rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k |
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pageFormat = job.defaultPage(); | pageFormat = new PageFormat(); pageFormat.setPaper(new Paper()); pageFormat.getPaper().setImageableArea(50, 50, pageFormat.getWidth()-(50*2), pageFormat.getHeight()-(50*2)); | public PrintPanel(PlayPen pp) { super(); setOpaque(true); setLayout(new BoxLayout(this, BoxLayout.X_AXIS)); this.pp = pp; add(new PrintPreviewPanel()); job = PrinterJob.getPrinterJob(); jobAttributes = new HashPrintRequestAttributeSet(); pageFormat = job.defaultPage(); JPanel formPanel = new JPanel(new Fo... |
setPageFormat(job.pageDialog(jobAttributes)); | setPageFormat(job.pageDialog(pageFormat)); | public PrintPanel(PlayPen pp) { super(); setOpaque(true); setLayout(new BoxLayout(this, BoxLayout.X_AXIS)); this.pp = pp; add(new PrintPreviewPanel()); job = PrinterJob.getPrinterJob(); jobAttributes = new HashPrintRequestAttributeSet(); pageFormat = job.defaultPage(); JPanel formPanel = new JPanel(new Fo... |
pageCountLabel = new JLabel("Page Count: "+getNumberOfPages()); formPanel.add(pageCountLabel); | public PrintPanel(PlayPen pp) { super(); setOpaque(true); setLayout(new BoxLayout(this, BoxLayout.X_AXIS)); this.pp = pp; add(new PrintPreviewPanel()); job = PrinterJob.getPrinterJob(); jobAttributes = new HashPrintRequestAttributeSet(); pageFormat = job.defaultPage(); JPanel formPanel = new JPanel(new Fo... | |
setPageFormat(job.pageDialog(jobAttributes)); | setPageFormat(job.pageDialog(pageFormat)); | public void actionPerformed(ActionEvent e) { setPageFormat(job.pageDialog(jobAttributes)); } |
g2.drawString("Page "+pageIndex+" of "+(pagesAcross*pagesDown), (float) (leftMargin+10.0), (float) (topMargin+10.0)); logger.debug("Printing page "+(pageIndex+1)+" of "+(pagesAcross*pagesDown) +" at ["+col+","+row+"]"); | AffineTransform backupXform = g2.getTransform(); | public int print(Graphics graphics, PageFormat pageFormat, int pageIndex) throws PrinterException { Graphics2D g2 = (Graphics2D) graphics; if (pageIndex < pagesAcross*pagesDown) { double leftMargin = pageFormat.getImageableX(); double topMargin = pageFormat.getImageableY(); double width = pageFormat.getImagea... |
g2.setTransform(backupXform); if (printPageNumbersBox.isSelected()) { g2.drawString("Page "+(pageIndex+1)+" of "+(pagesAcross*pagesDown), (float) (leftMargin+10.0), (float) (topMargin+10.0)); } | public int print(Graphics graphics, PageFormat pageFormat, int pageIndex) throws PrinterException { Graphics2D g2 = (Graphics2D) graphics; if (pageIndex < pagesAcross*pagesDown) { double leftMargin = pageFormat.getImageableX(); double topMargin = pageFormat.getImageableY(); double width = pageFormat.getImagea... | |
pageCountLabel.setText("Page Count: "+getNumberOfPages()); | public void validateLayout() { // widths are in points (1/72 inch units) Dimension ppSize = pp.getPreferredSize(); double ppWidth = ppSize.width; double ppHeight = ppSize.height; double paperWidth = pageFormat.getImageableWidth(); double paperHeight = pageFormat.getImageableHeight(); pagesAcross = (int) Math.... | |
int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ | HaploviewTab tab = (HaploviewTab)tabs.getSelectedComponent(); if (tab.equals(ldTab) || tab.equals(hapsTab)){ | public void stateChanged(ChangeEvent e) { if (tabs.getSelectedIndex() != -1){ window.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ ex... |
}else if (tabNum == VIEW_ASSOC_NUM || tabNum == VIEW_CHECK_NUM || tabNum == VIEW_TAGGER_NUM){ | }else if (tab.equals(associationTab) || tab.equals(checkTab) || tab.equals(taggerTab)){ | public void stateChanged(ChangeEvent e) { if (tabs.getSelectedIndex() != -1){ window.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ ex... |
if (tabNum == VIEW_ASSOC_NUM){ JTabbedPane metaAssoc= (JTabbedPane)tabs.getComponentAt(tabNum); | if (tab.equals(associationTab)){ JTabbedPane metaAssoc = (JTabbedPane)associationTab.getComponent(0); | public void stateChanged(ChangeEvent e) { if (tabs.getSelectedIndex() != -1){ window.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ ex... |
if (tabNum == VIEW_D_NUM){ | if (tab.equals(ldTab)){ | public void stateChanged(ChangeEvent e) { if (tabs.getSelectedIndex() != -1){ window.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ ex... |
export(tabs.getSelectedIndex(), PNG_MODE, 0, Chromosome.getUnfilteredSize()); | export((HaploviewTab)tabs.getSelectedComponent(), PNG_MODE, 0, Chromosome.getUnfilteredSize()); | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command.equals(READ_GENOTYPES)){ ReadDataDialog readDialog = new ReadDataDialog("Open new data", this); readDialog.pack(); readDialog.setVisible(true); } else if (command.equ... |
export(tabs.getSelectedIndex(), TXT_MODE, 0, Chromosome.getUnfilteredSize()); | export((HaploviewTab)tabs.getSelectedComponent(), TXT_MODE, 0, Chromosome.getUnfilteredSize()); | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command.equals(READ_GENOTYPES)){ ReadDataDialog readDialog = new ReadDataDialog("Open new data", this); readDialog.pack(); readDialog.setVisible(true); } else if (command.equ... |
