rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k |
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Storable newReplicaEntry = mReplicaStorage.prepare(); | S newReplicaEntry = mReplicaStorage.prepare(); | void resyncEntries(S replicaEntry, S masterEntry) throws FetchException, PersistException { if (replicaEntry == null && masterEntry == null) { return; } Log log = LogFactory.getLog(ReplicatedRepository.class); setReplicationDisabled(true); try { Transaction t... |
log.info("Adding missing entry: " + newReplicaEntry); | log.info("Adding missing replica entry: " + newReplicaEntry); | void resyncEntries(S replicaEntry, S masterEntry) throws FetchException, PersistException { if (replicaEntry == null && masterEntry == null) { return; } Log log = LogFactory.getLog(ReplicatedRepository.class); setReplicationDisabled(true); try { Transaction t... |
replicaEntry.copyUnequalProperties(newReplicaEntry); masterEntry.copyAllProperties(newReplicaEntry); log.info("Replacing stale entry with: " + newReplicaEntry); | transferToReplicaEntry(replicaEntry, masterEntry, newReplicaEntry); log.info("Replacing stale replica entry with: " + newReplicaEntry); | void resyncEntries(S replicaEntry, S masterEntry) throws FetchException, PersistException { if (replicaEntry == null && masterEntry == null) { return; } Log log = LogFactory.getLog(ReplicatedRepository.class); setReplicationDisabled(true); try { Transaction t... |
synchronized (lock) { while (true) { storage = mStorageMap.get(type); if (storage != null) { return storage; } if (doCreate) { break; } try { lock.wait(); } catch (InterruptedException e) { throw new RepositoryException("Interrupted"); } } StorableIntrospector.examine(type); storage = createStorage(type); mStorage... | if (Thread.holdsLock(lock)) { throw new IllegalStateException ("Recursively trying to create storage for type: " + type); | public <S extends Storable> Storage<S> storageFor(Class<S> type) throws MalformedTypeException, SupportException, RepositoryException { Storage storage = mStorageMap.get(type); if (storage != null) { return storage; } Object lock; boolean doCreate; sync... |
synchronized (mStorableTypeLockMap) { mStorableTypeLockMap.remove(type); | try { synchronized (lock) { while (true) { storage = mStorageMap.get(type); if (storage != null) { return storage; } if (doCreate) { break; } try { lock.wait(); } catch (InterruptedException e) { throw new RepositoryException("Interrupted"); } } StorableIntrospector.examine(type); storage = createStorage(type); mS... | public <S extends Storable> Storage<S> storageFor(Class<S> type) throws MalformedTypeException, SupportException, RepositoryException { Storage storage = mStorageMap.get(type); if (storage != null) { return storage; } Object lock; boolean doCreate; sync... |
logger.debug("added rectangles, new bounds: " + scrollTo); | public void actionPerformed(ActionEvent e) { playpen.setZoom(playpen.getZoom() + zoomStep); Rectangle scrollTo = null; Iterator it = playpen.getSelectedItems().iterator(); while (it.hasNext()) { Rectangle bounds = ((Component) it.next()).getBounds(); if (scrollTo == null) { scrollTo = new Rectangle(bounds);... | |
* Do not use delimiters for the database object names in SQWL statements. | * Do not use delimiters for the database object names in SQL statements. | public void createDatabase( String user, String passwd ) { // Get the database schema XML file InputStream schemaIS = getClass().getClassLoader().getResourceAsStream( "photovault_schema.xml" ); Database dbModel = new DatabaseIO().read( new InputStreamReader( schemaIS ) ); ... |
String localName = null; | public void doTag(XMLOutput output) throws Exception { String localName = null; int idx = name.indexOf(':'); if (idx >= 0) { localName = name.substring(idx + 1); } else { localName = name; } /** * @todo we should buffer up any S... | |
if (idx >= 0) { localName = name.substring(idx + 1); | final String localName = (idx >= 0) ? name.substring(idx + 1) : name; outputAttributes = false; XMLOutput newOutput = new XMLOutput(output) { public void startElement( String uri, String localName, String qName, Attributes atts) throws SAXException { initialize(); super.startElement(uri, localName, qName, atts); }... | public void doTag(XMLOutput output) throws Exception { String localName = null; int idx = name.indexOf(':'); if (idx >= 0) { localName = name.substring(idx + 1); } else { localName = name; } /** * @todo we should buffer up any S... |
