bugged stringlengths 6 599k | fixed stringlengths 10 599k | __index_level_0__ int64 0 1.13M |
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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[4]); } Chromosome.setDataBuild("ncbi_b35"); Vector sampleData = new Vector()... | 1,112,499 |
void readPedGenotypes(String[] f, int type){ //input is a 3 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = max comparison distance (don't compute d' if markers are greater than this dist apart) //type is either 3 or... | void readPedGenotypes(String[] f, int type){ //input is a 3 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = max comparison distance (don't compute d' if markers are greater than this dist apart) //type is either 3 or... | 1,112,501 |
public void paintComponent(Graphics g){ DPrimeTable dPrimeTable = theData.dpTable; if (Chromosome.getSize() < 2){ //if there zero or only one valid marker return; } Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zoomi... | public void paintComponent(Graphics g){ DPrimeTable dPrimeTable = theData.dpTable; if (Chromosome.getSize() < 2){ //if there zero or only one valid marker return; } Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zoomi... | 1,112,503 |
private JUnitOJBManager() { System.setProperty( "photovault.configfile", "conf/junittest_config.xml" ); log.error( "Initializing OB for JUnit tests" ); createDatabase(); PhotovaultSettings settings = PhotovaultSettings.getSettings(); settings.setConfiguration( "pv_junit" ); PVData... | private JUnitOJBManager() { System.setProperty( "photovault.configfile", "conf/junittest_config.xml" ); log.error( "Initializing OB for JUnit tests" ); createDatabase(); PhotovaultSettings settings = PhotovaultSettings.getSettings(); settings.setConfiguration( "pv_junit" ); PVData... | 1,112,505 |
private final void setDatabase(SQLDatabase newdb) { if (newdb == null) throw new NullPointerException("db must be non-null"); this.db = newdb; db.setIgnoreReset(true); if (db.getDataSource() == null) { ArchitectDataSource dbcs = new ArchitectDataSource(); dbcs.setName("Target Database"); dbcs.setDisplayName(... | private final void setDatabase(SQLDatabase newdb) { if (newdb == null) throw new NullPointerException("db must be non-null"); this.db = newdb; db.setIgnoreReset(true); if (db.getDataSource() == null) { ArchitectDataSource dbcs = new ArchitectDataSource(); dbcs.setName("Target Database"); dbcs.setDisplayName(... | 1,112,509 |
public PairwiseLinkage computeDPrime(int pos1, int pos2){ long sep = Chromosome.getMarker(pos2).getPosition() - Chromosome.getMarker(pos1).getPosition(); if (maxdist > 0){ if ((sep > maxdist || sep < negMaxdist)){ return null; } } compsDone++; ... | public PairwiseLinkage computeDPrime(int pos1, int pos2){ long sep = Chromosome.getMarker(pos2).getPosition() - Chromosome.getMarker(pos1).getPosition(); if (maxdist > 0){ if ((sep > maxdist || sep < negMaxdist)){ return null; } } compsDone++; ... | 1,112,510 |
public PairwiseLinkage computeDPrime(int pos1, int pos2){ long sep = Chromosome.getMarker(pos2).getPosition() - Chromosome.getMarker(pos1).getPosition(); if (maxdist > 0){ if ((sep > maxdist || sep < negMaxdist)){ return null; } } compsDone++; ... | public PairwiseLinkage computeDPrime(int pos1, int pos2){ long sep = Chromosome.getMarker(pos2).getPosition() - Chromosome.getMarker(pos1).getPosition(); if (maxdist > 0){ if ((sep > maxdist || sep < negMaxdist)){ return null; } } compsDone++; ... | 1,112,511 |
public PairwiseLinkage computeDPrime(int pos1, int pos2){ long sep = Chromosome.getMarker(pos2).getPosition() - Chromosome.getMarker(pos1).getPosition(); if (maxdist > 0){ if ((sep > maxdist || sep < negMaxdist)){ return null; } } compsDone++; ... | public PairwiseLinkage computeDPrime(int pos1, int pos2){ long sep = Chromosome.getMarker(pos2).getPosition() - Chromosome.getMarker(pos1).getPosition(); if (maxdist > 0){ if ((sep > maxdist || sep < negMaxdist)){ return null; } } compsDone++; ... | 1,112,512 |
public PairwiseLinkage computeDPrime(int pos1, int pos2){ long sep = Chromosome.getMarker(pos2).getPosition() - Chromosome.getMarker(pos1).getPosition(); if (maxdist > 0){ if ((sep > maxdist || sep < negMaxdist)){ return null; } } compsDone++; ... | public PairwiseLinkage computeDPrime(int pos1, int pos2){ long sep = Chromosome.getMarker(pos2).getPosition() - Chromosome.getMarker(pos1).getPosition(); if (maxdist > 0){ if ((sep > maxdist || sep < negMaxdist)){ return null; } } compsDone++; ... | 1,112,513 |
