rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k |
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InvocationTargetException, NoSuchMethodException { | InvocationTargetException, NoSuchMethodException, ArchitectException { | public void testAllSettersGenerateEvents() throws IllegalArgumentException, IllegalAccessException, InvocationTargetException, NoSuchMethodException { SQLObject so = getSQLObjectUnderTest(); Set<String>propertiesToIgnore = new HashSet<String>(); propertiesToIgnore.add("populated"); propertiesToIgnore.add("S... |
context.runScript(uri, output, getExport(), getInherit() ); | context.runScript(uri, output, isExport(), isInherit() ); | public void doTag(XMLOutput output) throws Exception { if (uri == null) { throw new MissingAttributeException( "uri" ); } // we need to create a new JellyContext of the URI // take off the script name from the URL context.runScript(uri, output, getExport(), getInherit()... |
bestPermPanel.setMaximumSize(bestPermPanel.getPreferredSize()); | public void run() { try { while(testSet.getPermutationCount() - testSet.getPermutationsPerformed() != 0) { permProgressBar.setValue(testSet.getPermutationsPerformed()); scoreBoardNumTotalLabel.setText(String.valueOf(testSet.getPermutationsPerformed... | |
bestObsPanel.setMaximumSize(bestObsPanel.getPreferredSize()); | public void finishedPerms() { scoreBoardNumTotalLabel.setText(String.valueOf(testSet.getPermutationsPerformed())); scoreBoardNumPassLabel.setText(String.valueOf(testSet.getBestExceededCount())); doPermutationsButton.setEnabled(true); stopPermutationsButton.setEnabled(false); this.... | |
bestPermPanel.setMaximumSize(bestPermPanel.getPreferredSize()); | public void finishedPerms() { scoreBoardNumTotalLabel.setText(String.valueOf(testSet.getPermutationsPerformed())); scoreBoardNumPassLabel.setText(String.valueOf(testSet.getBestExceededCount())); doPermutationsButton.setEnabled(true); stopPermutationsButton.setEnabled(false); this.... | |
if ( taglib instanceof DynamicTagLibrary ) { DynamicTagLibrary dynaLib = (DynamicTagLibrary) taglib; Tag newTag = dynaLib.createTag( tag.getLocalName(), getSaxAttributes() ); | if ( taglib != null ) { Tag newTag = taglib.createTag( tag.getLocalName(), getSaxAttributes() ); | protected Tag findDynamicTag(JellyContext context, StaticTag tag) throws JellyException { // lets see if there's a tag library for this URI... TagLibrary taglib = context.getTagLibrary( tag.getUri() ); if ( taglib instanceof DynamicTagLibrary ) { DynamicTagLibrary dynaLib = (DynamicT... |
null, getMBeanServer()); | env, getMBeanServer()); | private static void startJMXConnectorServer(int port){ try { /* attempt to start the rmi registry */ startRMIRegistry(port); /* start the connector server */ JMXServiceURL url = new JMXServiceURL( "service:jmx:rmi:///jndi/rmi://localhost:" + port + "/t... |
null, getMBeanServer()); | env, getMBeanServer()); | private static void startJMXMPConnectorServer(int port){ try { /* start the connector server */ JMXServiceURL url = new JMXServiceURL( "service:jmx:jmxmp://localhost:" + port); JMXConnectorServer cs = JMXConnectorServerFactory.newJMXConnectorServe... |
if (!(args[a].startsWith("-"))){ | if (args[a].indexOf(" ") > 0){ | public static void main(String[] args) { int exitValue = 0; //String dir = System.getProperty("user.dir"); //String ver = System.getProperty("java.version"); String sep = System.getProperty("file.separator"); String javaHome = System.getProperty("java.home"); //TODO:do some... |
public Tag createTag(String name) | public Tag createTag(String name, Attributes attributes) | public Tag createTag(String name) throws Exception { Object value = templates.get(name); if ( value instanceof Script ) { Script template = (Script) value; return new DynamicTag(template); } else if ( value instanceof TagFactory ) { Tag... |
return factory.createTag(); | return factory.createTag(name, attributes); | public Tag createTag(String name) throws Exception { Object value = templates.get(name); if ( value instanceof Script ) { Script template = (Script) value; return new DynamicTag(template); } else if ( value instanceof TagFactory ) { Tag... |