else { localName = name; } invokeBody(output); output.startElement(namespace, localName, name, attributes); | public void doTag(XMLOutput output) throws Exception { String localName = null; int idx = name.indexOf(':'); if (idx >= 0) { localName = name.substring(idx + 1); } else { localName = name; } /** * @todo we should buffer up any S... | |
public void setAttributeValue( String name, String value ) { | public void setAttributeValue( String name, String value ) throws JellyException { if (outputAttributes) { throw new JellyException( "Cannot set the value of attribute: " + name + " as we have already output the startElement() SAX event" ); } | public void setAttributeValue( String name, String value ) { // ### we'll assume that all attributes are in no namespace! // ### this is severely limiting! // ### we should be namespace aware int index = attributes.getIndex("", name); if (index >= 0) { attributes.remove... |
tableModelSortDecorator.initColumnSizes(viewTable); | public void actionPerformed(ActionEvent e) { if (dbTree == null) { logger.debug("dbtree was null when actionPerformed called"); return; } if ( dbTree.getSelectionPaths() == null ) { logger.debug("dbtree path selection was null when actionPerformed called"); ... | |
tableModelSortDecorator.initColumnSizes(viewTable); | public void run() { try { List<SQLTable> toBeProfiled = new ArrayList<SQLTable>(); for (SQLTable t: tables) { if (profileManager.getResult(t)== null) { toBeProfiled.add(t); ... | |
System.out.println(ufe); | log.warn(ufe); | public void drop(DropTargetDropEvent e) { hoverTimer.stop(); // Prevent hover timer from doing an unwanted expandPath or collapsePath if (!isDropAcceptable(e)) { e.rejectDrop(); return; } e.acceptDrop(e.getDropAction()); Transferable transferable = e.getTransferable(); DataFlavor[] flavors = tra... |
System.out.println(ioe); | log.warn(ioe); | public void drop(DropTargetDropEvent e) { hoverTimer.stop(); // Prevent hover timer from doing an unwanted expandPath or collapsePath if (!isDropAcceptable(e)) { e.rejectDrop(); return; } e.acceptDrop(e.getDropAction()); Transferable transferable = e.getTransferable(); DataFlavor[] flavors = tra... |
} else { niprint("populated=\"true\" "); | protected void saveSQLObject(SQLObject o) throws IOException, ArchitectException { String id = (String) objectIdMap.get(o); if (id != null) { println("<reference ref-id=\""+id+"\" />"); return; } String type; Map propNames = new TreeMap(); if (o instanceof SQLDatabase) { id = "DB"+objectIdMap.size(); t... | |
Map paramValues = config.getParamValues(); if(appForm.getJndiFactory() != null){ paramValues.put(ApplicationConfig.JNDI_FACTORY, appForm.getJndiFactory()); }else{ paramValues.remove(ApplicationConfig.JNDI_FACTORY); } if(appForm.getJndiURL() != null){ paramValues.put(ApplicationConfig.JNDI_URL, appForm.getJndiURL()); }... | public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) throws Exception { ... | |
getInherit() ) { | isInherit() ) { | public Object getVariable(String name) { Object value = variables.get(name); if ( value == null && getInherit() ) { value = getParent().findVariable( name ); } return value; } |
public void setExport(boolean shouldExport) { this.shouldExport = shouldExport; | public void setExport(boolean export) { this.export = export; | public void setExport(boolean shouldExport) { this.shouldExport = shouldExport; } |
public void setInherit(boolean shouldInherit) { this.shouldInherit = shouldInherit; | public void setInherit(boolean inherit) { this.inherit = inherit; | public void setInherit(boolean shouldInherit) { this.shouldInherit = shouldInherit; } |
if ( getExport() ) { | if ( isExport() ) { | public void setVariable(String name, Object value) { if ( getExport() ) { getParent().setVariable( name, value ); return; } if (value == null) { variables.remove(name); } else { variables.put(name, value); } } |
