rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k |
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Document xmlDocument = this.getXmlDocument(output); Document xslDocument = this.parse(this.xsl); | 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... | |
tf.setURIResolver(createURIResolver()); Transformer transformer = tf.newTransformer(new DocumentSource(xslDocument)); | if (null == this.getXslt()) { throw new IllegalArgumentException("The xslt attribute cannot be null"); } | 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... |
DocumentSource xmlDocSource = new DocumentSource(xmlDocument); | this.tf.setURIResolver(createURIResolver()); this.transformerHandler = this.tf.newTransformerHandler(this.getObjAsSAXSource(this.getXslt())); | 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... |
String var = getVar(); if (var == null) { | this.doNestedParamTag(output); XMLReader xmlReader = this.createXMLReader(); xmlReader.setContentHandler(this.transformerHandler); xmlReader.setProperty(LEXICAL_HANDLER_PROPERTY, this.transformerHandler); String varName = this.getVar(); if (null == varName) { | 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... |
Result result = createSAXResult(output); transformer.transform(xmlDocSource, result); | this.transformerHandler.setResult(this.createSAXResult(output)); xmlReader.parse(this.getXMLInputSource()); | 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... |
transformer.transform(xmlDocSource, result); | this.transformerHandler.setResult(result); xmlReader.parse(this.getXMLInputSource()); | 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... |
context.setVariable(var, transformedDoc); | this.context.setVariable(varName, transformedDoc); | 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... |
fc.setSelectedFile(null); | void doExportDPrime(){ int returnVal = fc.showSaveDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION){ try { int scaleSize = theData.dPrimeTable.length*30; DrawingMethods dm = new DrawingMethods(); BufferedImage image = new BufferedImage(scaleSize, scaleSize, BufferedImage.TYPE_3BYTE_BGR); dm.dPrime... | |
String saveDprimeName = infileName + ".LDout"; new TextMethods().saveDprimeToText(theData.dPrimeTable, saveDprimeName); | fc.setSelectedFile(null); int returnVal = fc.showSaveDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { new TextMethods().saveDprimeToText(theData.dPrimeTable, fc.getSelectedFile()); } | 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); } } |
fc.setSelectedFile(null); | void saveHapsPic(){ int returnVal = fc.showSaveDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION){ try { DrawingMethods dm = new DrawingMethods(); BufferedImage testImage = new BufferedImage(10,10,BufferedImage.TYPE_3BYTE_BGR); Dimension theSize = dm.haploGetPreferredSize(finishedHaplos, testImage.g... | |
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)){ int thisInt = Integer.parseInt(filez[i].substring(6,8)); if (thisInt > highCount){ highCount... | try{ fc.setSelectedFile(null); int returnVal = fc.showSaveDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { new TextMethods().saveHapsToText(finishedHaplos, fc.getSelectedFile()); | 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... |
} String saveName = "haptxt"; if (highCount < 9) saveName += "0"; saveName += (highCount+1); saveName += "."; saveName += infileName; try{ new TextMethods().saveHapsToText(finishedHaplos, saveName); | 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... | |
if (caller.hapDisplay != null){ caller.hapDisplay.setVisible(false); } | 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){ ... | |
if (caller.dPrimeDisplay != null){ caller.dPrimeDisplay.setVisible(false); } | 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){ ... | |
if ( isTrim() && ! hasTrimmed ) { trimBody(); } | public Script getBody() { if ( isTrim() && ! hasTrimmed ) { trimBody(); } return body; } | |
getBody().run(context, XMLOutput.createXMLOutput(writer)); | invokeBody(XMLOutput.createXMLOutput(writer)); | 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(); } |
getBody().run(context, output); | if ( isTrim() && ! hasTrimmed ) { trimBody(); } invokeBody(output); | protected void invokeBody(XMLOutput output) throws Exception { getBody().run(context, output); } |
if(Chromosome.getDataChrom().equals("chrx") && currentInd.getGender()==1){ | if(Chromosome.getDataChrom().equalsIgnoreCase("chrx") && currentInd.getGender()==1){ | 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(); ... |
if(Chromosome.getDataChrom().equals("chrx")){ if(currentInd.getGender() == 1) { if (!(momAllele1 == 0 || momAllele2 == 0 || dadAllele1 == 0)){ | if(Chromosome.getDataChrom().equalsIgnoreCase("chrx")){ if (dadAllele1 != dadAllele2){ dadAllele1 = 0; dadAllele2 = 0; } if (!(momAllele1 == 0 || momAllele2 == 0 || dadAllele1 == 0 || dadAllele2 ==0)){ if(currentInd.getGender() == 1) { | 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(); ... |