public PairwiseLinkage computeDPrime(int pos1, int pos2){ long sep = Chromosome.getMarker(pos2).getPosition() - Chromosome.getMarker(pos1).getPosition(); if (maxdist > 0){ if ((sep > maxdist || sep < negMaxdist)){ return null; } } compsDone++; ... | public PairwiseLinkage computeDPrime(int pos1, int pos2){ long sep = Chromosome.getMarker(pos2).getPosition() - Chromosome.getMarker(pos1).getPosition(); if (maxdist > 0){ if ((sep > maxdist || sep < negMaxdist)){ return null; } } compsDone++; ... | 1,112,514 |
public PairwiseLinkage computeDPrime(int pos1, int pos2){ long sep = Chromosome.getMarker(pos2).getPosition() - Chromosome.getMarker(pos1).getPosition(); if (maxdist > 0){ if ((sep > maxdist || sep < negMaxdist)){ return null; } } compsDone++; ... | public PairwiseLinkage computeDPrime(int pos1, int pos2){ long sep = Chromosome.getMarker(pos2).getPosition() - Chromosome.getMarker(pos1).getPosition(); if (maxdist > 0){ if ((sep > maxdist || sep < negMaxdist)){ return null; } } compsDone++; ... | 1,112,515 |
public PairwiseLinkage computeDPrime(int pos1, int pos2){ long sep = Chromosome.getMarker(pos2).getPosition() - Chromosome.getMarker(pos1).getPosition(); if (maxdist > 0){ if ((sep > maxdist || sep < negMaxdist)){ return null; } } compsDone++; ... | public PairwiseLinkage computeDPrime(int pos1, int pos2){ long sep = Chromosome.getMarker(pos2).getPosition() - Chromosome.getMarker(pos1).getPosition(); if (maxdist > 0){ if ((sep > maxdist || sep < negMaxdist)){ return null; } } compsDone++; ... | 1,112,516 |
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... | 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... | 1,112,517 |
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... | 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... | 1,112,518 |
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... | 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... | 1,112,519 |
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... | 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... | 1,112,520 |
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... | 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... | 1,112,521 |
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... | 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... | 1,112,522 |
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... | 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... | 1,112,523 |
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... | 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... | 1,112,524 |
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... | 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... | 1,112,525 |
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... | 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... | 1,112,526 |
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... | 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... | 1,112,527 |
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]; ... | 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]; ... | 1,112,528 |
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]; ... | 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]; ... | 1,112,529 |
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... | 1,112,530 |
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... | 1,112,531 |
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... | 1,112,532 |
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... | 1,112,533 |
protected void createUI() { tabPane = new JTabbedPane(); queryPane = new QueryPane(); treePane = new PhotoFolderTree(); tabPane.addTab( "Query", queryPane ); tabPane.addTab( "Folders", treePane ); viewPane = new TableCollectionView(); viewPane.setCollection( queryPane.getResultCollection() ); // Set listeners to bo... | protected void createUI() { tabPane = new JTabbedPane(); queryPane = new QueryPane(); treePane = new PhotoFolderTree(); tabPane.addTab( "Query", queryPane ); tabPane.addTab( "Folders", treePane ); viewPane = new TableCollectionView(); viewPane.setCollection( queryPane.getResultCollection() ); // Set listeners to bo... | 1,112,534 |
public void photoFolderTreeSelectionChanged( PhotoFolderTreeEvent e ) { viewPane.setCollection( e.getSelected() ); } | public void photoFolderTreeSelectionChanged( PhotoFolderTreeEvent e ) { PhotoFolder f = e.getSelected(); if ( f != null ) { viewPane.setCollection( f ); } } | 1,112,535 |
public Script compile() throws Exception { if (tag instanceof CompilableTag) { ((CompilableTag) tag).compile(); } List typeList = new ArrayList(); List methodList = new ArrayList(); List expressionList = new ArrayList(); BeanInfo info = Introspector.getBeanInfo(t... | public Script compile() throws Exception { if (tag instanceof CompilableTag) { ((CompilableTag) tag).compile(); } List typeList = new ArrayList(); List methodList = new ArrayList(); List expressionList = new ArrayList(); BeanInfo info = Introspector.getBeanInfo(t... | 1,112,536 |