Haplotype h = (Haplotype) alleles.get(i); | Haplotype h = (Haplotype) filteredAlleles.get(i); | public String getFreqString(int i ){ if (Options.getAssocTest() == ASSOC_TRIO){ return ""; } nf.setMinimumFractionDigits(3); nf.setMaximumFractionDigits(3); StringBuffer countSB = new StringBuffer(); Haplotype h = (Haplotype) alleles.get(i); double caseSum... |
public JSR160ServerConnection(JMXConnector jmxc ) | public JSR160ServerConnection(JMXConnector jmxc, MBeanServerConnection mbeanServer) | public JSR160ServerConnection(JMXConnector jmxc ) throws IOException { assert jmxc != null; this.jmxc = jmxc; this.mbeanServer = jmxc.getMBeanServerConnection(); } |
this.mbeanServer = jmxc.getMBeanServerConnection(); | this.mbeanServer = mbeanServer; | public JSR160ServerConnection(JMXConnector jmxc ) throws IOException { assert jmxc != null; this.jmxc = jmxc; this.mbeanServer = jmxc.getMBeanServerConnection(); } |
throw new RuntimeException("Notifications not supported"); | Class[] methodSignature = new Class[]{String.class, javax.management.ObjectName.class, new Object[0].getClass(), new String[0].getClass()}; Object[] methodArgs = new Object[]{className, toJMXObjectName(name), params, signature}; callMBeanServer("createMBean", methodSignature, methodArgs); | public void createMBean(String className, ObjectName name, Object[] params, String[] signature){ throw new RuntimeException("Notifications not supported"); } |
throw new RuntimeException("unregisterMBean not supported"); | Class[] methodSignature = new Class[]{javax.management.ObjectName.class}; Object[] methodArgs = new Object[]{toJMXObjectName(objectName)}; callMBeanServer("unregisterMBean", methodSignature, methodArgs); | public void unregisterMBean(ObjectName objectName){ throw new RuntimeException("unregisterMBean not supported"); } |
return ((Haplotype) alleles.get(i)).toString(); | return ((Haplotype) filteredAlleles.get(i)).toString(); | public String getAlleleName(int i) { return ((Haplotype) alleles.get(i)).toString(); } |
public String getFreq(int j) { double freq = ((Haplotype)alleles.get(j)).getPercentage(); | public String getFreq(int i) { double freq = ((Haplotype)alleles.get(i)).getPercentage(); | public String getFreq(int j) { double freq = ((Haplotype)alleles.get(j)).getPercentage(); if (freq < 0){ return (""); }else{ nf.setMinimumFractionDigits(3); nf.setMaximumFractionDigits(3); return nf.format(freq); } } |
return ((Haplotype) alleles.get(i)).toNumericString(); | return ((Haplotype) filteredAlleles.get(i)).toNumericString(); | public String getNumericAlleleName(int i){ return ((Haplotype) alleles.get(i)).toNumericString(); } |
tempRec.p = (float)(probMap.get(new Long(tempRec.h1))); | if (tempRec.h1 == tempRec.h2){ tempRec.p = (float)(probMap.get(new Long(tempRec.h1))); }else{ tempRec.p = 0; } | private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus, Vector kidAffStatus, boolean[] haploid) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_bloc... |
superdata[i].superposs[k].p = (float) (fullProbMap.get(new Long(superdata[i].superposs[k].h1))); | if (superdata[i].superposs[k].h1 == superdata[i].superposs[k].h2){ superdata[i].superposs[k].p = (float) (fullProbMap.get(new Long(superdata[i].superposs[k].h1))); }else{ superdata[i].superposs[k].p = 0; } | private void full_em_breakup( byte[][] input_haplos, int[] block_size, Vector affStatus, Vector kidAffStatus, boolean[] haploid) throws HaploViewException{ int num_poss, iter; double total = 0; int block, start_locus, end_locus, biggest_block_size; int num_indivs = 0; int num_bloc... |
this.zeroed = new Vector(); | public Individual(){ this.markers = new Vector(); } | |
this.zeroed.add(new Boolean(false)); | public void addMarker(byte[] marker){ this.markers.add(marker); } | |
byte zeroArray[] = {0,0}; this.markers.set(i, zeroArray); | this.zeroed.set(i, new Boolean(true)); | public void zeroOutMarker(int i){ byte zeroArray[] = {0,0}; this.markers.set(i, zeroArray); } |
public TagScript createTagScript(String name, Attributes attributes) throws Exception { | public TagScript createTagScript(final String name, Attributes attributes) throws Exception { | public TagScript createTagScript(String name, Attributes attributes) throws Exception { Project project = getProject(); // custom Ant tags if ( name.equals("fileScanner") ) { Tag tag = new FileScannerTag(new FileScanner(project)); return TagScript.newIn... |