public Tag createTag() throws Exception { Tag answer = DynamicTagLibrary.this.createTag(name); | public Tag createTag(String name, Attributes attributes) throws Exception { Tag answer = DynamicTagLibrary.this.createTag(name, attributes); | public TagScript createTagScript(final String name, final Attributes attributes) throws Exception { return new TagScript( new TagFactory() { public Tag createTag() throws Exception { Tag answer = DynamicTagLibrary.this.createTag(name); ... |
public Tag createTag() throws Exception { Tag answer = DynamicTagLibrary.this.createTag(name); | public Tag createTag(String name, Attributes attributes) throws Exception { Tag answer = DynamicTagLibrary.this.createTag(name, attributes); | public Tag createTag() throws Exception { Tag answer = DynamicTagLibrary.this.createTag(name); // delegate to my parent instead if ( answer == null && parent != null ) { return parent.createTag(name, attr... |
chart.setBorderPaint(new Color(230, 238, 249)); | private static JFreeChart createChart(final PieDataset dataset) { final JFreeChart chart = ChartFactory.createPieChart( null, // chart title dataset, // data false, // include legend false, false); // E6EEF9 chart.setBa... | |
plot.setOutlinePaint(new Color(230, 238, 249)); | private static JFreeChart createChart(final PieDataset dataset) { final JFreeChart chart = ChartFactory.createPieChart( null, // chart title dataset, // data false, // include legend false, false); // E6EEF9 chart.setBa... | |
DashboardContext dashboardContext = new DashboardContextImpl(context, request); | public static String drawComponent(WebContext context, HttpServletRequest request, String dashboardId, String componentId){ DashboardContext dashboardContext = new DashboardContextImpl(context, request); DashboardConfig dashboardConfig = DashboardRepository.getInstance().get(dashboardId); ... | |
DashboardContext dashboardContext = new DashboardContextImpl(context, dashboardConfig, request); | public static String drawComponent(WebContext context, HttpServletRequest request, String dashboardId, String componentId){ DashboardContext dashboardContext = new DashboardContextImpl(context, request); DashboardConfig dashboardConfig = DashboardRepository.getInstance().get(dashboardId); ... | |
public String makeDropForeignKeySQL(String fkCatalog, String fkSchema, String fkTable, String fkName) { | public String makeDropForeignKeySQL(String fkTable, String fkName) { | public String makeDropForeignKeySQL(String fkCatalog, String fkSchema, String fkTable, String fkName) { return "ALTER TABLE " +DDLUtils.toQualifiedName(fkCatalog, fkSchema, fkTable) +" DROP CONSTRAINT " +fkName; } |
+DDLUtils.toQualifiedName(fkCatalog, fkSchema, fkTable) +" DROP CONSTRAINT " +fkName; | + toQualifiedName(fkTable) + " DROP CONSTRAINT " + fkName; | public String makeDropForeignKeySQL(String fkCatalog, String fkSchema, String fkTable, String fkName) { return "ALTER TABLE " +DDLUtils.toQualifiedName(fkCatalog, fkSchema, fkTable) +" DROP CONSTRAINT " +fkName; } |
public void modifyColumn(SQLColumn c) throws ArchitectDiffException { | public void modifyColumn(SQLColumn c) { | public void modifyColumn(SQLColumn c) throws ArchitectDiffException { Map colNameMap = new HashMap(); SQLTable t = c.getParentTable(); print("\n ALTER TABLE "); print( DDLUtils.toQualifiedName(t.getCatalogName(),t.getSchemaName(),t.getPhysicalName()) ); print(" MODIFY "); print(columnDefinition(c,colNameMap)... |
print( DDLUtils.toQualifiedName(t.getCatalogName(),t.getSchemaName(),t.getPhysicalName()) ); | print(toQualifiedName(t.getPhysicalName())); | public void modifyColumn(SQLColumn c) throws ArchitectDiffException { Map colNameMap = new HashMap(); SQLTable t = c.getParentTable(); print("\n ALTER TABLE "); print( DDLUtils.toQualifiedName(t.getCatalogName(),t.getSchemaName(),t.getPhysicalName()) ); print(" MODIFY "); print(columnDefinition(c,colNameMap)... |
public String toIdentifier(String logicalName, String physicalName) { | private String toIdentifier(String logicalName, String physicalName) { | public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; if (logger.isDebugEnabled()) logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); if (logger.isDebugEnable... |
if (Options.getAssocTest() != 0){ | if (Options.getAssocTest() != ASSOC_NONE){ | public ExportDialog(HaploView h){ super(h, "Export Data"); hv = h; JPanel contents = new JPanel(); contents.setLayout(new BoxLayout(contents, BoxLayout.Y_AXIS)); JPanel tabPanel = new JPanel(); int currTab = hv.tabs.getSelectedIndex(); tabPanel.setBorder(new TitledBo... |