public void run(JellyContext context, XMLOutput output) throws Exception { tag.setContext(context); // initialize all the properties of the tag before its used // if there is a problem abort this tag for (int i = 0, size = expressions.length; i < size; i++) { Expressio... | public void run(JellyContext context, XMLOutput output) throws Exception { tag.setContext(context); // initialize all the properties of the tag before its used // if there is a problem abort this tag for (int i = 0, size = expressions.length; i < size; i++) { Expressio... | 1,112,537 |
public void run(JellyContext context, XMLOutput output) throws Exception { tag.setContext(context); // initialize all the properties of the tag before its used // if there is a problem abort this tag for (int i = 0, size = expressions.length; i < size; i++) { Expressio... | public void run(JellyContext context, XMLOutput output) throws Exception { tag.setContext(context); // initialize all the properties of the tag before its used // if there is a problem abort this tag for (int i = 0, size = expressions.length; i < size; i++) { Expressio... | 1,112,538 |
public void exit() { if (promptForUnsavedModifications()) { try { closeProject(getProject()); saveSettings(); } catch (ArchitectException e) { logger.error("Couldn't save settings: "+e); } System.exit(0); } } | public void exit() { if (getProject().isSaveInProgress()) { JOptionPane.showMessageDialog(this, "Project is saving, cannot exit the Power Architect. Please wait for the save to finish, and then try again.", "Warning", JOptionPane.WARNING_MESSAGE); return; } if (promptForUnsavedModifications()) { try { ... | 1,112,540 |
public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == READ_GENOTYPES){ ReadDataDialog readDialog = new ReadDataDialog("Open new data", this); readDialog.pack(); readDialog.setVisible(true); } else if (command == READ_... | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == READ_GENOTYPES){ ReadDataDialog readDialog = new ReadDataDialog("Open new data", this); readDialog.pack(); readDialog.setVisible(true); } else if (command == READ_... | 1,112,543 |
public void setSession(Session s) { this.session = session; } | public void setSession(Session s) { this.session = s; } | 1,112,544 |
public void doTag(XMLOutput output) throws Exception { Class throwableClass = getThrowableClass(); try { invokeBody(output); } catch (Throwable t) { if (t instanceof JellyException) { // unwrap Jelly exceptions which wrap other exceptions JellyException je = (Jelly... | public void doTag(XMLOutput output) throws Exception { Class throwableClass = getThrowableClass(); try { invokeBody(output); } catch (Throwable t) { if (t instanceof JellyException) { // unwrap Jelly exceptions which wrap other exceptions JellyException je = (Jelly... | 1,112,548 |
private void doColumnProfile(List<SQLColumn> columns, Connection conn) throws SQLException, ArchitectException { Statement stmt = null; ResultSet rs = null; String lastSQL = null; try { if ( columns.size() == 0 ) return; SQLColumn c... | private void doColumnProfile(List<SQLColumn> columns, Connection conn) throws SQLException, ArchitectException { Statement stmt = null; ResultSet rs = null; String lastSQL = null; try { if ( columns.size() == 0 ) return; SQLColumn c... | 1,112,550 |
private void doColumnProfile(List<SQLColumn> columns, Connection conn) throws SQLException, ArchitectException { Statement stmt = null; ResultSet rs = null; String lastSQL = null; try { if ( columns.size() == 0 ) return; SQLColumn c... | private void doColumnProfile(List<SQLColumn> columns, Connection conn) throws SQLException, ArchitectException { Statement stmt = null; ResultSet rs = null; String lastSQL = null; try { if ( columns.size() == 0 ) return; SQLColumn c... | 1,112,551 |
private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); final int i = 0; StringBuffer ... | 1,112,552 |
private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | 1,112,553 |
private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | 1,112,554 |
private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | 1,112,555 |
private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | 1,112,556 |
private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | 1,112,557 |
private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | 1,112,558 |
private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | 1,112,559 |