} }else { if(momAllele1 == momAllele2) { if(dadAllele1 == momAllele1) { if(allele1 != momAllele1 || allele2 != momAllele2){ | }else { if(momAllele1 == momAllele2) { if(dadAllele1 == momAllele1) { if(allele1 != momAllele1 || allele2 != momAllele2){ mendErrNum ++; MendelError mend = new MendelError(currentInd.getFamilyID(), currentInd.getIndividualID()); mendels.add(mend); currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.get... | 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(); ... |
}else { if(allele1 == allele2 ){ mendErrNum ++; MendelError mend = new MendelError(currentInd.getFamilyID(), currentInd.getIndividualID()); mendels.add(mend); currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(l... | 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(); ... | |
if (!Chromosome.getDataChrom().equals("chrx") || currentInd.getGender() != 1) { | if (!Chromosome.getDataChrom().equalsIgnoreCase("chrx") || currentInd.getGender() != 1) { | 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(); ... |
add( buttonPane, BorderLayout.SOUTH ); | protected void createUI() { setLayout(new BorderLayout()); setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10)); tabPane = new JTabbedPane(); add( tabPane, BorderLayout.CENTER ); // General pane JPanel generalPane = new JPanel(); tabPane.addTab( "General", generalPane ); // Create the fields & their labels /... | |
String text = getBodyText(); | public void doTag(XMLOutput output) throws Exception { Task task = getTask(); String text = getBodyText(); // if the task has an addText() Method method = MethodUtils.getAccessibleMethod( taskType, "addText", addTaskParamTypes ); if (method != null) { ... | |
} | } else { getBody().run(context, output); } | public void doTag(XMLOutput output) throws Exception { Task task = getTask(); String text = getBodyText(); // if the task has an addText() Method method = MethodUtils.getAccessibleMethod( taskType, "addText", addTaskParamTypes ); if (method != null) { ... |
if ( task == null ) { task = (Task) taskType.newInstance(); task.setProject(project); task.setTaskName(taskName); task.init(); setDynaBean( new ConvertingWrapDynaBean(task) ); | if ( this.task == null ) { if ( getTaskType() == null ) { setTaskType( (Class) getAntProject().getTaskDefinitions().get( getTaskName() ) ); } this.task = createTask( getTaskName(), getTaskType() ); setDynaBean( new ConvertingWrapDynaBean( this.task ) ); | public Task getTask() throws Exception { if ( task == null ) { task = (Task) taskType.newInstance(); task.setProject(project); task.setTaskName(taskName); task.init(); setDynaBean( new ConvertingWrapDynaBean(task) ); } return task; } |
return task; | return this.task; | public Task getTask() throws Exception { if ( task == null ) { task = (Task) taskType.newInstance(); task.setProject(project); task.setTaskName(taskName); task.init(); setDynaBean( new ConvertingWrapDynaBean(task) ); } return task; } |
setDynaBean( new ConvertingWrapDynaBean(task) ); | setDynaBean( new ConvertingWrapDynaBean( this.task ) ); | public void setTask(Task task) { this.task = task; setDynaBean( new ConvertingWrapDynaBean(task) ); } |
JMXConnector jmxc = JMXConnectorFactory.connect(url, null); | JMXConnector jmxc = JMXConnectorFactory.connect(url, env); | public ServerConnection getServerConnection(ApplicationConfig config) throws ConnectionFailedException { try { /* Create an RMI connector client */ HashMap env = new HashMap(); String[] credentials = new String[] {config.getUsername(), ... |
db.setIgnoreReset(true); | db.setPlayPenDatabase(true); | public void testDatabaseInsert()throws ArchitectException { // setup a playpen like database SQLDatabase db = new SQLDatabase(); UndoManager undoManager = new UndoManager(db); db.setIgnoreReset(true); SQLTable table1 = new SQLTable(db,"table1","remark1","TABLE",true); SQLTable table2 = new SQLTable(db,"table2"... |
folder = PhotoFolder.create( "Top", null ); | folder = PhotoFolder.create( "PhotoAdditionTest", PhotoFolder.getRoot() ); | public void testPhotoAddition() { String testImgDir = "c:\\java\\photovault\\testfiles"; String fname = "test1.jpg"; File f = new File( testImgDir, fname ); PhotoInfo photo = null; try { photo = PhotoInfo.addToDB( f ); } catch ( PhotoNotFoundException e ) { fail( "Could not find photo: " + e.getMessage() );... |
query.create( "select folders from " + PhotoFolder.class.getName() + " where name = \"Top\"" ); | query.create( "select folders from " + PhotoFolder.class.getName() + " where folderId = 1" ); | public void testRetrieve() { DList folders = null; Transaction tx = odmg.newTransaction(); tx.begin(); try { OQLQuery query = odmg.newOQLQuery(); query.create( "select folders from " + PhotoFolder.class.getName() + " where name = \"Top\"" ); folders = (DList) query.execute(); tx.commit(); } catch ( ... |
assertEquals( "Folder with id 0 should be the top", folder.getName(), "Top" ); | assertEquals( "Folder with id 1 should be the top", folder.getName(), "Top" ); | public void testRetrieve() { DList folders = null; Transaction tx = odmg.newTransaction(); tx.begin(); try { OQLQuery query = odmg.newOQLQuery(); query.create( "select folders from " + PhotoFolder.class.getName() + " where name = \"Top\"" ); folders = (DList) query.execute(); tx.commit(); } catch ( ... |