if (tabs.getSelectedIndex() == VIEW_HAP_NUM){ | if (tabs.getSelectedComponent().equals(hapsTab)){ | public void changeBlocks(int method){ if (method == BLOX_NONE || method == BLOX_CUSTOM){ blockMenuItems[BLOX_CUSTOM].setSelected(true); } if (method != BLOX_CUSTOM){ theData.guessBlocks(method); } dPrimeDisplay.repaint(); currentBlockDef = method; ... |
void export(int tabNum, int format, int start, int stop){ | void export(HaploviewTab tab, int format, int start, int stop){ | void export(int tabNum, int format, int start, int stop){ fc.setSelectedFile(new File("")); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION){ File outfile = fc.getSelectedFile(); if (format == PNG_MODE || format == COMPRESSED_PNG_MODE){ BufferedImage ima... |
if (tabNum == VIEW_D_NUM){ | if (tab.equals(ldTab)){ | void export(int tabNum, int format, int start, int stop){ fc.setSelectedFile(new File("")); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION){ File outfile = fc.getSelectedFile(); if (format == PNG_MODE || format == COMPRESSED_PNG_MODE){ BufferedImage ima... |
}else if (tabNum == VIEW_HAP_NUM){ | }else if (tab.equals(hapsTab)){ | void export(int tabNum, int format, int start, int stop){ fc.setSelectedFile(new File("")); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION){ File outfile = fc.getSelectedFile(); if (format == PNG_MODE || format == COMPRESSED_PNG_MODE){ BufferedImage ima... |
}else if (tabNum == VIEW_CHECK_NUM){ | }else if (tab.equals(checkTab)){ | void export(int tabNum, int format, int start, int stop){ fc.setSelectedFile(new File("")); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION){ File outfile = fc.getSelectedFile(); if (format == PNG_MODE || format == COMPRESSED_PNG_MODE){ BufferedImage ima... |
}else if (tabNum == VIEW_ASSOC_NUM){ Component selectedTab = ((JTabbedPane)tabs.getComponent(tabNum)).getSelectedComponent(); | }else if (tab.equals(associationTab)){ Component selectedTab = ((JTabbedPane)associationTab.getComponent(0)).getSelectedComponent(); | void export(int tabNum, int format, int start, int stop){ fc.setSelectedFile(new File("")); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION){ File outfile = fc.getSelectedFile(); if (format == PNG_MODE || format == COMPRESSED_PNG_MODE){ BufferedImage ima... |
}else if (tabNum == VIEW_TAGGER_NUM){ | }else if (tab.equals(taggerTab)){ | void export(int tabNum, int format, int start, int stop){ fc.setSelectedFile(new File("")); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION){ File outfile = fc.getSelectedFile(); if (format == PNG_MODE || format == COMPRESSED_PNG_MODE){ BufferedImage ima... |
if (dPrimeDisplay != null && tabs.getSelectedIndex() == VIEW_D_NUM){ | if (dPrimeDisplay != null && tabs.getSelectedComponent().equals(ldTab)){ | void readAnalysisFile(File inFile){ try{ theData.readAnalysisTrack(inFile); }catch (HaploViewException hve){ JOptionPane.showMessageDialog(this, hve.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); }catch (IOE... |
int currentTab = VIEW_D_NUM; | HaploviewTab currentTab = ldTab; | void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files re... |
JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); | void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files re... | |
panel.add(dPrimeScroller); tabs.addTab(viewItems[VIEW_D_NUM], panel); | ldTab = new HaploviewTab(dPrimeScroller); tabs.addTab(VIEW_DPRIME, ldTab); | void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files re... |
panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); | void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files re... | |
panel.add(hapScroller); panel.add(hdc); tabs.addTab(viewItems[VIEW_HAP_NUM], panel); | hapsTab = new HaploviewTab(hapScroller); hapsTab.add(hdc); tabs.addTab(VIEW_HAPLOTYPES, hapsTab); | void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files re... |
JPanel metaCheckPanel = new JPanel(); metaCheckPanel.setLayout(new BoxLayout(metaCheckPanel, BoxLayout.Y_AXIS)); metaCheckPanel.add(checkPanel); | checkTab = new HaploviewTab(checkPanel); | void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files re... |
metaCheckPanel.add(cdc); tabs.addTab(viewItems[VIEW_CHECK_NUM], metaCheckPanel); | checkTab.add(cdc); tabs.addTab(VIEW_CHECK_PANEL, checkTab); | void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files re... |
currentTab=VIEW_CHECK_NUM; } taggerConfigPanel = new TaggerConfigPanel(theData); JPanel metaTagPanel = new JPanel(); metaTagPanel.setLayout(new BoxLayout(metaTagPanel,BoxLayout.Y_AXIS)); metaTagPanel.add(taggerConfigPanel); JTabbedPane tagTabs = new JTabbedPane(); tagTabs.add("Configuration",metaTagPanel); JPanel... | currentTab=checkTab; } if (theData.infoKnown){ taggerConfigPanel = new TaggerConfigPanel(theData); JPanel metaTagPanel = new JPanel(); metaTagPanel.setLayout(new BoxLayout(metaTagPanel,BoxLayout.Y_AXIS)); metaTagPanel.add(taggerConfigPanel); JTabbedPane tagTabs = new JTabbedPane(); tagTabs.add("Configuration",met... | void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files re... |