private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | 1,112,560 |
private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | 1,112,561 |
private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | 1,112,562 |
private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | 1,112,563 |
private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | 1,112,564 |
private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | private ColumnProfileResult execProfileFunction(ProfileFunctionDescriptor pfd, SQLColumn col, DDLGenerator ddlg, Connection conn) throws SQLException { long createStartTime = System.currentTimeMillis(); int i = 0; StringBuffer sql = ... | 1,112,565 |
public void remove(SQLObject sqo){ results.remove(sqo); } | public void remove(SQLObject sqo) throws ArchitectException{ results.remove(sqo); } | 1,112,567 |
public void setCancelled(boolean cancelled) { synchronized (monitorableMutex) { userCancel = true; } } | public void setCancelled(boolean cancelled) { synchronized (monitorableMutex) { userCancel = cancelled; } } | 1,112,569 |
protected Document parse(Object source) throws Exception { // #### we should allow parsing to output XML events to // the output if no var is specified if (source instanceof String) { String uri = (String) source; InputStream in = context.getResourceAsStream(uri); ... | protected Document parse(Object source) throws Exception { // #### we should allow parsing to output XML events to // the output if no var is specified if (source instanceof String) { String uri = (String) source; InputStream in = context.getResourceAsStream(uri); ... | 1,112,570 |
protected Document parse(Object source) throws Exception { // #### we should allow parsing to output XML events to // the output if no var is specified if (source instanceof String) { String uri = (String) source; InputStream in = context.getResourceAsStream(uri); ... | protected Document parse(Object source) throws Exception { // #### we should allow parsing to output XML events to // the output if no var is specified if (source instanceof String) { String uri = (String) source; InputStream in = context.getResourceAsStream(uri); ... | 1,112,571 |
public void haploDraw(Graphics gr, boolean myuseThickness, int mycolorThresh, int mycrossThinThresh, int mycrossThickThresh, double[] gapDPrime, Haplotype[][] hapsInBlocks){ Graphics2D g = (Graphics2D) gr; final BasicStroke stroke = new BasicStroke(1.0f); final BasicStroke wideStroke = new BasicStroke(2.0f)... | public void haploDraw(Graphics gr, boolean myuseThickness, int mycolorThresh, int mycrossThinThresh, int mycrossThickThresh, double[] gapDPrime, Haplotype[][] hapsInBlocks){ Graphics2D g = (Graphics2D) gr; final BasicStroke stroke = new BasicStroke(1.0f); final BasicStroke wideStroke = new BasicStroke(2.0f)... | 1,112,572 |
public void haploDraw(Graphics gr, boolean myuseThickness, int mycolorThresh, int mycrossThinThresh, int mycrossThickThresh, double[] gapDPrime, Haplotype[][] hapsInBlocks){ Graphics2D g = (Graphics2D) gr; final BasicStroke stroke = new BasicStroke(1.0f); final BasicStroke wideStroke = new BasicStroke(2.0f)... | public void haploDraw(Graphics gr, boolean myuseThickness, int mycolorThresh, int mycrossThinThresh, int mycrossThickThresh, double[] gapDPrime, Haplotype[][] hapsInBlocks){ Graphics2D g = (Graphics2D) gr; final BasicStroke stroke = new BasicStroke(1.0f); final BasicStroke wideStroke = new BasicStroke(2.0f)... | 1,112,573 |
public void haploDraw(Graphics gr, boolean myuseThickness, int mycolorThresh, int mycrossThinThresh, int mycrossThickThresh, double[] gapDPrime, Haplotype[][] hapsInBlocks){ Graphics2D g = (Graphics2D) gr; final BasicStroke stroke = new BasicStroke(1.0f); final BasicStroke wideStroke = new BasicStroke(2.0f)... | public void haploDraw(Graphics gr, boolean myuseThickness, int mycolorThresh, int mycrossThinThresh, int mycrossThickThresh, double[] gapDPrime, Haplotype[][] hapsInBlocks){ Graphics2D g = (Graphics2D) gr; final BasicStroke stroke = new BasicStroke(1.0f); final BasicStroke wideStroke = new BasicStroke(2.0f)... | 1,112,574 |
public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) throws Exception { ... | public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) throws Exception { ... | 1,112,575 |
public void remove(SQLObject sqo) throws ArchitectException{ ProfileResult old = results.remove(sqo); if ( sqo instanceof SQLTable ) { for ( SQLColumn col: ((SQLTable)sqo).getColumns()) { results.remove(col); } } else if ( sqo ... | public void remove(SQLObject sqo) throws ArchitectException{ results.remove(sqo); if ( sqo instanceof SQLTable ) { for ( SQLColumn col: ((SQLTable)sqo).getColumns()) { results.remove(col); } } else if ( sqo instanceof SQLColumn... | 1,112,576 |