makePhoto( cal, "Lassille kuuluu hyv" ); | makePhoto( cal, "Lassille kuuluu hyvaa" ); | public void setUp() { // Create several photos with different shooting dates // Add them to a collection so that they are easy to delete afterwards Calendar cal = Calendar.getInstance(); photos = new Vector(); uids = new Vector(); cal.set( 2002, 11, 23 ); makePhoto( cal, "Katsokaa kun Lassi ui" ); cal.set( 2002, 11... |
Iterator it = sqlObjectListeners.iterator(); while (it.hasNext()) { ((SQLObjectListener) it.next()).dbChildrenRemoved(e); | SQLObjectListener[] listeners = sqlObjectListeners.toArray(new SQLObjectListener[0]); for(int i = listeners.length-1;i>=0;i--) { listeners[i].dbChildrenRemoved(e); | protected void fireDbChildrenRemoved(int[] oldIndices, List oldChildren) { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbChildrenRemoved event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent (this, oldIndices... |
Iterator it = sqlObjectListeners.iterator(); while (it.hasNext()) { | SQLObjectListener[] listeners = sqlObjectListeners.toArray(new SQLObjectListener[0]); for(int i = listeners.length-1;i>=0;i--) { | protected void fireDbObjectChanged(String propertyName, Object oldValue, Object newValue) { SQLObjectEvent e = new SQLObjectEvent( this, propertyName, oldValue, newValue, isSecondaryChangeMode()); boolean same = (oldValue == null ? oldValue == newValue : oldValue.equals(newValue)); if (same) { logg... |
((SQLObjectListener) it.next()).dbObjectChanged(e); | listeners[i].dbObjectChanged(e); | protected void fireDbObjectChanged(String propertyName, Object oldValue, Object newValue) { SQLObjectEvent e = new SQLObjectEvent( this, propertyName, oldValue, newValue, isSecondaryChangeMode()); boolean same = (oldValue == null ? oldValue == newValue : oldValue.equals(newValue)); if (same) { logg... |
Iterator it = sqlObjectListeners.iterator(); while (it.hasNext()) { | SQLObjectListener[] listeners = sqlObjectListeners.toArray(new SQLObjectListener[0]); for(int i = listeners.length-1;i>=0;i--) { | public void fireDbStructureChanged() { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbStructureChanged event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent( this, null, isSecondaryChangeMode()); int coun... |
((SQLObjectListener) it.next()).dbStructureChanged(e); | listeners[i].dbStructureChanged(e); | public void fireDbStructureChanged() { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbStructureChanged event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent( this, null, isSecondaryChangeMode()); int coun... |
Iterator it = undoEventListeners.iterator(); | UndoCompoundEventListener[] listeners = sqlObjectListeners.toArray(new UndoCompoundEventListener[0]); | protected void fireUndoCompoundEvent(UndoCompoundEvent e) { Iterator it = undoEventListeners.iterator(); if (e.getType().isStartEvent()) { while (it.hasNext()) { ((UndoCompoundEventListener) it.next()).compoundEditStart(e); } } else { while (it.hasNext()) { ((UndoCompoundEventListener) it.next()).compou... |
while (it.hasNext()) { ((UndoCompoundEventListener) it.next()).compoundEditStart(e); | for(int i = listeners.length-1;i>=0;i--) { listeners[i].compoundEditStart(e); | protected void fireUndoCompoundEvent(UndoCompoundEvent e) { Iterator it = undoEventListeners.iterator(); if (e.getType().isStartEvent()) { while (it.hasNext()) { ((UndoCompoundEventListener) it.next()).compoundEditStart(e); } } else { while (it.hasNext()) { ((UndoCompoundEventListener) it.next()).compou... |
while (it.hasNext()) { ((UndoCompoundEventListener) it.next()).compoundEditEnd(e); | for(int i = listeners.length-1;i>=0;i--) { listeners[i].compoundEditEnd(e); | protected void fireUndoCompoundEvent(UndoCompoundEvent e) { Iterator it = undoEventListeners.iterator(); if (e.getType().isStartEvent()) { while (it.hasNext()) { ((UndoCompoundEventListener) it.next()).compoundEditStart(e); } } else { while (it.hasNext()) { ((UndoCompoundEventListener) it.next()).compou... |
+ ": " | + "): " | protected SAXException createSAXException(String message, Exception e) { log.warn("Underlying exception: " + e); e.printStackTrace(); if (locator != null) { String error = "Error at (" + locator.getLineNumber() + ", " ... |
} catch (IllegalAccessException e) { log.warn("Constructor for class is not accessible: " + uri + " so disabling the taglib"); } catch (InstantiationException e) { log.warn("Class could not be instantiated: " + uri + " so disabling the taglib"); } catch (ClassCastException e) { log.warn("Class is not a TagLibrary: " + ... | protected TagScript createTag( String namespaceURI, String localName, Attributes list) throws SAXException { try { // use the URI to load a taglib TagLibrary taglib = context.getTagLibrary(namespaceURI); if (taglib == null) { if (nam... | |