tabs.addTab(VIEW_ASSOC, metaAssoc); | associationTab = new HaploviewTab(metaAssoc); tabs.addTab(VIEW_ASSOC, associationTab); | void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files re... |
tabs.setSelectedIndex(currentTab); | tabs.setSelectedComponent(currentTab); | void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files re... |
int currentTab = VIEW_D_NUM; | HaploviewTab currentTab = ldTab; | public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ... |
JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); | public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ... | |
panel.add(dPrimeScroller); tabs.addTab(viewItems[VIEW_D_NUM], panel); | ldTab = new HaploviewTab(dPrimeScroller); tabs.addTab(VIEW_DPRIME, ldTab); | public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ... |
panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); | public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ... | |
panel.add(hapScroller); panel.add(hdc); tabs.addTab(viewItems[VIEW_HAP_NUM], panel); | hapsTab = new HaploviewTab(hapScroller); hapsTab.add(hdc); tabs.addTab(VIEW_HAPLOTYPES, hapsTab); | public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ... |
JPanel metaCheckPanel = new JPanel(); metaCheckPanel.setLayout(new BoxLayout(metaCheckPanel, BoxLayout.Y_AXIS)); metaCheckPanel.add(checkPanel); | checkTab = new HaploviewTab(checkPanel); | public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ... |
metaCheckPanel.add(cdc); | checkTab.add(cdc); | public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ... |
tabs.addTab(viewItems[VIEW_CHECK_NUM], metaCheckPanel); | tabs.addTab(VIEW_CHECK_PANEL, checkTab); | public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ... |
currentTab=VIEW_CHECK_NUM; | currentTab=checkTab; | public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ... |
taggerConfigPanel = new TaggerConfigPanel(theData); | if (theData.infoKnown){ taggerConfigPanel = new TaggerConfigPanel(theData); | public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ... |
resMetaPanel.add(tagResultsPanel); tagTabs.addTab("Results",resMetaPanel); tabs.addTab(VIEW_TAGGER,tagTabs); viewMenuItems[VIEW_TAGGER_NUM].setEnabled(true); | resMetaPanel.add(tagResultsPanel); tagTabs.addTab("Results",resMetaPanel); taggerTab = new HaploviewTab(tagTabs); tabs.addTab(VIEW_TAGGER,taggerTab); viewMenuItems[VIEW_TAGGER_NUM].setEnabled(true); } | public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ... |
tabs.addTab(VIEW_ASSOC, metaAssoc); | associationTab = new HaploviewTab(metaAssoc); tabs.addTab(VIEW_ASSOC, associationTab); | public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ... |
tabs.setSelectedIndex(currentTab); | tabs.setSelectedComponent(currentTab); | public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first ... |
Container checkTab = (Container)tabs.getComponentAt(VIEW_CHECK_NUM); | void readMarkers(File inputFile, String[][] hminfo){ try { theData.prepareMarkerInput(inputFile, hminfo); if (theData.infoKnown){ analysisItem.setEnabled(true); gbrowseItem.setEnabled(true); spacingItem.setEnabled(true); }else{ ... | |
TaskSource tag = (TaskSource) findAncestorWithClass( TaskSource.class ); if ( tag == null ) { throw new JellyException( "You should only use Ant DataType tags within an Ant Task" ); } Object task = tag.getTaskObject(); Object dataType = getDataType(); | public void doTag(XMLOutput output) throws Exception { TaskSource tag = (TaskSource) findAncestorWithClass( TaskSource.class ); if ( tag == null ) { throw new JellyException( "You should only use Ant DataType tags within an Ant Task" ); } Object task = tag.getT... | |
DynaBean dynaBean = tag.getDynaBean(); DynaClass dynaClass = dynaBean.getDynaClass(); DynaProperty dynaProperty = dynaClass.getDynaProperty(name); if ( dynaProperty != null ) { dynaBean.set( name, dataType ); | getBody().run(context, output); AntTagSupport parentTag = (AntTagSupport) findAncestorWithClass( AntTagSupport.class); if ( parentTag == null ) { return; | public void doTag(XMLOutput output) throws Exception { TaskSource tag = (TaskSource) findAncestorWithClass( TaskSource.class ); if ( tag == null ) { throw new JellyException( "You should only use Ant DataType tags within an Ant Task" ); } Object task = tag.getT... |
else { String methodName = "add" + name.substring(0,1).toUpperCase() + name.substring(1); Class taskClass = task.getClass(); Class[] parameterTypes = new Class[] { dataType.getClass() }; Method method = MethodUtils.getAccessibleMethod( taskClass, methodName, parameterTypes ); if ( method == null ) { throw new JellyExc... | Object targetObj = parentTag.getObject(); DataType dataType = getDataType(); if ( targetObj == null ) { return; } if( parentTag instanceof DynaBeanTagSupport ) { DynaBean dynaBean = ((DynaBeanTagSupport)parent).getDynaBean(); DynaClass dynaClass = dynaBean.getDynaClass(); DynaProperty dynaProperty = dynaClass.g... | public void doTag(XMLOutput output) throws Exception { TaskSource tag = (TaskSource) findAncestorWithClass( TaskSource.class ); if ( tag == null ) { throw new JellyException( "You should only use Ant DataType tags within an Ant Task" ); } Object task = tag.getT... |