Project project = getProject(); if ( name.equals("fileScanner") ) { Tag tag = new FileScannerTag(new FileScanner(project)); return TagScript.newInstance(tag); | TagScript answer = createCustomTagScript(name, attributes); if ( answer == null ) { answer = new DynaTagScript( new TagFactory() { public Tag createTag() throws Exception { return AntTagLibrary.this.createTag(name); } } ); | public TagScript createTagScript(String name, Attributes attributes) throws Exception { Project project = getProject(); // custom Ant tags if ( name.equals("fileScanner") ) { Tag tag = new FileScannerTag(new FileScanner(project)); return TagScript.newIn... |
AntTag tag = new AntTag( getProject(), name ); if ( name.equals( "echo" ) ) { tag.setTrim(false); } return TagScript.newInstance(tag); | return answer; | public TagScript createTagScript(String name, Attributes attributes) throws Exception { Project project = getProject(); // custom Ant tags if ( name.equals("fileScanner") ) { Tag tag = new FileScannerTag(new FileScanner(project)); return TagScript.newIn... |
this( AntTagLibrary.createProject() ); | this.antTagLib = new AntTagLibrary(); | public JeezTagLibrary() { this( AntTagLibrary.createProject() ); } |
public TagScript createTagScript(String name, Attributes attrs) throws Exception { TagScript script = super.createTagScript( name, attrs ); | public TagScript createTagScript( final String name, Attributes attrs ) throws Exception { | public TagScript createTagScript(String name, Attributes attrs) throws Exception { TagScript script = super.createTagScript( name, attrs ); if ( script == null ) { // script = this.coreTagLib.createTagScript( name, attrs ); if ( script == nu... |
script = antTagLib.createCustomTagScript( name, attrs ); | public TagScript createTagScript(String name, Attributes attrs) throws Exception { TagScript script = super.createTagScript( name, attrs ); if ( script == null ) { // script = this.coreTagLib.createTagScript( name, attrs ); if ( script == nu... | |
script = this.werkzTagLib.createTagScript( name, attrs ); if ( script == null ) { if ( isRuntimeTask( name ) ) { if ( ! project.getTaskDefinitions().containsKey( name ) ) { script = this.antTagLib.createRuntimeTaskTagScript( name, attrs ); } else { this.runtimeTasks.remove( name ); | return new DynaTagScript( new TagFactory() { public Tag createTag() throws Exception { Tag tag = JeezTagLibrary.this.createTag(name); if ( tag != null ) { return tag; } else { return antTagLib.createTag( name ); } | public TagScript createTagScript(String name, Attributes attrs) throws Exception { TagScript script = super.createTagScript( name, attrs ); if ( script == null ) { // script = this.coreTagLib.createTagScript( name, attrs ); if ( script == nu... |
if ( script == null ) { script = this.antTagLib.createTagScript( name, attrs ); } if ( name.equals( "taskdef" ) ) { addRuntimeTask( attrs.getValue( "name" ) ); } } | ); | public TagScript createTagScript(String name, Attributes attrs) throws Exception { TagScript script = super.createTagScript( name, attrs ); if ( script == null ) { // script = this.coreTagLib.createTagScript( name, attrs ); if ( script == nu... |
public TagScript createTagScript(String name, Attributes attributes) | public TagScript createTagScript(final String name, Attributes attributes) | public TagScript createTagScript(String name, Attributes attributes) throws Exception { Object value = templates.get(name); if ( value instanceof Script ) { Script template = (Script) value; DynamicTag tag = new DynamicTag(template); // XXXX: somehow... |
Object value = templates.get(name); if ( value instanceof Script ) { Script template = (Script) value; DynamicTag tag = new DynamicTag(template); return new DynaTagScript(tag); } else if ( value instanceof DynaTag ) { DynaTag tag = (DynaTag) value; return new DynaTagScript(tag); } return null; | return new DynaTagScript( new TagFactory() { public Tag createTag() throws Exception { return DynamicTagLibrary.this.createTag(name); } } ); | public TagScript createTagScript(String name, Attributes attributes) throws Exception { Object value = templates.get(name); if ( value instanceof Script ) { Script template = (Script) value; DynamicTag tag = new DynamicTag(template); // XXXX: somehow... |