Object value = evaluateAsValue(context); | Object value = evaluateRecurse(context); | public boolean evaluateAsBoolean(JellyContext context) { Object value = evaluateAsValue(context); if ( value instanceof Boolean ) { Boolean b = (Boolean) value; return b.booleanValue(); } else if ( value instanceof String ) { // return Boolean.getBoolean(... |
Object value = evaluateAsValue(context); | Object value = evaluateRecurse(context); | public Iterator evaluateAsIterator(JellyContext context) { Object value = evaluateAsValue(context); if ( value == null ) { return EMPTY_ITERATOR; } else if ( value instanceof Iterator ) { return (Iterator) value; } else if ( value instanceof Lis... |
Object value = evaluateAsValue(context); | Object value = evaluateRecurse(context); | public String evaluateAsString(JellyContext context) { Object value = evaluateAsValue(context); // sometimes when Jelly is used inside Maven the value // of an expression can actually be an expression. // e.g. ${foo.bar} can lookup "foo.bar" in a Maven context // which could actua... |
return bodyPart.getSize(); | try { Object content = bodyPart.getContent(); if (content instanceof InputStream) { ByteArrayOutputStream os = new ByteArrayOutputStream(); IOUtil.copy(((InputStream) content), os); return os.size(); } else if (content instanceof String) { return ((String) content).length(); } else { throw new IllegalStateException("Un... | public static int getMimePartSize(MimeMultipart parts, String mimeType) { if (parts != null) { try { for (int i = 0; i < parts.getCount(); i++) { BodyPart bodyPart = parts.getBodyPart(i); if (bodyPart.getContentType().startsWith(mimeType)) { ... |
TableUtils.fitColumnWidth(table, colIndex); | TableUtils.fitColumnWidth(table, colIndex, 0); | public void initSingleColumnSize(int colIndex) { TableUtils.fitColumnWidth(table, colIndex); } |
JFrame jf = new JFrame(); | int exitValue = 0; | public static void main(String[] args) { JFrame jf = new JFrame(); String dir = System.getProperty("user.dir"); String sep = System.getProperty("file.separator"); String ver = System.getProperty("java.version"); System.out.println(ver); String jarfile = System.getProperty("... |
int c; boolean dead = false; StringBuffer errorMsg = new StringBuffer(); InputStream es = child.getErrorStream(); InputStream is = child.getInputStream(); | StreamGobbler isg = new StreamGobbler(child.getInputStream()); isg.start(); | public static void main(String[] args) { JFrame jf = new JFrame(); String dir = System.getProperty("user.dir"); String sep = System.getProperty("file.separator"); String ver = System.getProperty("java.version"); System.out.println(ver); String jarfile = System.getProperty("... |
while ((c=es.read())!=-1) { errorMsg.append((char)c); if (!dead){ child.destroy(); dead = true; } | boolean dead = false; StringBuffer errorMsg = new StringBuffer("Fatal Error:\n"); BufferedReader besr = new BufferedReader(new InputStreamReader(child.getErrorStream())); String line = null; if ((line = besr.readLine()) != null) { errorMsg.append(line); child.destroy(); dead = true; | public static void main(String[] args) { JFrame jf = new JFrame(); String dir = System.getProperty("user.dir"); String sep = System.getProperty("file.separator"); String ver = System.getProperty("java.version"); System.out.println(ver); String jarfile = System.getProperty("... |
while ((c=is.read())!=-1){ System.out.print((char)c); } | public static void main(String[] args) { JFrame jf = new JFrame(); String dir = System.getProperty("user.dir"); String sep = System.getProperty("file.separator"); String ver = System.getProperty("java.version"); System.out.println(ver); String jarfile = System.getProperty("... | |
JOptionPane.showMessageDialog(jf, "Fatal Error:\n" + errorMsg, null, JOptionPane.ERROR_MESSAGE); | if (headless){ System.out.println(errorMsg); }else{ JFrame jf = new JFrame(); JOptionPane.showMessageDialog(jf, errorMsg, null, JOptionPane.ERROR_MESSAGE); } exitValue = -1; | public static void main(String[] args) { JFrame jf = new JFrame(); String dir = System.getProperty("user.dir"); String sep = System.getProperty("file.separator"); String ver = System.getProperty("java.version"); System.out.println(ver); String jarfile = System.getProperty("... |
JOptionPane.showMessageDialog(jf, "Error:\nUnable to launch Haploview.", null, JOptionPane.ERROR_MESSAGE); | if (headless){ System.out.println("Error:\nUnable to launch Haploview.\n"+e.getMessage()); }else{ JFrame jf = new JFrame(); JOptionPane.showMessageDialog(jf, "Error:\nUnable to launch Haploview.\n"+e.getMessage(), null, JOptionPane.ERROR_MESSAGE); } | public static void main(String[] args) { JFrame jf = new JFrame(); String dir = System.getProperty("user.dir"); String sep = System.getProperty("file.separator"); String ver = System.getProperty("java.version"); System.out.println(ver); String jarfile = System.getProperty("... |