public void doTag(XMLOutput output) throws Exception { context.setVariable( "org.apache.commons.jelly.werkz.Project", project ); | public void doTag(XMLOutput output) throws Exception { | public void doTag(XMLOutput output) throws Exception { // project.clear(); context.setVariable( "org.apache.commons.jelly.werkz.Project", project ); getBody().run(context, output); } |
if ( project == null ) { project = (Project) context.getVariable( "org.apache.commons.jelly.werkz.Project" ); if ( project == null ) { project = new Project(); context.setVariable( "org.apache.commons.jelly.werkz.Project", project ); } } | public Project getProject() { return project; } | |
super("ApplicationHeartBeatThread:" + appConfig.getName()); | protected ApplicationHeartBeatThread(ApplicationConfig appConfig) { this.appConfig = appConfig; } | |
String text = getBodyText(); | String text = getBodyText(false); | public void doTag(XMLOutput output) throws JellyTagException { try { JellyInterpreter interpreter = BeanShellExpressionFactory.getInterpreter(context); // @todo it'd be really nice to create a JellyNameSpace to pass into // this method so that any variables declared b... |
public void doTag(XMLOutput output) throws Exception { | public void doTag(XMLOutput output) throws JellyTagException { | public void doTag(XMLOutput output) throws Exception { if (log.isDebugEnabled()) log.debug("********Executing DummyTag Body*********"); if (m_classToBeLoaded != null) { try { Class clazz = getClass().getClassLoader().loadClass(m_classToBeLoaded);... |
byte[] markers = currentInd.getMarker(loc); allele1 = markers[0]; allele2 = markers[1]; | allele1 = currentInd.getMarkerA(loc); allele2 = currentInd.getMarkerB(loc); | private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable... |
byte[] marker = (currentFamily.getMember(currentInd.getMomID())).getMarker(loc); int momAllele1 = marker[0]; int momAllele2 = marker[1]; marker = (currentFamily.getMember(currentInd.getDadID())).getMarker(loc); int dadAllele1 = marker[0]; int dadAllele2 = marker[1]; | int momAllele1 = (currentFamily.getMember(currentInd.getMomID())).getMarkerA(loc); int momAllele2 = (currentFamily.getMember(currentInd.getMomID())).getMarkerB(loc); int dadAllele1 = (currentFamily.getMember(currentInd.getDadID())).getMarkerA(loc); int dadAllele2 = (currentFamily.getMember(currentInd.getDadID())).getMa... | private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable... |
byte[] markers; byte[] zeroArray = {0,0}; | private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable... | |
markers = zeroArray; | allele1 = 0; allele2 = 0; | private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable... |
markers = currentInd.getMarker(loc); | allele1 = currentInd.getMarkerA(loc); allele2 = currentInd.getMarkerB(loc); | private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable... |
allele1 = markers[0]; allele2 = markers[1]; | private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable... | |
logger.log(Level.FINE, "Unknown error", e); | logger.log(Level.SEVERE, "Unknown error", e); | public boolean isQualified(ApplicationConfig applicationConfig) { ServerConnection serverConnection = null; try { serverConnection = ServerConnector.getServerConnection(applicationConfig); String value = (String)serverConnection.getAttribute(objectName, ... |
ConnectorRegistry.remove(config); | public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) throws Exception { ... | |
stylesheet.setValueOfAction( new Action() { public void run(Node node) throws Exception { String text = node.getStringValue(); if ( text != null && text.length() > 0 ) { output.write( text ); } } } ); | public StylesheetTag() { // add default actions stylesheet.setValueOfAction( new Action() { public void run(Node node) throws Exception { String text = node.getStringValue(); if ( text != null && text.length() > 0 ) { ... | |
stylesheet.addRule( rule ); | getStylesheet().addRule( rule ); | public void addTemplate( Rule rule ) { stylesheet.addRule( rule ); } |