Object[] parameters = new Object[] { dataType }; method.invoke( task, parameters ); | } if ( targetObj instanceof Path && dataType instanceof Path ) { ((Path)targetObj).append( (Path)dataType ); return; | public void doTag(XMLOutput output) throws Exception { TaskSource tag = (TaskSource) findAncestorWithClass( TaskSource.class ); if ( tag == null ) { throw new JellyException( "You should only use Ant DataType tags within an Ant Task" ); } Object task = tag.getT... |
getBody().run(context, output); | try { ih.storeElement( getAntProject(), targetObj, dataType, getName() ); } catch (Exception e) { String dataTypeName = dataType.getClass().getName(); String baseName = dataTypeName.substring( dataTypeName.lastIndexOf( "." ) + 1 ); String methName = "add" + baseName; Method m = MethodUtils.getAccessibleMethod( target... | public void doTag(XMLOutput output) throws Exception { TaskSource tag = (TaskSource) findAncestorWithClass( TaskSource.class ); if ( tag == null ) { throw new JellyException( "You should only use Ant DataType tags within an Ant Task" ); } Object task = tag.getT... |
public Object getDataType() { | public DataType getDataType() { | public Object getDataType() { return dataType; } |
public void setDataType(Object dataType) { | public void setDataType(DataType dataType) { | public void setDataType(Object dataType) { this.dataType = dataType; setDynaBean( new ConvertingWrapDynaBean(dataType) ); } |
suite.addTestSuite(TestSQLDatabase.class); | suite.addTestSuite(SQLObjectTest.class); suite.addTest(TestSQLDatabase.suite()); suite.addTest(TestSQLTable.suite()); suite.addTest(TestSQLColumn.suite()); suite.addTestSuite(TestSQLRelationship.class); | public static Test suite() { TestSuite suite = new TestSuite("Test for regress"); //$JUnit-BEGIN$ suite.addTestSuite(TestSQLDatabase.class); suite.addTestSuite(ArchitectExceptionTest.class); suite.addTestSuite(SaveLoadTest.class); suite.addTestSuite(PLDotIniTest.class); suite.addTest(TestSQLColumn.suite()); su... |
suite.addTest(TestSQLColumn.suite()); | public static Test suite() { TestSuite suite = new TestSuite("Test for regress"); //$JUnit-BEGIN$ suite.addTestSuite(TestSQLDatabase.class); suite.addTestSuite(ArchitectExceptionTest.class); suite.addTestSuite(SaveLoadTest.class); suite.addTestSuite(PLDotIniTest.class); suite.addTest(TestSQLColumn.suite()); su... | |
suite.addTestSuite(SQLObjectTest.class); suite.addTestSuite(TestSQLTable.class); suite.addTestSuite(TestSQLRelationship.class); | public static Test suite() { TestSuite suite = new TestSuite("Test for regress"); //$JUnit-BEGIN$ suite.addTestSuite(TestSQLDatabase.class); suite.addTestSuite(ArchitectExceptionTest.class); suite.addTestSuite(SaveLoadTest.class); suite.addTestSuite(PLDotIniTest.class); suite.addTest(TestSQLColumn.suite()); su... | |
SimpleDateFormat fmt = new SimpleDateFormat( "yyyy" ); | System.err.println( "getNewFname " + date + " " + strExtension ); SimpleDateFormat fmt = new SimpleDateFormat( "yyyy" ); | private File getNewFname( java.util.Date date, String strExtension ) { SimpleDateFormat fmt = new SimpleDateFormat( "yyyy" ); String strYear = fmt.format( date ); fmt.applyPattern( "yyyyMM" ); String strMonth = fmt.format( date ); fmt.applyPattern( "yyyyMMdd" ); String strDate = fmt.format( date ); File yearDir = n... |
yearDir.mkdir(); | System.err.println( "making yeardir" ); if ( !yearDir.mkdir() ) { log.error( "Failed to create directory " + yearDir.getAbsoluteFile() ); } | private File getNewFname( java.util.Date date, String strExtension ) { SimpleDateFormat fmt = new SimpleDateFormat( "yyyy" ); String strYear = fmt.format( date ); fmt.applyPattern( "yyyyMM" ); String strMonth = fmt.format( date ); fmt.applyPattern( "yyyyMMdd" ); String strDate = fmt.format( date ); File yearDir = n... |
monthDir.mkdir(); | System.err.println( "making yeardir" ); if ( !monthDir.mkdir() ) { log.error( "Failed to create " + monthDir.getAbsolutePath() ); } | private File getNewFname( java.util.Date date, String strExtension ) { SimpleDateFormat fmt = new SimpleDateFormat( "yyyy" ); String strYear = fmt.format( date ); fmt.applyPattern( "yyyyMM" ); String strMonth = fmt.format( date ); fmt.applyPattern( "yyyyMMdd" ); String strDate = fmt.format( date ); File yearDir = n... |
Vector addMe = new Vector(); | static Vector do4Gamete(DPrimeTable dPrime){ Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first make a list of marker pairs with < 4 gametes, sorted by distance apart for (int x = 0; x < Chromosome.getSize()-1; x++){ for (int y = x+1; y < Chromosome.getSi... | |