public void setDisplayThresh(int amount) { parent.displayThresh = amount; parent.adjustDisplay(); | public void setDisplayThresh(int amount){ if (parent.displayThresh != amount){ parent.adjustDisplay(amount); } | public void setDisplayThresh(int amount) { parent.displayThresh = amount; parent.adjustDisplay(); } |
if (this.getParent() != null){ if (this.getPreferredSize().height > this.getParent().getHeight()){ ((JScrollPane)this.getParent().getParent()).setVerticalScrollBarPolicy( JScrollPane.VERTICAL_SCROLLBAR_ALWAYS ); }else{ ((JScrollPane)this.getParent().getParent()).setVerticalScrollBarPolicy( JScrollPane.VERTICAL_SCROLLBA... | public void adjustDisplay(int dt){ //this is called when the controller wants to change the haps //displayed, instead of directly repainting so that none of this math //is done when the screen repaints for other reasons (resizing, focus change, etc) //first filter haps on displaythresh ... | |
assertEquals("displayName", l.getLastPropertyChange()); | assertEquals("name", l.getLastPropertyChange()); | public void testSetDisplayName() { CountingPropertyChangeListener l = new CountingPropertyChangeListener(); ds.addPropertyChangeListener(l); ds.setDisplayName("test"); assertEquals(1, l.getPropertyChangeCount()); assertEquals("displayName", l.getLastPropertyChange()); assertEquals("test", ds.getDisplayName());... |
ind.setZeroedArray(sortedZeroed); | void prepareMarkerInput(File infile, String[][] hapmapGoodies) throws IOException, HaploViewException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position. the maxdist ... | |
editColumnAction.setDBTree(dbTree); insertColumnAction.setDBTree(dbTree); editRelationshipAction.setDBTree(dbTree); deleteSelectedAction.setDBTree(dbTree); editTableAction.setDBTree(dbTree); | protected void setupActions() { aboutAction.setPlayPen(playpen); printAction.setPlayPen(playpen); deleteSelectedAction.setPlayPen(playpen); editColumnAction.setPlayPen(playpen); insertColumnAction.setPlayPen(playpen); editTableAction.setPlayPen(playpen); createTableAction.setPlayPen(playpen); createIdentifying... | |
public void dPrimeDraw(String[][] table, Graphics g){ | public void dPrimeDraw(String[][] table, boolean info, Vector snps, Graphics g){ | public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo... |
g.fillRect(0,0,scale,scale); | g.fillRect(0,0,scale+activeOffset,scale); | public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo... |
g.drawString("1", shifts[0], shifts[1]); | g.drawString("1", activeOffset + shifts[0], shifts[1]); | public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo... |
if (info){ g.setFont(regFont); for (int y = 0; y < table.length; y++){ String name = ((SNP)snps.elementAt(y)).getName(); g.drawString(name, labeloffset-3-regfm.stringWidth(name), y*30 + shifts[1]); } if (table.length > 3){ g.drawLine(labeloffset+90,5,labeloffset+scale-5,scale-90); double lineLength = Math.sqrt((scale... | public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo... | |
g.fillRect(x*30+1, y*30+1, 28, 28); | g.fillRect(x*30+1+activeOffset, y*30+1, 28, 28); | public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo... |
g.drawRect(x*30, y*30, 30, 30); | g.drawRect(x*30+activeOffset, y*30, 30, 30); | public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo... |
g.drawString(Float.toString(d), shifts[0]+(x*30) ,(y*30)+shifts[1]); | g.drawString(Float.toString(d), shifts[0]+(x*30)+activeOffset,(y*30)+shifts[1]); | public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo... |
g.drawString(Integer.toString(x+2), shifts[0]+(x+1)*30, shifts[1]+(x+1)*30); | g.drawString(Integer.toString(x+2), shifts[0]+(x+1)*30+activeOffset, shifts[1]+(x+1)*30); | public void dPrimeDraw(String[][] table, Graphics g){ int scale = table.length*30; float d, l, blgr; Color myColor; int[] shifts; Font regFont = new Font("Lucida Sans Regular", Font.PLAIN, 10); FontMetrics regfm = g.getFontMetrics(regFont); Font boldFont = new Font("Lucida Sans Bold", Font.BOLD, 14); FontMetrics bo... |