public DataFlavor bestImportFlavor(JComponent c, DataFlavor[] flavors) { logger.debug("PlayPenTransferHandler: can I import "+Arrays.asList(flavors)); for (int i = 0; i < flavors.length; i++) { String cls = flavors[i].getDefaultRepresentationClassAsString(); logger.debug("representation class = "+cls); ... | public DataFlavor bestImportFlavor(JComponent c, DataFlavor[] flavors) { logger.debug("PlayPenTransferHandler: can I import "+Arrays.asList(flavors)); for (int i = 0; i < flavors.length; i++) { String cls = flavors[i].getDefaultRepresentationClassAsString(); logger.debug("representation class = "+cls); ... | 1,112,579 |
public DataFlavor bestImportFlavor(JComponent c, DataFlavor[] flavors) { logger.debug("PlayPenTransferHandler: can I import "+Arrays.asList(flavors)); for (int i = 0; i < flavors.length; i++) { String cls = flavors[i].getDefaultRepresentationClassAsString(); logger.debug("representation class = "+cls); ... | public DataFlavor bestImportFlavor(JComponent c, DataFlavor[] flavors) { logger.debug("PlayPenTransferHandler: can I import "+Arrays.asList(flavors)); for (int i = 0; i < flavors.length; i++) { String cls = flavors[i].getDefaultRepresentationClassAsString(); logger.debug("representation class = "+cls); ... | 1,112,580 |
public void drop(DropTargetDropEvent dtde) { Transferable t = dtde.getTransferable(); PlayPen c = (PlayPen) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if (importFlavor == null) { dtde.rejectDrop(); } else { try { Object so... | public void drop(DropTargetDropEvent dtde) { Transferable t = dtde.getTransferable(); PlayPen c = (PlayPen) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if (importFlavor == null) { dtde.rejectDrop(); } else { try { Object so... | 1,112,581 |
public PlayPen(SQLDatabase db) { super(); if (db == null) throw new NullPointerException("db must be non-null"); this.db = db; relationships = new LinkedList(); try { ArchitectUtils.listenToHierarchy(this, db); } catch (ArchitectException ex) { logger.error("Couldn't listen to database", ex); } setLayout(n... | public PlayPen(SQLDatabase db) { super(); if (db == null) throw new NullPointerException("db must be non-null"); this.db = db; relationships = new LinkedList(); try { ArchitectUtils.listenToHierarchy(this, db); } catch (ArchitectException ex) { logger.error("Couldn't listen to database", ex); } setLayout(n... | 1,112,582 |
public PlayPen(SQLDatabase db) { super(); if (db == null) throw new NullPointerException("db must be non-null"); this.db = db; relationships = new LinkedList(); try { ArchitectUtils.listenToHierarchy(this, db); } catch (ArchitectException ex) { logger.error("Couldn't listen to database", ex); } setLayout(n... | public PlayPen(SQLDatabase db) { super(); if (db == null) throw new NullPointerException("db must be non-null"); this.db = db; relationships = new LinkedList(); try { ArchitectUtils.listenToHierarchy(this, db); } catch (ArchitectException ex) { logger.error("Couldn't listen to database", ex); } setLayout(n... | 1,112,583 |
public void sendWelcomeLetters(MailTopic topic,String email)throws RemoteException,FinderException{ Collection letters = MailFinder.getInstance().getEmailLetters(((Integer)topic.getPrimaryKey()).intValue(),EmailLetter.TYPE_SUBSCRIPTION); if(letters!=null &&!letters.isEmpty()){ this.sendLetter((EmailLetter)lett... | public void sendWelcomeLetters(MailTopic topic,String email)throws RemoteException,FinderException{ Collection letters = MailFinder.getInstance().getEmailLetters(((Integer)topic.getPrimaryKey()).intValue(),EmailLetter.TYPE_SUBSCRIPTION); if(letters!=null &&!letters.isEmpty()){ Email eEmail =MailFinder.getInsta... | 1,112,584 |
protected RGB parseRGB(String value) { StringTokenizer enum = new StringTokenizer(value, ","); int red = 0; int green = 0; int blue = 0; if (enum.hasMoreTokens()) { red = parseNumber(enum.nextToken()); } | protected RGB parseRGB(String value) { StringTokenizer items = new StringTokenizer(value, ","); int red = 0; int green = 0; int blue = 0; if (enum.hasMoreTokens()) { red = parseNumber(enum.nextToken()); } | 1,112,586 |
protected RGB parseRGB(String value) { StringTokenizer enum = new StringTokenizer(value, ","); int red = 0; int green = 0; int blue = 0; if (enum.hasMoreTokens()) { red = parseNumber(enum.nextToken()); } | protected RGB parseRGB(String value) { StringTokenizer enum = new StringTokenizer(value, ","); int red = 0; int green = 0; int blue = 0; if (enum.hasMoreTokens()) { red = parseNumber(enum.nextToken()); } | 1,112,587 |