System.exit(0); | System.exit(exitValue); | public static void main(String[] args) { JFrame jf = new JFrame(); String dir = System.getProperty("user.dir"); String sep = System.getProperty("file.separator"); String ver = System.getProperty("java.version"); System.out.println(ver); String jarfile = System.getProperty("... |
for (int i = 0, size = whenTags.length; i < size; i++) { TagScript script = whenTags[i]; script.run(context, output); WhenTag tag = (WhenTag) script.getTag(); if (tag.getValue()) { return; } } if (otherwiseTag != null) { otherwiseTag.run(context, output); } | setBlockEvaluated(false); invokeBody(output); | public void doTag(XMLOutput output) throws Exception { for (int i = 0, size = whenTags.length; i < size; i++) { TagScript script = whenTags[i]; script.run(context, output); WhenTag tag = (WhenTag) script.getTag(); if (tag.getValue()) { return; ... |
PreparedStatement ps = conn.prepareStatement(sqlStatement); setParameters(ps, parameters); result = ps.executeUpdate(); | if ( parameters == null || parameters.size() == 0 ) { Statement statement = conn.createStatement(); result = statement.executeUpdate(sqlStatement); } else { PreparedStatement ps = conn.prepareStatement(sqlStatement); setParameters(ps, parameters); result = ps.executeUpdate(); } | public void doTag(XMLOutput output) throws Exception { try { conn = getConnection(); } catch (SQLException e) { throw new JellyException(sql + ": " + e.getMessage(), e); } /* * Use the SQL statement specified by the sql attribute, if any, * ot... |
pp.addTablePane(new TablePane(t1, pp), new Point(0,0)); | pp.addTablePane(tp1 = new TablePane(t1, pp), new Point(0,0)); | protected void setUp() throws Exception { super.setUp(); pp = ArchitectFrame.getMainInstance().getProject().getPlayPen(); SQLTable t1 = new SQLTable(pp.getDatabase(), true); pp.getDatabase().addChild(t1); pp.addTablePane(new TablePane(t1, pp), new Point(0,0)); SQLTable t2 = new SQLTable(pp.getDatabase(), true); ... |
pp.addTablePane(new TablePane(t2, pp), new Point(0,0)); | pp.addTablePane(tp2 = new TablePane(t2, pp), new Point(0,0)); | protected void setUp() throws Exception { super.setUp(); pp = ArchitectFrame.getMainInstance().getProject().getPlayPen(); SQLTable t1 = new SQLTable(pp.getDatabase(), true); pp.getDatabase().addChild(t1); pp.addTablePane(new TablePane(t1, pp), new Point(0,0)); SQLTable t2 = new SQLTable(pp.getDatabase(), true); ... |
sqlrel.addMapping(t1.getColumnByName("pkcol_1"), t2.getColumnByName("fkcol")); | protected void setUp() throws Exception { super.setUp(); pp = ArchitectFrame.getMainInstance().getProject().getPlayPen(); SQLTable t1 = new SQLTable(pp.getDatabase(), true); pp.getDatabase().addChild(t1); pp.addTablePane(new TablePane(t1, pp), new Point(0,0)); SQLTable t2 = new SQLTable(pp.getDatabase(), true); ... | |
odmg = OJB.getInstance(); db = odmg.newDatabase(); try { db.open( "repository.xml", Database.OPEN_READ_WRITE ); } catch ( ODMGException e ) { db = null; } | odmg = ODMG.getODMGImplementation(); db = ODMG.getODMGDatabase(); | public void setUp() { odmg = OJB.getInstance(); db = odmg.newDatabase(); try { db.open( "repository.xml", Database.OPEN_READ_WRITE ); } catch ( ODMGException e ) { // log.warn( "Could not open database: " + e.getMessage() ); db = null; } tx = odmg.newTransaction(); tx.begin(); DList folders = null; ... |
}else if (e.getActionCommand().equals("dump tags")){ try{ HaploView.fc.setSelectedFile(new File("")); if (HaploView.fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION){ File outfile = HaploView.fc.getSelectedFile(); tc.dumpTags(outfile); } }catch (IOException ioe){ JOptionPane.showMessageDialog(this, ioe.getMessage... | public void actionPerformed(ActionEvent e) { if (e.getActionCommand().equals("taggingdone")){ TaggerConfigPanel tcp = (TaggerConfigPanel) e.getSource(); setTags(tcp.getTaggerController()); }else if (e.getActionCommand().equals("dump")){ try{ HaploView.fc... | |
listsPanel.add(dumpTestsButton); | JButton dumpTagsButton = new JButton("Dump Tags File"); dumpTagsButton.setActionCommand("dump tags"); dumpTagsButton.addActionListener(this); JPanel listsButtonPanel = new JPanel(); listsButtonPanel.add(dumpTestsButton); listsButtonPanel.add(dumpTagsButton); listsPanel.add(listsButtonPanel); | public void setTags(TaggerController t) { tc = t; removeAll(); setLayout(new BoxLayout(this,BoxLayout.X_AXIS)); Vector colNames = new Vector(); Vector tableData = new Vector(); colNames.add("Allele"); colNames.add("Test"); colNames.add("r\u00b2"); for (... |
addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent e) { System.exit(0); } } ); | public BrowserWindow() { super( "Photovault Browser"); SwingUtilities.invokeLater(new java.lang.Runnable() { public void run() { createUI(); } }); addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent e) { System.exit(0); } } ); } | |
setDefaultCloseOperation( JFrame.DISPOSE_ON_CLOSE ); | protected void createUI() { tabPane = new JTabbedPane(); queryPane = new QueryPane(); treePane = new PhotoFolderTree(); tabPane.addTab( "Query", queryPane ); tabPane.addTab( "Folders", treePane ); // viewPane = new TableCollectionView(); viewPane = new PhotoCollectionThumbView(); viewPane.setCollection( queryPane.g... | |