public Dimension dPrimeGetPreferredSize(int size){ return new Dimension(size*30, size*30); | public Dimension dPrimeGetPreferredSize(int size, boolean info){ if (info){ return new Dimension((labeloffset+size*30), size*30); }else{ return new Dimension(size*30, size*30); } | public Dimension dPrimeGetPreferredSize(int size){ return new Dimension(size*30, size*30); } |
h.put(name, value); | h.put(name, value.toString()); | public Hashtable getProperties() { Hashtable h = new Hashtable(); for (Iterator i = this.context.getVariableNames(); i.hasNext(); ) { String name = (String) i.next(); Object value = this.context.getVariable(name); if (value != null) { h.put(name, value);... |
properties = new HashMap(); | properties = new HashMap<String,String>(); | public ArchitectDataSource() { properties = new HashMap(); } |
return (String) properties.get(key); | return properties.get(key); | public String get(String key) { return (String) properties.get(key); } |
return (String) properties.get(PL_DSN); | return properties.get(PL_DSN); | public String getOdbcDsn() { return (String) properties.get(PL_DSN); } |
protected PropertyChangeSupport getPcs() { | private PropertyChangeSupport getPcs() { | protected PropertyChangeSupport getPcs() { if (pcs == null) pcs = new PropertyChangeSupport(this); return pcs; } |
return (String) properties.get(PL_TYPE); | return properties.get(PL_TYPE); | public String getPlDbType() { return (String) properties.get(PL_TYPE); } |
return (String) properties.get(PL_SCHEMA_OWNER); | return properties.get(PL_SCHEMA_OWNER); | public String getPlSchema() { return (String) properties.get(PL_SCHEMA_OWNER); } |
public Map getPropertiesMap() { return properties; | public Map<String,String> getPropertiesMap() { return Collections.unmodifiableMap(properties); | public Map getPropertiesMap() { return properties; } |
Window.setDefaultImage(image); | window.getShell().setImage(image); | private void setWindowImage(Window window, Image image) { Window.setDefaultImage(image); } |
throw new JellyTagException("This tag must be nested within a widget"); | throw new JellyTagException("This tag must be nested within a Widget or a Window"); | public void doTag(XMLOutput output) throws JellyTagException { // invoke by body just in case some nested tag configures me invokeBody(output); Widget parent = getParentWidget(); if (parent == null) { throw new JellyTagException("This tag must be nested within a widget"); ... |
Image image = new Image(parent.getDisplay(), getSrc()); | public void doTag(XMLOutput output) throws JellyTagException { // invoke by body just in case some nested tag configures me invokeBody(output); Widget parent = getParentWidget(); if (parent == null) { throw new JellyTagException("This tag must be nested within a widget"); ... | |
if (parent instanceof Label) { Label label = (Label) parent; label.setImage(image); } else if (parent instanceof Button) { Button button = (Button) parent; button.setImage(image); } else if (parent instanceof Item) { Item item = (Item) parent; item.setImage(image); } else if (parent instanceof Decorations) { Decorat... | Image image = new Image(parent.getDisplay(), getSrc()); setWidgetImage(parent, image); } | public void doTag(XMLOutput output) throws JellyTagException { // invoke by body just in case some nested tag configures me invokeBody(output); Widget parent = getParentWidget(); if (parent == null) { throw new JellyTagException("This tag must be nested within a widget"); ... |
colorMenuItems[0].setSelected(true); | colorMenuItems[Options.getLDColorScheme()].setSelected(true); | public HaploView(){ try{ fc = new JFileChooser(System.getProperty("user.dir")); }catch(NullPointerException n){ try{ UIManager.setLookAndFeel(UIManager.getCrossPlatformLookAndFeelClassName()); fc = new JFileChooser(System.getProperty("user.dir")); ... |
drp.addMenuElement(tpc.toString(), tpc.getName()); | drp.addMenuElement(tpc.getIdentifier().toString(), tpc.getName()); | public PresentationObject getLetterForm(IWContext iwc) { Table T = new Table(); TextInput fromAddress = new TextInput("from_address"); fromAddress.setLength(80); TextInput fromName = new TextInput("from_name"); fromName.setLength(80); TextInput subject = new TextInput("subject"); subject.setLength(80); TextAre... |