public void parseHapMap(File inFile) throws PedFileException, IOException { int colNum = -1; Vector lines = new Vector(); BufferedReader reader = new BufferedReader(new FileReader(inFile)); String line; while((line = reader.readLine())!=null){ if (line.length() == 0){ ... | public void parseHapMap(File inFile) throws PedFileException, IOException { int colNum = -1; Vector lines = new Vector(); BufferedReader reader = new BufferedReader(new FileReader(inFile)); String line; while((line = reader.readLine())!=null){ if (line.length() == 0){ ... | 1,112,589 |
public void parseHapMap(File inFile) throws PedFileException, IOException { int colNum = -1; Vector lines = new Vector(); BufferedReader reader = new BufferedReader(new FileReader(inFile)); String line; while((line = reader.readLine())!=null){ if (line.length() == 0){ ... | public void parseHapMap(File inFile) throws PedFileException, IOException { int colNum = -1; Vector lines = new Vector(); BufferedReader reader = new BufferedReader(new FileReader(inFile)); String line; while((line = reader.readLine())!=null){ if (line.length() == 0){ ... | 1,112,590 |
public void parseLinkage(File inputFile) throws PedFileException, IOException { int colNum = -1; boolean withOptionalColumn = false; int numLines = 0; Individual ind; this.allIndividuals = new Vector(); BufferedReader reader = new BufferedReader(new FileReader(inputFile)); ... | public void parseLinkage(File inputFile) throws PedFileException, IOException { int colNum = -1; boolean withOptionalColumn = false; int numLines = 0; Individual ind; this.allIndividuals = new Vector(); BufferedReader reader = new BufferedReader(new FileReader(inputFile)); ... | 1,112,591 |
public void parseLinkage(File inputFile) throws PedFileException, IOException { int colNum = -1; boolean withOptionalColumn = false; int numLines = 0; Individual ind; this.allIndividuals = new Vector(); BufferedReader reader = new BufferedReader(new FileReader(inputFile)); ... | public void parseLinkage(File inputFile) throws PedFileException, IOException { int colNum = -1; boolean withOptionalColumn = false; int numLines = 0; Individual ind; this.allIndividuals = new Vector(); BufferedReader reader = new BufferedReader(new FileReader(inputFile)); ... | 1,112,592 |
public void parseLinkage(File inputFile) throws PedFileException, IOException { int colNum = -1; boolean withOptionalColumn = false; int numLines = 0; Individual ind; this.allIndividuals = new Vector(); BufferedReader reader = new BufferedReader(new FileReader(inputFile)); ... | public void parseLinkage(File inputFile) throws PedFileException, IOException { int colNum = -1; boolean withOptionalColumn = false; int numLines = 0; Individual ind; this.allIndividuals = new Vector(); BufferedReader reader = new BufferedReader(new FileReader(inputFile)); ... | 1,112,593 |
public void parseLinkage(File inputFile) throws PedFileException, IOException { int colNum = -1; boolean withOptionalColumn = false; int numLines = 0; Individual ind; this.allIndividuals = new Vector(); BufferedReader reader = new BufferedReader(new FileReader(inputFile)); ... | public void parseLinkage(File inputFile) throws PedFileException, IOException { int colNum = -1; boolean withOptionalColumn = false; int numLines = 0; Individual ind; this.allIndividuals = new Vector(); BufferedReader reader = new BufferedReader(new FileReader(inputFile)); ... | 1,112,594 |
public TransformTag() { super(); tf = TransformerFactory.newInstance(); } | public TransformTag() { super(); this.tf = (SAXTransformerFactory) TransformerFactory.newInstance(); } | 1,112,595 |
protected URIResolver createURIResolver() { return new URIResolver() { public Source resolve(String href, String base) throws TransformerException { if (log.isDebugEnabled() ) { log.info( "base: " + base + " href: " + href ); } ... | protected URIResolver createURIResolver() { return new URIResolver() { public Source resolve(String href, String base) throws TransformerException { if (log.isDebugEnabled() ) { log.debug( "base: " + base + " href: " + href ); } ... | 1,112,596 |
protected URIResolver createURIResolver() { return new URIResolver() { public Source resolve(String href, String base) throws TransformerException { if (log.isDebugEnabled() ) { log.info( "base: " + base + " href: " + href ); } ... | protected URIResolver createURIResolver() { return new URIResolver() { public Source resolve(String href, String base) throws TransformerException { if (log.isDebugEnabled() ) { log.info( "base: " + base + " href: " + href ); } ... | 1,112,597 |