this.output = output; try { getBody().run(context, output); if ( log.isDebugEnabled() ) { log.debug( "About to evaluate stylesheet on source: " + source ); } stylesheet.setModeName( getMode() ); stylesheet.run( source ); } finally { this.output = null; stylesheet.clear(); } } | this.output = output; Stylesheet stylesheet = getStylesheet(); stylesheet.clear(); getBody().run(context, output); stylesheet.setModeName(getMode()); if (var != null) { context.setVariable(var, stylesheet); } else { Object source = getSource(); if (log.isDebugEnabled()) { log.debug("About to evaluate stylesheet on... | public void doTag(XMLOutput output) throws Exception { // for use by inner classes this.output = output; try { // run the body to add the rules getBody().run(context, output); if ( log.isDebugEnabled() ) { log.debug( "A... |
if ( stylesheet == null ) { stylesheet = createStylesheet(); } | public Stylesheet getStylesheet() { return stylesheet; } | |
this.variables = variables; | this.variables.putAll( variables ); | public void setVariables(Map variables) { this.variables = variables; } |
logger.info("Making Changes to the key of the column"); | public void setPrimaryKeySeq(Integer argPrimaryKeySeq) { Integer oldPrimaryKeySeq = primaryKeySeq; if (argPrimaryKeySeq != null && !this.autoIncrement) { setNullable(DatabaseMetaData.columnNoNulls); } if (this.primaryKeySeq != null && this.primaryKeySeq.equals(argPrimaryKeySeq)) return; this.primaryKeySeq = arg... | |
getBody().run(context, output); | invokeBody(output); | public void doTag(XMLOutput output) throws Exception { if (test != null) { if (test.evaluateAsBoolean(context)) { getBody().run(context, output); } } else { throw new MissingAttributeException( "test" ); } } |
super("Insert Column", | super("New Column", | public InsertColumnAction() { super("Insert Column", ASUtils.createIcon("NewColumn", "Insert Column", ArchitectFrame.getMainInstance().sprefs.getInt(SwingUserSettings.ICON_SIZE, 24))); } |
"Insert Column", | "New Column", | public InsertColumnAction() { super("Insert Column", ASUtils.createIcon("NewColumn", "Insert Column", ArchitectFrame.getMainInstance().sprefs.getInt(SwingUserSettings.ICON_SIZE, 24))); } |
putValue(SHORT_DESCRIPTION, "New Column"); | public InsertColumnAction() { super("Insert Column", ASUtils.createIcon("NewColumn", "Insert Column", ArchitectFrame.getMainInstance().sprefs.getInt(SwingUserSettings.ICON_SIZE, 24))); } | |
Haplotype[] crossHaplos = generateHaplotypes(inputVector, 1)[0]; | Haplotype[] crossHaplos = generateHaplotypes(inputVector, 1,true)[0]; | Haplotype[][] generateCrossovers(Haplotype[][] haplos) throws HaploViewException{ Vector crossBlock = new Vector(); double CROSSOVER_THRESHOLD = 0.01; //to what percentage do we want to consider crossings? if (haplos.length == 0) return null; //seed first block with ordering numbers ... |
Haplotype[][] generateHaplotypes(Vector blocks, int hapthresh) throws HaploViewException{ | Haplotype[][] generateHaplotypes(Vector blocks, int hapthresh, boolean crossover) throws HaploViewException{ | 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... |
} if (!crossover){ haplotypes = results; | 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... | |
PokeDBThread (SQLDatabase sd) { | PokeDBThread (SQLObject so) { | PokeDBThread (SQLDatabase sd) { super(); this.sd = sd; } |
this.sd = sd; | this.so = so; | PokeDBThread (SQLDatabase sd) { super(); this.sd = sd; } |
ArchitectUtils.pokeDatabase(sd); | ArchitectUtils.pokeDatabase(so); | public void run() { try { ArchitectUtils.pokeDatabase(sd); } catch (ArchitectException ex) { logger.error("problem poking database " + sd.getName(),ex); } logger.debug("finished poking database " + sd.getName()); } |
logger.error("problem poking database " + sd.getName(),ex); | logger.error("problem poking database " + so.getName(),ex); | public void run() { try { ArchitectUtils.pokeDatabase(sd); } catch (ArchitectException ex) { logger.error("problem poking database " + sd.getName(),ex); } logger.debug("finished poking database " + sd.getName()); } |
logger.debug("finished poking database " + sd.getName()); | logger.debug("finished poking database " + so.getName()); | public void run() { try { ArchitectUtils.pokeDatabase(sd); } catch (ArchitectException ex) { logger.error("problem poking database " + sd.getName(),ex); } logger.debug("finished poking database " + sd.getName()); } |
GraphApplet.this.repaint(); | public void run(){ while(true){ try { Thread.sleep(pollingInterval * 1000); } catch (InterruptedException e) { } /* get new data */ poll(); /* repaint */ GraphApplet.this.repain... | |