T.add(new HiddenInput("topic_id", tpc.toString()), 2, row++); | T.add(new HiddenInput("topic_id",tpc.getIdentifier().toString()), 2, row++); | public PresentationObject getLetterForm(IWContext iwc) { Table T = new Table(); TextInput fromAddress = new TextInput("from_address"); fromAddress.setLength(80); TextInput fromName = new TextInput("from_name"); fromName.setLength(80); TextInput subject = new TextInput("subject"); subject.setLength(80); TextAre... |
public void doTag(XMLOutput output) throws Exception { | public void doTag(XMLOutput output) throws MissingAttributeException, Exception { | public void doTag(XMLOutput output) throws Exception { if (test != null) { while (test.evaluateAsBoolean(getContext())) { if (log.isDebugEnabled()) { log.debug("evaluated to true! gonna keep on chuggin!"); } invokeBody(output); ... |
final long maxCompDist = Long.parseLong(filenames[2])*1000; | maxCompDist = Long.parseLong(filenames[2])*1000; | void processData(){ final long maxCompDist = Long.parseLong(filenames[2])*1000; try{ this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); final SwingWorker worker = new SwingWorker(){ public Object construct(){ dPrimeDisplay=null; ... |
int good = theData.prepareMarkerInput(inputFile); | int good = theData.prepareMarkerInput(inputFile,maxCompDist); | void readMarkers(File inputFile){ try { int good = theData.prepareMarkerInput(inputFile); if (good == -1){ JOptionPane.showMessageDialog(this, "Number of markers in info file does not match number of markers in dataset.", "Err... |
throw new LockedColumnException(this); | throw new LockedColumnException(this,col); | public void checkColumnLocked(SQLColumn col) throws LockedColumnException { for (SQLRelationship.ColumnMapping cm : getMappings()) { if (cm.getFkColumn() == col) { throw new LockedColumnException(this); } } } |
Iterator iter = modelFields.values().iterator(); while( iter.hasNext() ) { FieldController fieldCtrl = (FieldController) iter.next(); fieldCtrl.updateAllViews(); } | public void setView( PhotoInfoView view ) { views.clear(); views.add( view ); } | |
Context context = new Context(); | JellyContext context = new JellyContext(); | public void testParse() throws Exception { InputStream in = getClass().getResourceAsStream( "example.jelly" ); XMLParser parser = new XMLParser(); Script script = parser.parse( in ); script = script.compile(); log.debug( "Found: " + script ); assertTrue( "Script is ... |
setDynaBean( new WrapDynaBean(dataType) ); | setDynaBean( new ConvertingWrapDynaBean(dataType) ); | public void setDataType(Object dataType) { this.dataType = dataType; setDynaBean( new WrapDynaBean(dataType) ); } |
} | }else{ g2.fillRect(0,0,size.width, size.height); } g2.setColor(Color.black); | public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... |
g2.setColor(BG_GREY); g2.fillRect(0,0,pref.width,pref.height); g2.setColor(Color.black); | public void paintComponent(Graphics g){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ ... | |
if (a1 == 5 && a2 == 5){ | if (a1 >= 5 && a2 >= 5){ | public void tallyCCInd(byte a1, byte a2, int cc){ //case = 0, control = 1 for int cc if (a1 == 5 && a2 == 5){ counts[cc][0]++; counts[cc][1]++; }else{ //seed the alleles as soon as they're found if (allele1 == 0){ allele1 = a1; ... |
if(alleleT == 5 && alleleU == 5) { | if(alleleT >= 5 && alleleU >= 5) { | public void tallyTrioInd(byte alleleT, byte alleleU) { if(alleleT == 5 && alleleU == 5) { if(tallyHet){ counts[0][0]++; counts[1][1]++; counts[0][1]++; counts[1][0]++; this.tallyHet = false; } else { ... |
int size = entry.size; | private void findAllMatchingTestMail(String username) throws SamplingException { try { org.apache.commons.net.pop3.POP3Client pop3Client = openConnection(username); // retrieve all messages POP3MessageInfo[] entries = null; try { entries = pop3Client... | |
