringTokenizer enum = new StringTokenizer( text, "," ); int x = 0; int y = 0; if ( enum.hasMoreTokens() ) { x = parseNumber( enum.nex... | public Object convert(Class type, Object value) { if ( value != null ) { String text = value.toString(); StringTokenizer enum = new StringTokenizer( text, "," ); int x = 0; int y = 0; if ( enum.hasMoreTokens() ) { x = parseNumber( enum.nex... | 1,110,795 |
public Object convert(Class type, Object value) { if ( value != null ) { String text = value.toString(); StringTokenizer enum = new StringTokenizer( text, "," ); int x = 0; int y = 0; if ( enum.hasMoreTokens() ) { x = parseNumber( enum.nex... | public Object convert(Class type, Object value) { if ( value != null ) { String text = value.toString(); StringTokenizer enum = new StringTokenizer( text, "," ); int x = 0; int y = 0; if ( enum.hasMoreTokens() ) { x = parseNumber( enum.nex... | 1,110,796 |
public FileScannerTag(FileScanner fileScanner) { this.fileScanner = fileScanner; this.dynaBean = new ConvertingWrapDynaBean(fileScanner); } | public FileScannerTag(FileScanner fileScanner) { this.fileScanner = fileScanner; } | 1,110,798 |
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); ... | 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); ... | 1,110,799 |
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); ... | 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); ... | 1,110,800 |
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); ... | 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); ... | 1,110,801 |
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