if(output == null) return null; | private Properties getNewValues(){ String output = doHttpPost(); Properties properties = new Properties(); try { properties.load(new ByteArrayInputStream(output.getBytes())); } catch (IOException e) { throw new RuntimeException(e); } return properties;... | |
if(properties == null) return; | private void poll() { Properties properties = getNewValues(); long timestamp = Long.parseLong(properties.getProperty("timestamp")); // todo: this is not used String attributes = properties.getProperty("attributes"); String values = properties.getProperty("values"); if(datas... | |
EventSystem.getInstance().fireEvent(new ApplicationChangedEvent(config)); | public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) throws Exception { ... | |
getBody().run(context, output); | invokeBody(output); | public void doTag(XMLOutput output) throws Exception { if ( var == null ) { var = "org.apache.commons.jelly.ojb.Broker"; } if ( broker != null ) { context.setVariable(var, broker); getBody().run(context, output); } else ... |
t.initFolders(); | t.initFolders(true); | public void actionPerformed(ActionEvent evt) { SQLTable t = new SQLTable(); t.initFolders(); t.setTableName("New_Table"); TablePane tp = new TablePane(t); pp.addFloating(tp); } |
String ident = logicalName.replace(' ','_').toUpperCase(); | String ident = logicalName.replace(' ','_'); | public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); /... |
String tempString = ident; Pattern p2 = Pattern.compile("[^a-xA-Z0-9_@$#]"); Matcher m2 = p2.matcher(ident); while (m2.find()) { tempString = tempString.replace(m2.group(),"_"); } | ident = ident.replaceAll("[^a-zA-Z0-9_@$#]", "_"); | public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); /... |
variables.put("context", this); variables.put("systemScope", System.getProperties()); } | variables.put("context",this); try { variables.put("systemScope", System.getProperties() ); } catch (SecurityException e) { } } | private void init() { variables.put("context", this); variables.put("systemScope", System.getProperties()); } |
if(parentGeno>=2 && kidsGeno>=1) tdtfams += parentGeno/2; | if(parentGeno>=2 && kidsGeno>=1){ if (parentGeno/2 > kidsGeno){ tdtfams += kidsGeno; }else{ tdtfams += parentGeno/2; } } | private int getNumOfFamTrio(Enumeration famList, Hashtable parentgeno, Hashtable kidgeno){ //int totalfams = 0; int tdtfams =0; while(famList.hasMoreElements()){ //totalfams++; int parentGeno=0, kidsGeno =0; String key = (String)famList.nextElement(); ... |
expandedFolders = new HashSet(); | public FolderController( PhotoInfo[] model ) { super( model ); addedToFolders = new HashSet(); removedFromFolders = new HashSet(); initTree(); } | |
expandedFolders.add( folder ); | void addPhotoToTree( PhotoInfo photo ) { Collection folders = photo.getFolders(); Iterator iter = folders.iterator(); while ( iter.hasNext() ) { PhotoFolder folder = (PhotoFolder) iter.next(); FolderNode fn = (FolderNode) nodeMapper.mapFolderToNode( folder ); fn.addPhoto( photo ); } } | |
expandedFolders.clear(); | public void setModel( Object[] model, boolean preserveState ) { this.model = model; if ( !preserveState && addedToFolders != null ) { addedToFolders.clear(); removedFromFolders.clear(); } initTree(); } | |
expandTreePaths(); | public void updateAllViews() { Iterator iter = views.iterator(); while ( iter.hasNext() ) { PhotoInfoView view = (PhotoInfoView) iter.next(); view.setFolderTreeModel( treeModel ); } } | |
this(s,include,exclude,ac,DEFAULT_RSQ_CUTOFF,AGGRESSIVE_TRIPLE); | this(s,include,exclude,ac,DEFAULT_RSQ_CUTOFF,AGGRESSIVE_TRIPLE, DEFAULT_MAXDIST); | public Tagger(Vector s, Vector include, Vector exclude, AlleleCorrelator ac){ this(s,include,exclude,ac,DEFAULT_RSQ_CUTOFF,AGGRESSIVE_TRIPLE); } |
if( getPairwiseCompRsq(currentVarSeq,(VariantSequence) snps.get(j)) >= minRSquared) { tempPT.addTagged((VariantSequence) snps.get(j)); | if( maxComparisonDistance == 0 || Math.abs(((SNP)currentVarSeq).getLocation() - ((SNP)snps.get(j)).getLocation()) <= maxComparisonDistance) { if( getPairwiseCompRsq(currentVarSeq,(VariantSequence) snps.get(j)) >= minRSquared) { tempPT.addTagged((VariantSequence) snps.get(j)); } | public Vector findTags() { tags = new Vector(); untagged = new Vector(); taggedSoFar = 0; //potentialTagsHash stores the PotentialTag objects keyed on the corresponding sequences Hashtable potentialTagHash = new Hashtable(); PotentialTagComparator ptcomp = new PotentialTagC... |