addMe.add(String.valueOf(x)); addMe.add(String.valueOf(y)); addMe.add(String.valueOf(sep)); if (strongPairs.size() == 0){ strongPairs.add(addMe); }else{ boolean unplaced = true; for (int v = 0; v < strongPairs.size(); v ++){ if (sep >= Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(2))){ strongP... | strongPairs.add(new MarkerInfo(x,y,sep)); | static Vector do4Gamete(DPrimeTable dPrime){ Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first make a list of marker pairs with < 4 gametes, sorted by distance apart for (int x = 0; x < Chromosome.getSize()-1; x++){ for (int y = x+1; y < Chromosome.getSi... |
int first = Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(0)); int last = Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(1)); | int first =((MarkerInfo)strongPairs.elementAt(v)).marker1; int last =((MarkerInfo)strongPairs.elementAt(v)).marker2; | static Vector do4Gamete(DPrimeTable dPrime){ Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first make a list of marker pairs with < 4 gametes, sorted by distance apart for (int x = 0; x < Chromosome.getSize()-1; x++){ for (int y = x+1; y < Chromosome.getSi... |
if (numGam > 3){ isABlock = false; } | if (numGam > 3){ isABlock = false; break OUTER; } | static Vector do4Gamete(DPrimeTable dPrime){ Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first make a list of marker pairs with < 4 gametes, sorted by distance apart for (int x = 0; x < Chromosome.getSize()-1; x++){ for (int y = x+1; y < Chromosome.getSi... |
Vector addMe = new Vector(); | static Vector doGabriel(DPrimeTable dPrime){ int numStrong = 0; int numRec = 0; int numInGroup = 0; Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first set up a filter of markers which fail the MAF threshhold boolean[] skipMarker = new boolean[Chromosome.getSi... | |
addMe.add(String.valueOf(x)); addMe.add(String.valueOf(y)); addMe.add(String.valueOf(sep)); if (strongPairs.size() == 0){ strongPairs.add(addMe); }else{ boolean unplaced = true; for (int v = 0; v < strongPairs.size(); v ++){ if (sep >= Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(2))){ strongP... | strongPairs.add(new MarkerInfo(x,y,sep)); | static Vector doGabriel(DPrimeTable dPrime){ int numStrong = 0; int numRec = 0; int numInGroup = 0; Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first set up a filter of markers which fail the MAF threshhold boolean[] skipMarker = new boolean[Chromosome.getSi... |
int first = Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(0)); int last = Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(1)); int sep = Math.abs(Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(2))); | int first =((MarkerInfo)strongPairs.elementAt(v)).marker1; int last =((MarkerInfo)strongPairs.elementAt(v)).marker2; long sep = ((MarkerInfo)strongPairs.elementAt(v)).sep.longValue(); | static Vector doGabriel(DPrimeTable dPrime){ int numStrong = 0; int numRec = 0; int numInGroup = 0; Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first set up a filter of markers which fail the MAF threshhold boolean[] skipMarker = new boolean[Chromosome.getSi... |
ODMGXAWrapper txw = new ODMGXAWrapper(); PhotoFolder folder = new PhotoFolder(); folder.setName( name ); folder.setParentFolder( parent ); txw.lock( folder, Transaction.WRITE ); txw.commit(); return folder; | ODMGXAWrapper txw = new ODMGXAWrapper(); PhotoFolder folder = new PhotoFolder(); try { folder.setName( name ); folder.setParentFolder( parent ); txw.lock( folder, Transaction.WRITE ); } catch (IllegalArgumentException e ) { throw e; } finally { txw.commit(); } return folder; | public static PhotoFolder create( String name, PhotoFolder parent ) { ODMGXAWrapper txw = new ODMGXAWrapper(); PhotoFolder folder = new PhotoFolder(); folder.setName( name ); folder.setParentFolder( parent ); txw.lock( folder, Transaction.WRITE ); txw.commit(); return folder; } |
ODMGXAWrapper txw = new ODMGXAWrapper(); | checkStringProperty( "Name", v, NAME_LENGTH ); ODMGXAWrapper txw = new ODMGXAWrapper(); | public void setName(String v) { ODMGXAWrapper txw = new ODMGXAWrapper(); txw.lock( this, Transaction.WRITE ); this.name = v; modified(); txw.commit(); } |
} | private double getPValue(Hashtable parentHom, int parentHet) throws PedFileException{ //ie: 11 13 31 33 -> homA =1 homB = 1 parentHet=2 int homA=0, homB=0, num; double pvalue=0; Enumeration enu = parentHom.elements(); while(enu.hasMoreElements()){ num = Integer.parseInt((String)enu.nextElement()); if(homA>0) ... | |
if (diplotypes <= 0){ throw new PedFileException("No valid genotypes or no complete trios!"); } | private double hwCalculate(int obsAA, int obsAB, int obsBB) throws PedFileException{ //Calculates exact two-sided hardy-weinberg p-value. Parameters //are number of genotypes, number of rare alleles observed and //number of heterozygotes observed. // // (c) 2003 Jan Wigginton, Goncal... | |