public Source resolve(String href, String base) throws TransformerException { if (log.isDebugEnabled() ) { log.info( "base: " + base + " href: " + href ); } // pass if we don't have a syste... | public Source resolve(String href, String base) throws TransformerException { if (log.isDebugEnabled() ) { log.debug( "base: " + base + " href: " + href ); } // pass if we don't have a syst... | 1,112,598 |
public Source resolve(String href, String base) throws TransformerException { if (log.isDebugEnabled() ) { log.info( "base: " + base + " href: " + href ); } // pass if we don't have a syste... | public Source resolve(String href, String base) throws TransformerException { if (log.isDebugEnabled() ) { log.info( "base: " + base + " href: " + href ); } // pass if we don't have a syste... | 1,112,599 |
public void doTag(XMLOutput output) throws Exception { Document xmlDocument = this.getXmlDocument(output); Document xslDocument = this.parse(this.xsl); tf.setURIResolver(createURIResolver()); Transformer transformer = tf.newTransformer(new DocumentSource(xslDocument)); DocumentSou... | public void doTag(XMLOutput output) throws Exception { Document xmlDocument = this.getXmlDocument(output); Document xslDocument = this.parse(this.xsl); tf.setURIResolver(createURIResolver()); Transformer transformer = tf.newTransformer(new DocumentSource(xslDocument)); DocumentSou... | 1,112,600 |
public void doTag(XMLOutput output) throws Exception { Document xmlDocument = this.getXmlDocument(output); Document xslDocument = this.parse(this.xsl); tf.setURIResolver(createURIResolver()); Transformer transformer = tf.newTransformer(new DocumentSource(xslDocument)); DocumentSou... | public void doTag(XMLOutput output) throws Exception { Document xmlDocument = this.getXmlDocument(output); Document xslDocument = this.parse(this.xsl); tf.setURIResolver(createURIResolver()); Transformer transformer = tf.newTransformer(new DocumentSource(xslDocument)); DocumentSou... | 1,112,601 |
public void doTag(XMLOutput output) throws Exception { Document xmlDocument = this.getXmlDocument(output); Document xslDocument = this.parse(this.xsl); tf.setURIResolver(createURIResolver()); Transformer transformer = tf.newTransformer(new DocumentSource(xslDocument)); DocumentSou... | public void doTag(XMLOutput output) throws Exception { Document xmlDocument = this.getXmlDocument(output); Document xslDocument = this.parse(this.xsl); tf.setURIResolver(createURIResolver()); Transformer transformer = tf.newTransformer(new DocumentSource(xslDocument)); this.tf.set... | 1,112,602 |
public void doTag(XMLOutput output) throws Exception { Document xmlDocument = this.getXmlDocument(output); Document xslDocument = this.parse(this.xsl); tf.setURIResolver(createURIResolver()); Transformer transformer = tf.newTransformer(new DocumentSource(xslDocument)); DocumentSou... | public void doTag(XMLOutput output) throws Exception { Document xmlDocument = this.getXmlDocument(output); Document xslDocument = this.parse(this.xsl); tf.setURIResolver(createURIResolver()); Transformer transformer = tf.newTransformer(new DocumentSource(xslDocument)); DocumentSou... | 1,112,603 |
public void doTag(XMLOutput output) throws Exception { Document xmlDocument = this.getXmlDocument(output); Document xslDocument = this.parse(this.xsl); tf.setURIResolver(createURIResolver()); Transformer transformer = tf.newTransformer(new DocumentSource(xslDocument)); DocumentSou... | public void doTag(XMLOutput output) throws Exception { Document xmlDocument = this.getXmlDocument(output); Document xslDocument = this.parse(this.xsl); tf.setURIResolver(createURIResolver()); Transformer transformer = tf.newTransformer(new DocumentSource(xslDocument)); DocumentSou... | 1,112,604 |
public void doTag(XMLOutput output) throws Exception { Document xmlDocument = this.getXmlDocument(output); Document xslDocument = this.parse(this.xsl); tf.setURIResolver(createURIResolver()); Transformer transformer = tf.newTransformer(new DocumentSource(xslDocument)); DocumentSou... | public void doTag(XMLOutput output) throws Exception { Document xmlDocument = this.getXmlDocument(output); Document xslDocument = this.parse(this.xsl); tf.setURIResolver(createURIResolver()); Transformer transformer = tf.newTransformer(new DocumentSource(xslDocument)); DocumentSou... | 1,112,605 |
public void doTag(XMLOutput output) throws Exception { Document xmlDocument = this.getXmlDocument(output); Document xslDocument = this.parse(this.xsl); tf.setURIResolver(createURIResolver()); Transformer transformer = tf.newTransformer(new DocumentSource(xslDocument)); DocumentSou... | public void doTag(XMLOutput output) throws Exception { Document xmlDocument = this.getXmlDocument(output); Document xslDocument = this.parse(this.xsl); tf.setURIResolver(createURIResolver()); Transformer transformer = tf.newTransformer(new DocumentSource(xslDocument)); DocumentSou... | 1,112,606 |