if(history == null){ if(logger.isLoggable(Level.INFO)){ logger.info("Added application " + appConfig.getName() + " to the downtimesMap."); } final long recordingSince = System.currentTimeMillis(); addApplicationToDB(appConfig.getApplicationId(), recordingSince); history = new ApplicationDowntimeHistory(recordingSince)... | assert history != null; | public ApplicationDowntimeHistory getDowntimeHistory(ApplicationConfig appConfig){ if(appConfig == null){ throw new NullPointerException("appConfig must be specified"); } ApplicationDowntimeHistory history = downtimesMap.get(appConfig); if(history == null){ /* it is... |
if(event instanceof NewApplicationEvent){ addApplication((NewApplicationEvent)event); return; } | public void handleEvent(EventObject event) { if(!(event instanceof ApplicationEvent)){ throw new IllegalArgumentException("event must of type ApplicationEvent"); } ApplicationEvent appEvent = (ApplicationEvent)event; ApplicationDowntimeHistory downtimeHistory = getDowntimeHist... | |
if (lowCI > FindBlocks.cutLowCI && highCI >= FindBlocks.cutHighCI) { | if (lowCI >= FindBlocks.cutLowCI && highCI >= FindBlocks.cutHighCI) { | public void colorDPrime(int scheme){ PairwiseLinkage dPrime[][] = theData.filteredDPrimeTable; if (scheme == STD_SCHEME){ // set coloring based on LOD and D' for (int i = 0; i < dPrime.length; i++){ for (int j = i+1; j < dPrime[i].length; j++){ P... |
}else if (highCI > FindBlocks.recHighCI) { | }else if (highCI >= FindBlocks.recHighCI) { | public void colorDPrime(int scheme){ PairwiseLinkage dPrime[][] = theData.filteredDPrimeTable; if (scheme == STD_SCHEME){ // set coloring based on LOD and D' for (int i = 0; i < dPrime.length; i++){ for (int j = i+1; j < dPrime[i].length; j++){ P... |
public void handleEvent(Event event) { if(sourceConfig.getApplicationConfig().equals(event.getApplicationConfig()) && event instanceof ApplicationDownEvent){ | public void handleEvent(EventObject event) { if(event instanceof ApplicationDownEvent && sourceConfig.getApplicationConfig().equals( ((ApplicationDownEvent)event).getApplicationConfig())){ | public void handleEvent(Event event) { if(sourceConfig.getApplicationConfig().equals(event.getApplicationConfig()) && event instanceof ApplicationDownEvent){ handler.handle(new AlertInfo()); } } |
ApplicationDowntimeService.getInstance().addListener(new ApplicationDowntimeEventListener()); | EventSystem.getInstance().addListener(new ApplicationDowntimeEventListener(), ApplicationDownEvent.class); | public void register(AlertHandler handler, String alertId, String alertName) { this.handler = handler; ApplicationDowntimeService.getInstance().addListener(new ApplicationDowntimeEventListener()); } |
xmlWriter.setEscapeText(isEscapeText()); | protected XMLOutput createXMLOutput(Writer writer) throws Exception { OutputFormat format = null; if (prettyPrint) { format = OutputFormat.createPrettyPrint(); } else { format = new OutputFormat(); } if ( encoding != null ) { format.... | |
UserManager userManager = UserManager.getInstance(); User completeUser = userManager.getUser(user.getUsername()); if(!user.getPassword().equals(completeUser.getPassword()) || !User.STATUS_ACTIVE.equals(completeUser.getStatus())){ throw new RuntimeException("Invalid user credentials."); | AuthService authService = ServiceFactory.getAuthService(); try { authService.login(context, user.getUsername(), user._getPlaintextPassword()); } catch (Exception e) { throw new RuntimeException(e); | private static void authenticate(ServiceContextImpl context, String className, String methodName){ User user = context.getUser(); if(user == null){ /* only the login method in AuthService is allowed without ... |
context.setUser(completeUser); | private static void authenticate(ServiceContextImpl context, String className, String methodName){ User user = context.getUser(); if(user == null){ /* only the login method in AuthService is allowed without ... | |
if( ! (curFam.containsKey(currentInd.getDadID()))) { | if( !currentInd.getDadID().equals("0") && ! (curFam.containsKey(currentInd.getDadID()))) { | public void parseLinkage(Vector pedigrees) throws PedFileException { int colNum = -1; boolean withOptionalColumn = false; int numLines = pedigrees.size(); Individual ind; this.order = new Vector(); for(int k=0; k<numLines; k++){ StringTokenizer tokenizer = new St... |