public void addChild(Component component) { | public void addChild(Component component, Object constraints) { | public void addChild(Component component) { Object parent = getBean(); if ( parent instanceof JFrame && component instanceof JMenuBar ) { JFrame frame = (JFrame) parent; frame.setJMenuBar( (JMenuBar) component ); } else if ( parent instanceof RootPaneContainer ) { ... |
container.add( component ); | if (constraints != null) { container.add( component, constraints ); } else { container.add( component ); } | public void addChild(Component component) { Object parent = getBean(); if ( parent instanceof JFrame && component instanceof JMenuBar ) { JFrame frame = (JFrame) parent; frame.setJMenuBar( (JMenuBar) component ); } else if ( parent instanceof RootPaneContainer ) { ... |
else { Component component = getComponent(); if ( component != null ) { ComponentTag parentTag = (ComponentTag) findAncestorWithClass( ComponentTag.class ); if ( parentTag != null ) { parentTag.addChild(component); } else { throw new JellyException( "This tag must be used within a JellySwing widget tag or the 'var' att... | Component component = getComponent(); if ( component != null ) { ContainerTag parentTag = (ContainerTag) findAncestorWithClass( ContainerTag.class ); if ( parentTag != null ) { parentTag.addChild(component, getConstraint()); } else { if (var == null) { throw new JellyException( "The 'var' attribute must be specified or... | protected void processBean(String var, Object bean) throws Exception { if (var != null) { context.setVariable(var, bean); } else { Component component = getComponent(); if ( component != null ) { ComponentTag parentTag = (ComponentTag) findAncesto... |
} | } else if ( name.equalsIgnoreCase("background") || name.equalsIgnoreCase("foreground")) { Color c = null; if (value instanceof Color) { c = (Color) value; } else if (value != null) { c = (Color) ConvertUtils.convert( value.toString(), Color.class); } if (name.equalsIgnoreCase("background")) { component.setBackground(c... | protected void setBeanProperties(Object bean, Map attributes) throws Exception { for (Iterator iter = attributes.entrySet().iterator(); iter.hasNext(); ) { Map.Entry entry = (Map.Entry) iter.next(); String name = (String) entry.getKey(); Object value = entry.getValue(); ... |
} catch(Exception e){ if(e instanceof InstanceNotFoundException || e.getCause() instanceof InstanceNotFoundException){ logger.log(Level.INFO, "Specified object name/ attribute not found"); }else{ logger.log(Level.FINE, "Unknown error", e); } | public boolean isQualified(ApplicationConfig applicationConfig) { ServerConnection serverConnection = null; try { serverConnection = ServerConnector.getServerConnection(applicationConfig); String value = (String)serverConnection.getAttribute(objectName, ... | |
protected abstract void init(Map<String, String> properties); | public void init(Element qualifyingCriteria) { properties = new Properties(qualifyingCriteria); init(properties); } | protected abstract void init(Map<String, String> properties); |
return false; | return true; | public boolean canAccess(String acl){ String authorizedList = ACLStore.getInstance().getProperty(acl); if(authorizedList == null) return false; StringTokenizer tokenizer = new StringTokenizer(authorizedList, ","); while(tokenizer.hasMoreTokens()){ if(getUsername().e... |
if(authorizedList == null) return true; | public boolean canAccess(String acl){ boolean canAccess = false; String authorizedList = ACLStore.getInstance().getProperty(acl); StringTokenizer tokenizer = new StringTokenizer(authorizedList, ","); while(tokenizer.hasMoreTokens()){ if(getName().equals(tokenizer.nextToken()))... | |
public String computeDPrime(int a, int b, int c, int d, int e, double f){ | public PairwiseLinkage computeDPrime(int a, int b, int c, int d, int e, double f){ | public String computeDPrime(int a, int b, int c, int d, int e, double f){ int i,j,k,count,itmp; int low_i = 0; int high_i = 0; double[] nAA = new double[1]; double[] nBB = new double[1]; double[] nAB = new double[1]; double[] nBA = new double[1]; double[] pAA = new double[1]; double[] pBB = new double[1]; double[... |
String returnStr = new String(""); NumberFormat nf = NumberFormat.getInstance(); nf.setMinimumFractionDigits(2); nf.setMaximumFractionDigits(2); returnStr += nf.format(dprime); returnStr += "\t"; returnStr += nf.format(loglike1-loglike0); returnStr += "\t"; returnStr += nf.format(r2); returnStr += "\t"; | public String computeDPrime(int a, int b, int c, int d, int e, double f){ int i,j,k,count,itmp; int low_i = 0; int high_i = 0; double[] nAA = new double[1]; double[] nBB = new double[1]; double[] nAB = new double[1]; double[] nBA = new double[1]; double[] pAA = new double[1]; double[] pBB = new double[1]; double[... | |
returnStr += (double) low_i/100.0; returnStr += "\t"; returnStr += (double) high_i/100.0; return returnStr; | double[] freqarray = {pAA[0], pAB[0], pBB[0], pBA[0]}; PairwiseLinkage linkage = new PairwiseLinkage(roundDouble(dprime), roundDouble((loglike1-loglike0)), roundDouble(r2), ((double)low_i/100.0), ((double)high_i/100.0), freqarray); return linkage; | public String computeDPrime(int a, int b, int c, int d, int e, double f){ int i,j,k,count,itmp; int low_i = 0; int high_i = 0; double[] nAA = new double[1]; double[] nBB = new double[1]; double[] nAB = new double[1]; double[] nBA = new double[1]; double[] pAA = new double[1]; double[] pBB = new double[1]; double[... |