void saveDprimeToText(){ try{ String saveDprimeName = infileName + ".LDout"; new TextMethods().saveDprimeToText(theData.dPrimeTable, saveDprimeName); }catch (IOException ioexec){ JOptionPane.showMessageDialog(this, ioexec.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); } } | void saveDprimeToText(){ try{ String saveDprimeName = infileName + ".LDout"; new TextMethods().saveDprimeToText(theData.dPrimeTable, saveDprimeName); }catch (IOException ioexec){ JOptionPane.showMessageDialog(this, ioexec.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); } } | 1,112,608 |
void saveHapsToText(){ //first we see what files are in this directory File currentDir = new File(System.getProperty("user.dir")); int highCount = 0; String[] filez = currentDir.list(); for (int i = 0; i < filez.length; i++){ if (filez[i].startsWith("haptxt")){ if (filez[i].endsWith(infileName)){ //get co... | void saveHapsToText(){ //first we see what files are in this directory File currentDir = new File(System.getProperty("user.dir")); int highCount = 0; String[] filez = currentDir.list(); for (int i = 0; i < filez.length; i++){ if (filez[i].startsWith("haptxt")){ if (filez[i].endsWith(infileName)){ //get co... | 1,112,610 |
void saveHapsToText(){ //first we see what files are in this directory File currentDir = new File(System.getProperty("user.dir")); int highCount = 0; String[] filez = currentDir.list(); for (int i = 0; i < filez.length; i++){ if (filez[i].startsWith("haptxt")){ if (filez[i].endsWith(infileName)){ //get co... | void saveHapsToText(){ //first we see what files are in this directory File currentDir = new File(System.getProperty("user.dir")); int highCount = 0; String[] filez = currentDir.list(); for (int i = 0; i < filez.length; i++){ if (filez[i].startsWith("haptxt")){ if (filez[i].endsWith(infileName)){ //get co... | 1,112,611 |
public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command==RAW_DATA){ load(PED); }else if (command == PHASED_DATA){ load(HAPS); }else if (command == HAPMAP_DATA){ load(HMP); }else if (command == BROWSE_GENO){ ... | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command==RAW_DATA){ load(PED); }else if (command == PHASED_DATA){ load(HAPS); }else if (command == HAPMAP_DATA){ load(HMP); }else if (command == BROWSE_GENO){ ... | 1,112,612 |
public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command==RAW_DATA){ load(PED); }else if (command == PHASED_DATA){ load(HAPS); }else if (command == HAPMAP_DATA){ load(HMP); }else if (command == BROWSE_GENO){ ... | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command==RAW_DATA){ load(PED); }else if (command == PHASED_DATA){ load(HAPS); }else if (command == HAPMAP_DATA){ load(HMP); }else if (command == BROWSE_GENO){ ... | 1,112,613 |
public Script getBody() { if ( isTrim() && ! hasTrimmed ) { trimBody(); } return body; } | public Script getBody() { if ( isTrim() && ! hasTrimmed ) { trimBody(); } return body; } | 1,112,614 |
protected String getBodyText() throws Exception { // XXX: could maybe optimise this later on by having a pool of buffers StringWriter writer = new StringWriter(); getBody().run(context, XMLOutput.createXMLOutput(writer)); return writer.toString(); } | protected String getBodyText() throws Exception { // XXX: could maybe optimise this later on by having a pool of buffers StringWriter writer = new StringWriter(); invokeBody(XMLOutput.createXMLOutput(writer)); return writer.toString(); } | 1,112,615 |
protected void invokeBody(XMLOutput output) throws Exception { getBody().run(context, output); } | protected void invokeBody(XMLOutput output) throws Exception { if ( isTrim() && ! hasTrimmed ) { trimBody(); } invokeBody(output); } | 1,112,616 |
private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0, haploid = 0; Hashtable founderGenoCount = new Hashtable(); ... | private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0, haploid = 0; Hashtable founderGenoCount = new Hashtable(); ... | 1,112,617 |
private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0, haploid = 0; Hashtable founderGenoCount = new Hashtable(); ... | private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0, haploid = 0; Hashtable founderGenoCount = new Hashtable(); ... | 1,112,618 |
private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0, haploid = 0; Hashtable founderGenoCount = new Hashtable(); ... | private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0, haploid = 0; Hashtable founderGenoCount = new Hashtable(); ... | 1,112,619 |
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