MailProcessingRecord mailProcessingRecord = new MailProcessingRecord(); mailProcessingRecord.setReceivingQueue("pop3"); mailProcessingRecord.setTimeFetchStart(System.currentTimeMillis()); String mailText; BufferedReader mailReader = null; Reader reader = null; | private void findAllMatchingTestMail(String username) throws SamplingException { try { org.apache.commons.net.pop3.POP3Client pop3Client = openConnection(username); // retrieve all messages POP3MessageInfo[] entries = null; try { entries = pop3Client... | |
reader = pop3Client.retrieveMessage(entry.number); mailReader = new BufferedReader(reader); analyzeAndMatch(mailReader, mailProcessingRecord, pop3Client, i); } catch (Exception e) { log.info("failed to read pop3 mail #" + i + " for " + username); continue; } finally { if (reader != null) { try { reader.close(); } catc... | new POP3MailAnalyzeStrategy("pop3", m_results, pop3Client, entry.number, i).handle(); } catch (Exception exception) { log.warn("error processing pop3 mail", exception); } | private void findAllMatchingTestMail(String username) throws SamplingException { try { org.apache.commons.net.pop3.POP3Client pop3Client = openConnection(username); // retrieve all messages POP3MessageInfo[] entries = null; try { entries = pop3Client... |
return text; | return "${" + text + "}"; | public Expression createExpression(final String text) throws Exception {/* org.apache.commons.jexl.Expression expr = org.apache.commons.jexl.ExpressionFactory.createExpression(text); if ( isSupportAntVariables() ) { expr.addPostResolver(new FlatResolv... |
return text; | return "${" + text + "}"; | public String getExpressionText() { return text; } |
throw new MissingAttributeException( "var" ); | throw new MissingAttributeException( "delim" ); | public void doTag(final XMLOutput output) throws Exception { if ( this.var == null ) { throw new MissingAttributeException( "var" ); } if ( this.delim == null ) { throw new MissingAttributeException( "var" ); } StringTokenizer tokenizer = new... |
String className = (String) entry.getValue(); context.registerTagLibrary("jelly:" + uri, className); | String className = (String) entry.getValue(); String libraryURI = "jelly:" + uri; if ( context.getTagLibrary(libraryURI) == null ) { context.registerTagLibrary(libraryURI, className); } | protected void configure() { // load the properties file of libraries available InputStream in = null; URL url = getClassLoader().getResource("org/apache/commons/jelly/jelly.properties"); if (url != null) { log.debug("Loading Jelly default tag libraries from: " + ur... |
public String getElementName(); | String getElementName(); | public String getElementName(); |
public void setColumnNumber(int columnNumber); | void setColumnNumber(int columnNumber); | public void setColumnNumber(int columnNumber); |
public void setElementName(String elementName); | void setElementName(String elementName); | public void setElementName(String elementName); |
public void setFileName(String fileName); | void setFileName(String fileName); | public void setFileName(String fileName); |
public void setLineNumber(int lineNumber); | void setLineNumber(int lineNumber); | public void setLineNumber(int lineNumber); |
return super.getMessage() + " At line: " | return super.getMessage() + " File: " + fileName + " At tag <" + elementName + ">: line: " | public String getMessage() { return super.getMessage() + " At line: " + lineNumber + " column: " + columnNumber; } |
fc.setSelectedFile(null); | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == "Open"){ int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { try{ theData = new HaploData(fc.getSelectedFile()); infileName = fc.getSelectedFile().getName(); ... | |
else if(args[i].equalsIgnoreCase("-ha") || args[i].equalsIgnoreCase("-l") || args[i].equalsIgnoreCase("-haps")) { | else if(args[i].equalsIgnoreCase("-ha") || args[i].equalsIgnoreCase("-haps")) { | private void argHandler(String[] args){ argHandlerMessages = new Vector(); int maxDistance = -1; //this means that user didn't specify any output type if it doesn't get changed below blockOutputType = -1; double hapThresh = -1; double minimumMAF=-1; double spacingThr... |
UserActivityLogger.getInstance().logActivity(userName, userName+" logged out successfully"); | public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) throws Exception { ... |
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