String[][] generateDPrimeTable(final Vector chromosomes){ | PairwiseLinkage[][] generateDPrimeTable(final Vector chromosomes){ | String[][] generateDPrimeTable(final Vector chromosomes){ numCompleted = 0; //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset String [][] dPrimeTable = new String[((Chromosome) chromosomes.firstElement()).size()][((Chromosome) chromosomes.firstElement()).size()]; int dou... |
String [][] dPrimeTable = new String[((Chromosome) chromosomes.firstElement()).size()][((Chromosome) chromosomes.firstElement()).size()]; | PairwiseLinkage[][] dPrimeTable = new PairwiseLinkage[((Chromosome) chromosomes.firstElement()).size()][((Chromosome) chromosomes.firstElement()).size()]; | String[][] generateDPrimeTable(final Vector chromosomes){ numCompleted = 0; //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset String [][] dPrimeTable = new String[((Chromosome) chromosomes.firstElement()).size()][((Chromosome) chromosomes.firstElement()).size()]; int dou... |
dPrimeTable[pos1][pos2] = "0\t0\t0\t0\t0"; | dPrimeTable[pos1][pos2] = new PairwiseLinkage(0,0,0,0,0,nullArray); | String[][] generateDPrimeTable(final Vector chromosomes){ numCompleted = 0; //calculating D prime requires the number of each possible 2 marker //haplotype in the dataset String [][] dPrimeTable = new String[((Chromosome) chromosomes.firstElement()).size()][((Chromosome) chromosomes.firstElement()).size()]; int dou... |
Vector guessBlocks(String[][] dPrime, int method){ | Vector guessBlocks(PairwiseLinkage[][] dPrime, int method){ | Vector guessBlocks(String[][] dPrime, int method){ Vector returnVec = new Vector(); switch(method){ case 0: returnVec = new FindBlocks(dPrime).doSFS(); break; case 1: returnVec = new FindBlocks(dPrime).doMJD(); break; } return returnVec; } |
case 1: returnVec = new FindBlocks(dPrime).doMJD(); break; | case 1: returnVec = new FindBlocks(dPrime).do4Gamete(); break; case 2: returnVec = new FindBlocks(dPrime).doMJD(); break; | Vector guessBlocks(String[][] dPrime, int method){ Vector returnVec = new Vector(); switch(method){ case 0: returnVec = new FindBlocks(dPrime).doSFS(); break; case 1: returnVec = new FindBlocks(dPrime).doMJD(); break; } return returnVec; } |
System.out.println(numa1 + " " + numa2); | int prepareMarkerInput(File infile) throws IOException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position String currentLine; Vector markers = new Vector(); //read the file: BufferedRead... | |
if (theData.dpTable.getLDStats(p,j+p).getLOD() >= Options.getTaggerLODCutoff()){ | PairwiseLinkage pl = theData.dpTable.getLDStats(p,j+p); if (pl != null && pl.getLOD() >= Options.getTaggerLODCutoff()){ | public TaggerController(HaploData hd, Vector included, Vector excluded, Vector sitesToCapture, int aggressionLevel) { theData = hd; taggerSNPs = new Vector(); snpHash = new Hashtable(); for(int i=0;i<sitesToCapture.size();i++) { SNP tempSNP = (SNP) s... |
tagger = new Tagger(taggerSNPs,includedSNPs,excludedSNPs, hac, Options.getTaggerRsqCutoff(), aggressionLevel); | tagger = new Tagger(taggerSNPs,includedSNPs,excludedSNPs, hac, Options.getTaggerRsqCutoff(), aggressionLevel, Options.getMaxDistance()); | public TaggerController(HaploData hd, Vector included, Vector excluded, Vector sitesToCapture, int aggressionLevel) { theData = hd; taggerSNPs = new Vector(); snpHash = new Hashtable(); for(int i=0;i<sitesToCapture.size();i++) { SNP tempSNP = (SNP) s... |
while(sitesToCapture.size() > 0) { potentialTags = new Vector(potentialTagByVarSeq.values()); if(potentialTags.size() == 0) { break; | if (findTags){ while(sitesToCapture.size() > 0) { potentialTags = new Vector(potentialTagByVarSeq.values()); if(potentialTags.size() == 0) { break; } Collections.sort(potentialTags,ptcomp); PotentialTag currentBestTag = (PotentialTag) potentialTags.lastElement(); HashSet newlyTagged = addTag(currentBestTag,pote... | public Vector findTags() { tags = new Vector(); untagged = new Vector(); taggedSoFar = 0; //potentialTagsHash stores the PotentialTag objects keyed on the corresponding sequences Hashtable potentialTagByVarSeq = new Hashtable(); PotentialTagComparator ptcomp = new Potential... |
Collections.sort(potentialTags,ptcomp); PotentialTag currentBestTag = (PotentialTag) potentialTags.lastElement(); HashSet newlyTagged = addTag(currentBestTag,potentialTagByVarSeq,sitesToCapture); countTagged += newlyTagged.size(); sitesToCapture.removeAll(newlyTagged); sitesToCapture.remove(currentBestTag.sequence); | public Vector findTags() { tags = new Vector(); untagged = new Vector(); taggedSoFar = 0; //potentialTagsHash stores the PotentialTag objects keyed on the corresponding sequences Hashtable potentialTagByVarSeq = new Hashtable(); PotentialTagComparator ptcomp = new Potential... | |