if(! (curFam.containsKey(currentInd.getMomID()))) { | if(!currentInd.getMomID().equals("0") && ! (curFam.containsKey(currentInd.getMomID()))) { | public void parseLinkage(Vector pedigrees) throws PedFileException { int colNum = -1; boolean withOptionalColumn = false; int numLines = pedigrees.size(); Individual ind; this.order = new Vector(); for(int k=0; k<numLines; k++){ StringTokenizer tokenizer = new St... |
public void clearDriverJarList() { driverJarList.clear(); } | public void clearDriverJarList(); | public void clearDriverJarList() { driverJarList.clear(); } |
public boolean removeDriverJar(String fullPath) { return driverJarList.remove(fullPath); } | public boolean removeDriverJar(String fullPath); | public boolean removeDriverJar(String fullPath) { return driverJarList.remove(fullPath); } |
return date; | return date != null ? (Date)date.clone() : null; | public Date getDate() { return date; } |
private void createDatabase() { | private boolean createDatabase() { | private void createDatabase() { // Ask for the admin password PVDatabase db = new PVDatabase(); String user = ""; String passwd = ""; if ( dbServerBtn.isSelected() ) { AdminLoginDlg loginDlg = new AdminLoginDlg( this, true ); if ( loginDlg.showDialog() == Adm... |
PVDatabase db = new PVDatabase(); String user = ""; String passwd = ""; if ( dbServerBtn.isSelected() ) { AdminLoginDlg loginDlg = new AdminLoginDlg( this, true ); if ( loginDlg.showDialog() == AdminLoginDlg.LOGIN_DLG_OK ) { user = loginDlg.getUsername(); passwd = loginDlg.getPasswd(); | try { PVDatabase db = new PVDatabase(); db.setName( nameFld.getText() ); PhotovaultSettings settings = PhotovaultSettings.getSettings(); settings.addDatabase( db ); String user = ""; String passwd = ""; if ( dbServerBtn.isSelected() ) { AdminLoginDlg loginDlg = new AdminLoginDlg( this, true ); if ( loginDlg.showDialog(... | private void createDatabase() { // Ask for the admin password PVDatabase db = new PVDatabase(); String user = ""; String passwd = ""; if ( dbServerBtn.isSelected() ) { AdminLoginDlg loginDlg = new AdminLoginDlg( this, true ); if ( loginDlg.showDialog() == Adm... |
db.setDbName( dbNameFld.getText() ); db.setDbHost( dbHostFld.getText() ); db.setName( nameFld.getText() ); Volume vol = new Volume( "defaultVolume", volumeDirFld.getText() ); db.addVolume( vol ); } else { db.setName( nameFld.getText() ); db.setInstanceType( PVDatabase.TYPE_EMBEDDED ); db.setEmbeddedDirectory( new File... | db.createDatabase( user, passwd ); settings.saveConfig(); } catch (PhotovaultException ex) { JOptionPane.showMessageDialog( this, ex.getMessage(), "Error creating database", JOptionPane.ERROR_MESSAGE ); return false; | private void createDatabase() { // Ask for the admin password PVDatabase db = new PVDatabase(); String user = ""; String passwd = ""; if ( dbServerBtn.isSelected() ) { AdminLoginDlg loginDlg = new AdminLoginDlg( this, true ); if ( loginDlg.showDialog() == Adm... |
db.createDatabase( user, passwd ); PhotovaultSettings settings = PhotovaultSettings.getSettings(); settings.addDatabase( db ); settings.saveConfig(); | private void createDatabase() { // Ask for the admin password PVDatabase db = new PVDatabase(); String user = ""; String passwd = ""; if ( dbServerBtn.isSelected() ) { AdminLoginDlg loginDlg = new AdminLoginDlg( this, true ); if ( loginDlg.showDialog() == Adm... | |
return true; | private void createDatabase() { // Ask for the admin password PVDatabase db = new PVDatabase(); String user = ""; String passwd = ""; if ( dbServerBtn.isSelected() ) { AdminLoginDlg loginDlg = new AdminLoginDlg( this, true ); if ( loginDlg.showDialog() == Adm... | |
String componentDisplay = component.draw(new DashboardContextImpl(context, | String componentDisplay = component.draw(new DashboardContextImpl(context, currentDashboardConfig, | public int doStartTag() throws JspException{ HttpServletRequest request = (HttpServletRequest)pageContext.getRequest(); WebContext context = null; try{ context = WebContext.get(request); ApplicationConfig appConfig = context.getApplicationConfig(); ... |
if (catalogTerm == null) { | if (getCatalogTerm() == null) { | public String getCatalogSeparator() throws SQLException { if (catalogTerm == null) { throw new SQLException("Catalogs are not supported"); } else { return "."; } } |