BrowserWindow br = new BrowserWindow(); | importFile(); | public void actionPerformed( ActionEvent e ) { BrowserWindow br = new BrowserWindow(); // br.setVisible( true ); } |
importFile(); | System.exit( 0 ); | public void actionPerformed( ActionEvent e ) { importFile(); } |
registerWidgetTag( "tableTree", TableTree.class ); registerWidgetTag( "tableTreeItem", TableTreeItem.class ); | public SwtTagLibrary() { // widgets registerWidgetTag( "button", Button.class ); registerWidgetTag( "canvas", Canvas.class ); registerWidgetTag( "caret", Caret.class ); registerWidgetTag( "combo", Combo.class ); registerWidgetTag( "composite", Composite.class ); regi... | |
JButton okButton = new JButton("Ok"); | JButton okButton = new JButton(ArchitectPanelBuilder.OK_BUTTON_LABEL); | public synchronized void setupDialog() { logger.debug("running setupDialog()"); if (plexp == null) { throw new NullPointerException("setupDialog: plexp was null"); } // always refresh Target Database (it might have changed) plexp.setTargetDataSource(ArchitectFrame.getMainInstance().getProject().getTargetDatabas... |
Options.setAssocTest(1); | Options.setAssocTest(ASSOC_TRIO); | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command.equals(RAW_DATA)){ load(PED); }else if (command.equals(PHASED_DATA)){ load(HAPS); }else if (command.equals(HAPMAP_DATA)){ load(HMP); }else if (command.e... |
Options.setAssocTest(2); | Options.setAssocTest(ASSOC_CC); | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command.equals(RAW_DATA)){ load(PED); }else if (command.equals(PHASED_DATA)){ load(HAPS); }else if (command.equals(HAPMAP_DATA)){ load(HMP); }else if (command.e... |
Options.setAssocTest(0); | Options.setAssocTest(ASSOC_NONE); | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command.equals(RAW_DATA)){ load(PED); }else if (command.equals(PHASED_DATA)){ load(HAPS); }else if (command.equals(HAPMAP_DATA)){ load(HMP); }else if (command.e... |
String[] returnStrings = {genoFileField.getText(), infoFileField.getText(), maxComparisonDistField.getText()}; | if (maxComparisonDistField.getText().equals("")){ Options.setMaxDistance(0); }else{ Options.setMaxDistance(Integer.parseInt(maxComparisonDistField.getText())); } String[] returnStrings = {genoFileField.getText(), infoFileField.getText()}; | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command.equals(RAW_DATA)){ load(PED); }else if (command.equals(PHASED_DATA)){ load(HAPS); }else if (command.equals(HAPMAP_DATA)){ load(HMP); }else if (command.e... |
addPhotoToTree( (PhotoInfo) model[n] ); | if ( model[n] != null ) { addPhotoToTree( (PhotoInfo) model[n] ); } | protected void initTree() { folderNodes = new HashMap(); topNode = null; if ( model == null ) { return; } // Add all photos in the model to folder tree for ( int n = 0; n < model.length; n++ ) { addPhotoToTree( (PhotoInfo) model[n] ); } treeModel.nodeStructureChanged(topNode); } |
print(" ADD FOREIGN KEY "); | print(" ADD CONSTRAINT "); | public void addRelationship(SQLRelationship r) throws ArchitectDiffException { print("\n ALTER TABLE "); printQualified(r.getFkTable().getPhysicalName()); print(" ADD FOREIGN KEY "); print(r.getName()); print(" ( "); Map<String, SQLColumn> colNameMap = new HashMap<String, SQLColumn> (); boolean firstColumn =... |
print(" ( "); | print(" FOREIGN KEY ( "); | public void addRelationship(SQLRelationship r) throws ArchitectDiffException { print("\n ALTER TABLE "); printQualified(r.getFkTable().getPhysicalName()); print(" ADD FOREIGN KEY "); print(r.getName()); print(" ( "); Map<String, SQLColumn> colNameMap = new HashMap<String, SQLColumn> (); boolean firstColumn =... |
private String columnDefinition(SQLColumn c, Map colNameMap) throws ArchitectDiffException | protected String columnDefinition(SQLColumn c, Map colNameMap) throws ArchitectDiffException | private String columnDefinition(SQLColumn c, Map colNameMap) throws ArchitectDiffException { StringBuffer def = new StringBuffer(); getPhysicalName(colNameMap,c); // also adds generated physical name to the map GenericTypeDescriptor td = (GenericTypeDescriptor) typeMap.get(new Integer(c.getType())); if (td == nul... |
print(" DROP FOREIGN KEY "); | print(" DROP CONSTRAINT "); | public void dropRelationship(SQLRelationship r) { print("\n ALTER TABLE "); printQualified(r.getFkTable().getPhysicalName()); print(" DROP FOREIGN KEY "); print(r.getName()); endStatement(DDLStatement.StatementType.DROP, r); } |
setVisible( false ); | private void CancelBtnActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_CancelBtnActionPerformed retval = CANCEL_OPTION; }//GEN-LAST:event_CancelBtnActionPerformed | |
public void run(Context context, XMLOutput output) throws Exception { | public void run(JellyContext context, XMLOutput output) throws Exception { | public void run(Context context, XMLOutput output) throws Exception { log.info( "Invoking dynamic tag with attributes: " + attributes ); attributes.put( "org.apache.commons.jelly.body", getBody() ); // create new context based on current attributes Context newContext = context.ne... |