double numr, denom; if(counts == null) { numr = Math.pow(curHap.getTransCount() -curHap.getUntransCount() ,2) ; denom = curHap.getTransCount() + curHap.getUntransCount(); | double numr = Math.pow(curHap.getTransCount() + counts[3] + counts[7] + 2*counts[6] - (curHap.getUntransCount() + counts[1] + counts[5] + 2*counts[2]),2); double denom = (curHap.getTransCount() + curHap.getUntransCount() + counts[3] + counts[7] + counts[1] + counts[5] + 4*(counts[2] + counts[6])); | protected void calculateChiSquares() { chiSquares = new Vector(); pValues = new Vector(); if (Options.getAssocTest() == ASSOC_TRIO) { Iterator faitr = filteredAlleles.iterator(); while(faitr.hasNext()) { if(Options.getTdtType() == TDT_STD) { ... |
}else{ numr = Math.pow(curHap.getTransCount() + counts[3] + counts[7] + 2*counts[6] - (curHap.getUntransCount() + counts[1] + counts[5] + 2*counts[2]),2); denom = (curHap.getTransCount() + curHap.getUntransCount() + counts[3] + counts[7] + counts[1] + counts[5] + 4*(counts[2] + counts[6])); } | protected void calculateChiSquares() { chiSquares = new Vector(); pValues = new Vector(); if (Options.getAssocTest() == ASSOC_TRIO) { Iterator faitr = filteredAlleles.iterator(); while(faitr.hasNext()) { if(Options.getTdtType() == TDT_STD) { ... | |
throw new PedFileException("Column number mismatch in pedfile. line " + (numLines+1)); | throw new PedFileException("Column number mismatch in pedfile. line " + (k+1)); | public void parseLinkage(Vector pedigrees) throws PedFileException { int colNum = -1; boolean withOptionalColumn = false; int numMarkers = 0; boolean genoError = false; int numLines = pedigrees.size(); if (numLines == 0){ throw new PedFileException("Data format e... |
throw new PedFileException("Incorrect number of fields on line " + (numLines+1)); | throw new PedFileException("Incorrect number of fields on line " + (k+1)); | public void parseLinkage(Vector pedigrees) throws PedFileException { int colNum = -1; boolean withOptionalColumn = false; int numMarkers = 0; boolean genoError = false; int numLines = pedigrees.size(); if (numLines == 0){ throw new PedFileException("Data format e... |
throw new PedFileException("Pedfile error: invalid gender or affected status on line " + (numLines+1)); | throw new PedFileException("Pedfile error: invalid gender or affected status on line " + (k+1)); | public void parseLinkage(Vector pedigrees) throws PedFileException { int colNum = -1; boolean withOptionalColumn = false; int numMarkers = 0; boolean genoError = false; int numLines = pedigrees.size(); if (numLines == 0){ throw new PedFileException("Data format e... |
throw new PedFileException("Pedigree file input error: invalid genotype on line " + (numLines+1) ); | throw new PedFileException("Pedigree file input error: invalid genotype on line " + (k+1) ); | public void parseLinkage(Vector pedigrees) throws PedFileException { int colNum = -1; boolean withOptionalColumn = false; int numMarkers = 0; boolean genoError = false; int numLines = pedigrees.size(); if (numLines == 0){ throw new PedFileException("Data format e... |
throw new JellyException(e); | throw new JellyException("Unable to create expression: " + text, e); | public Expression createExpression(String text) throws JellyException {/* org.apache.commons.jexl.Expression expr = org.apache.commons.jexl.ExpressionFactory.createExpression(text); if ( isSupportAntVariables() ) { expr.addPostResolver(new FlatResolve... |
tSpec.setDisplayName(dbcs.getDisplayName()); | public void actionPerformed(ActionEvent e) { logger.debug("Setting data source of "+db+" to "+dbcs); // copy over the values from the selected DB. ArchitectDataSource tSpec = db.getDataSource(); tSpec.setDriverClass(dbcs.getDriverClass()); tSpec.setUrl(dbcs.getUrl()); tSpec.setUser(dbcs.getUser()); tSpec.setP... | |
output.append(String.valueOf((char) ch)); | msg.append(String.valueOf((char) ch)); if ( ch == '\n' ) { output.append(msg.toString()); output.setCaretPosition(output.getText().length()); msg.delete(0,msg.length()); } } if ( msg.length() > 0 ) { output.append(msg.toString()); output.setCaretPosition(output.getText().length()); | public void run() { int ch; try { while ( (ch = is.read()) >= 0) { output.append(String.valueOf((char) ch)); } } catch (IOException ex) { ex.printStackTrace(); } } |
abortButton = new JButton("Abort"); abortButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { proc.destroy(); | abortAction = new AbstractAction("Abort") { public void actionPerformed(ActionEvent e) { proc.destroy(); if ( output != null && output.isEnabled() ) { output.append("Aborted ..."); output.setEnabled(false); | public EngineExecPanel(String header, Process pr) { super(new BorderLayout()); proc = pr; abortButton = new JButton("Abort"); abortButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { proc.destroy(); } }); JPanel p = new JPanel(new FlowLayout(FlowLayout.CENTER))... |
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