if (logger.isDebugEnabled()) logger.debug("getCatalogs: added '"+catName+"'"); | public ResultSet getCatalogs() throws SQLException { String catalogList = connection.getProperties().getProperty("catalogs"); MockJDBCResultSet rs = new MockJDBCResultSet(null, 1); rs.setColumnName(1, "TABLE_CAT"); if (getCatalogTerm() != null) { for (String catName : Arrays.asList(catalogList.split(","))) { ... | |
return null; | MockJDBCResultSet rs = new MockJDBCResultSet(null, 22); rs.setColumnName(1, "TABLE_CAT"); rs.setColumnName(2, "TABLE_SCHEM"); rs.setColumnName(3, "TABLE_NAME"); rs.setColumnName(4, "COLUMN_NAME"); rs.setColumnName(5, "DATA_TYPE"); rs.setColumnName(6, "TYPE_NAME"); rs.setColumnName(7, "COLUMN_SIZE"); rs.setColumnName(8,... | public ResultSet getColumns(String catalog, String schemaPattern, String tableNamePattern, String columnNamePattern) throws SQLException { // TODO Auto-generated method stub return null; } |
throw new UnsupportedOperationException("Not implemented"); | MockJDBCResultSet rs = new MockJDBCResultSet(null, 14); rs.setColumnName(1, "PKTABLE_CAT"); rs.setColumnName(2, "PKTABLE_SCHEM"); rs.setColumnName(3, "PKTABLE_NAME"); rs.setColumnName(4, "PKCOLUMN_NAME"); rs.setColumnName(5, "FKTABLE_CAT"); rs.setColumnName(6, "FKTABLE_SCHEM"); rs.setColumnName(7, "FKTABLE_NAME"); rs.s... | public ResultSet getExportedKeys(String catalog, String schema, String table) throws SQLException { throw new UnsupportedOperationException("Not implemented"); } |
throw new UnsupportedOperationException("Not implemented"); | MockJDBCResultSet rs = new MockJDBCResultSet(null, 14); rs.setColumnName(1, "PKTABLE_CAT"); rs.setColumnName(2, "PKTABLE_SCHEM"); rs.setColumnName(3, "PKTABLE_NAME"); rs.setColumnName(4, "PKCOLUMN_NAME"); rs.setColumnName(5, "FKTABLE_CAT"); rs.setColumnName(6, "FKTABLE_SCHEM"); rs.setColumnName(7, "FKTABLE_NAME"); rs.s... | public ResultSet getImportedKeys(String catalog, String schema, String table) throws SQLException { throw new UnsupportedOperationException("Not implemented"); } |
throw new UnsupportedOperationException("Not implemented"); | MockJDBCResultSet rs = new MockJDBCResultSet(null, 6); rs.setColumnName(1, "TABLE_CAT"); rs.setColumnName(2, "TABLE_SCHEM"); rs.setColumnName(3, "TABLE_NAME"); rs.setColumnName(4, "COLUMN_NAME"); rs.setColumnName(5, "KEY_SEQ"); rs.setColumnName(6, "PK_NAME"); return rs; | public ResultSet getPrimaryKeys(String catalog, String schema, String table) throws SQLException { throw new UnsupportedOperationException("Not implemented"); } |
logger.debug("getSchemas: schemaTerm==null; returning empty result set"); | public ResultSet getSchemas() throws SQLException { String catalogList = connection.getProperties().getProperty("catalogs"); MockJDBCResultSet rs = new MockJDBCResultSet(null, 2); rs.setColumnName(1, "TABLE_SCHEM"); rs.setColumnName(2, "TABLE_CATALOG"); if (getSchemaTerm() == null) { // no schemas. return emp... | |
rs.updateObject(1, null); rs.updateObject(2, schName); | rs.updateObject(1, schName); rs.updateObject(2, null); if (logger.isDebugEnabled()) logger.debug("getSchemas: added '"+schName+"'"); | public ResultSet getSchemas() throws SQLException { String catalogList = connection.getProperties().getProperty("catalogs"); MockJDBCResultSet rs = new MockJDBCResultSet(null, 2); rs.setColumnName(1, "TABLE_SCHEM"); rs.setColumnName(2, "TABLE_CATALOG"); if (getSchemaTerm() == null) { // no schemas. return emp... |
logger.debug("getSchemas: database has catalogs and schemas!"); | public ResultSet getSchemas() throws SQLException { String catalogList = connection.getProperties().getProperty("catalogs"); MockJDBCResultSet rs = new MockJDBCResultSet(null, 2); rs.setColumnName(1, "TABLE_SCHEM"); rs.setColumnName(2, "TABLE_CATALOG"); if (getSchemaTerm() == null) { // no schemas. return emp... | |
rs.updateObject(1, catName); rs.updateObject(2, schName); | rs.updateObject(1, schName); rs.updateObject(2, catName); if (logger.isDebugEnabled()) logger.debug("getSchemas: added '"+catName+"'.'"+schName+"'"); | public ResultSet getSchemas() throws SQLException { String catalogList = connection.getProperties().getProperty("catalogs"); MockJDBCResultSet rs = new MockJDBCResultSet(null, 2); rs.setColumnName(1, "TABLE_SCHEM"); rs.setColumnName(2, "TABLE_CATALOG"); if (getSchemaTerm() == null) { // no schemas. return emp... |
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