Context newContext = context.newContext( attributes ); | JellyContext newJellyContext = context.newJellyContext( attributes ); | public void run(Context context, XMLOutput output) throws Exception { log.info( "Invoking dynamic tag with attributes: " + attributes ); attributes.put( "org.apache.commons.jelly.body", getBody() ); // create new context based on current attributes Context newContext = context.ne... |
getTemplate().run( newContext, output ); | getTemplate().run( newJellyContext, output ); | public void run(Context context, XMLOutput output) throws Exception { log.info( "Invoking dynamic tag with attributes: " + attributes ); attributes.put( "org.apache.commons.jelly.body", getBody() ); // create new context based on current attributes Context newContext = context.ne... |
File propFile = new File( propFname ); | log.debug( "Using property file " + propFname ); File propFile = new File( propFname ); | static public void init() { // Determine the property file name String propFname = System.getProperty( "photovault.propFname", defaultPropFname ); File propFile = new File( propFname ); props = new Properties(); try { InputStream is = new FileInputStream( propFile ); props.load( is ); } catch ( FileNotFound... |
log.debug( "paintThumbnail entry " + photo.getUid() ); | private void paintThumbnail( Graphics2D g2, PhotoInfo photo, int startx, int starty, boolean isSelected ) { // Current position in which attributes can be drawn int ypos = starty + rowHeight/2; if ( photo != null ) { Thumbnail thumbnail = null; if ( photo.hasThumbnail() ) { log.debug( ... | |
if ( photo.hasThumbnail() ) { | log.debug( "finding thumb" ); boolean hasThumbnail = photo.hasThumbnail(); log.debug( "asked if has thumb" ); if ( hasThumbnail ) { | private void paintThumbnail( Graphics2D g2, PhotoInfo photo, int startx, int starty, boolean isSelected ) { // Current position in which attributes can be drawn int ypos = starty + rowHeight/2; if ( photo != null ) { Thumbnail thumbnail = null; if ( photo.hasThumbnail() ) { log.debug( ... |
log.debug( "drawing thumbnail" ); | private void paintThumbnail( Graphics2D g2, PhotoInfo photo, int startx, int starty, boolean isSelected ) { // Current position in which attributes can be drawn int ypos = starty + rowHeight/2; if ( photo != null ) { Thumbnail thumbnail = null; if ( photo.hasThumbnail() ) { log.debug( ... | |
log.debug( "paintThumbnail: exit " + photo.getUid() ); | private void paintThumbnail( Graphics2D g2, PhotoInfo photo, int startx, int starty, boolean isSelected ) { // Current position in which attributes can be drawn int ypos = starty + rowHeight/2; if ( photo != null ) { Thumbnail thumbnail = null; if ( photo.hasThumbnail() ) { log.debug( ... | |
log.debug( "No thumbnail" ); | public void thumbnailCreated( PhotoInfo photo ) { repaintPhoto( photo ); Container parent = getParent(); Rectangle viewRect = null; if ( parent instanceof JViewport ) { viewRect = ((JViewport)parent).getViewRect(); } PhotoInfo nextPhoto = null; // Walk through all phoso until we find a photo that is visible //... | |
super.setUp(); SQLDatabase mydb = new SQLDatabase(db.getDataSource()); Connection con = mydb.getConnection(); Statement stmt = con.createStatement(); try { stmt.executeUpdate("DROP TABLE REGRESSION_TEST1"); stmt.executeUpdate("DROP TABLE REGRESSION_TEST2"); } catch (SQLException sqle ){ System.out.println("+++ TestS... | super.setUp(); } | protected void setUp() throws Exception { super.setUp(); SQLDatabase mydb = new SQLDatabase(db.getDataSource()); Connection con = mydb.getConnection(); /* * Setting up a clean db for each of the tests */ Statement stmt = con.createStatement(); try { stmt.executeUpdate("DROP TABLE REGRESSION... |
public void testInherit() throws ArchitectException { SQLTable table1; SQLTable table2; table1 = db.getTableByName("REGRESSION_TEST1"); table2 = db.getTableByName("REGRESSION_TEST2"); | public void testInherit() throws ArchitectException { SQLTable table1; SQLTable table2; table1 = db.getTableByName("REGRESSION_TEST1"); table2 = db.getTableByName("REGRESSION_TEST2"); assertEquals(2, table1.getColumns().size()); assertEquals(1, table2.getColumns().size()); | public void testInherit() throws ArchitectException { SQLTable table1; SQLTable table2; table1 = db.getTableByName("REGRESSION_TEST1"); table2 = db.getTableByName("REGRESSION_TEST2"); table2.inherit(table1); assertEquals("The wrong 1st column was inherited",table2.getColumn(0).toString(),table1.getColu... |
table2.inherit(table1); assertEquals("The wrong 1st column was inherited",table2.getColumn(0).toString(),table1.getColumn(0).toString()); assertEquals("The wrong 2nd column was inherited",table2.getColumn(1).toString(),table1.getColumn(1).toString()); assertEquals("The wrong number of columns were inherited",table2.get... | table2.inherit(table1); assertEquals("The wrong 1st column was inherited", table1.getColumn(0).toString(), table2.getColumn(1).toString()); assertEquals("The wrong 2nd column was inherited", table1.getColumn(1).toString(), table2.getColumn(2).toString()); assertEquals("The wrong number of columns were inherited", table... | public void testInherit() throws ArchitectException { SQLTable table1; SQLTable table2; table1 = db.getTableByName("REGRESSION_TEST1"); table2 = db.getTableByName("REGRESSION_TEST2"); table2.inherit(table1); assertEquals("The wrong 1st column was inherited",table2.getColumn(0).toString(),table1.getColu... |
} | public void testInherit() throws ArchitectException { SQLTable table1; SQLTable table2; table1 = db.getTableByName("REGRESSION_TEST1"); table2 = db.getTableByName("REGRESSION_TEST2"); table2.inherit(table1); assertEquals("The wrong 1st column was inherited",table2.getColumn(0).toString(),table1.getColu... | |
public void testRemoveColumn() throws ArchitectException { SQLTable table1; SQLColumn col1; SQLColumn col2; table1 = db.getTableByName("REGRESSION_TEST1"); col1 = table1.getColumn(0); col2 = table1.getColumn(1); | public void testRemoveColumn() throws ArchitectException { SQLTable table1; SQLColumn col1; SQLColumn col2; | public void testRemoveColumn() throws ArchitectException { SQLTable table1; SQLColumn col1; SQLColumn col2; table1 = db.getTableByName("REGRESSION_TEST1"); col1 = table1.getColumn(0); col2 = table1.getColumn(1); assertEquals("We removed a column when we shouldn't have",table1.getColumns().size(),2)... |
assertEquals("We removed a column when we shouldn't have",table1.getColumns().size(),2); table1.removeColumn(col1); assertEquals("Either 0 or 2+ columns were removed",table1.getColumns().size(),1); assertEquals("The wrong column was removed",col2,table1.getColumn(0)); | table1 = db.getTableByName("REGRESSION_TEST1"); col1 = table1.getColumn(0); col2 = table1.getColumn(1); assertEquals("We removed a column when we shouldn't have", table1.getColumns().size(), 2); table1.removeColumn(col1); assertEquals("Either 0 or 2+ columns were removed", table1.getColumns().size(), 1); assertEquals(... | public void testRemoveColumn() throws ArchitectException { SQLTable table1; SQLColumn col1; SQLColumn col2; table1 = db.getTableByName("REGRESSION_TEST1"); col1 = table1.getColumn(0); col2 = table1.getColumn(1); assertEquals("We removed a column when we shouldn't have",table1.getColumns().size(),2)... |
assertEquals("Last Column failed to be removed",table1.getColumns().size(),0); Exception exc = null; try { table1.removeColumn(0); } catch (IndexOutOfBoundsException e) { System.out.println("Method throws proper error"); exc = e; } assertNotNull("Should have thrown an exception",exc); | } catch (IndexOutOfBoundsException e) { System.out.println("Method throws proper error"); exc = e; | public void testRemoveColumn() throws ArchitectException { SQLTable table1; SQLColumn col1; SQLColumn col2; table1 = db.getTableByName("REGRESSION_TEST1"); col1 = table1.getColumn(0); col2 = table1.getColumn(1); assertEquals("We removed a column when we shouldn't have",table1.getColumns().size(),2)... |
assertNotNull("Should have thrown an exception", exc); } | public void testRemoveColumn() throws ArchitectException { SQLTable table1; SQLColumn col1; SQLColumn col2; table1 = db.getTableByName("REGRESSION_TEST1"); col1 = table1.getColumn(0); col2 = table1.getColumn(1); assertEquals("We removed a column when we shouldn't have",table1.getColumns().size(),2)... | |
public void testRemoveColumnOutBounds() throws ArchitectException { SQLTable table1; SQLColumn col1; SQLColumn col2; table1 = db.getTableByName("REGRESSION_TEST1"); Exception exc = null; try { table1.removeColumn(16); } catch (IndexOutOfBoundsException e) { System.out.println("Method throws proper error"); exc=e; } a... | public void testRemoveColumnOutBounds() throws ArchitectException { SQLTable table1; table1 = db.getTableByName("REGRESSION_TEST1"); Exception exc = null; try { table1.removeColumn(16); } catch (IndexOutOfBoundsException e) { System.out.println("Method throws proper error"); exc = e; | public void testRemoveColumnOutBounds() throws ArchitectException { SQLTable table1; SQLColumn col1; SQLColumn col2; table1 = db.getTableByName("REGRESSION_TEST1"); Exception exc = null; try { table1.removeColumn(16); } catch (IndexOutOfBoundsException e) { System.out.println("Method throws p... |
assertNotNull("Should have thrown an exception", exc); } | public void testRemoveColumnOutBounds() throws ArchitectException { SQLTable table1; SQLColumn col1; SQLColumn col2; table1 = db.getTableByName("REGRESSION_TEST1"); Exception exc = null; try { table1.removeColumn(16); } catch (IndexOutOfBoundsException e) { System.out.println("Method throws p... | |
outputType = -1; | private void argHandler(String[] args){ //TODO: -specify values from HaplotypeDisplayController (min hap percentage etc) //TODO: -want to be able to output haps file from pedfile /* boolean nogui = false; String batchMode = ""; String hapsFileName = ""; String pedFileNa... |
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