rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k |
|---|---|---|
config.put(dbName, currentDB); | if (config.containsKey(dbName)) { ((List) config.get(dbName)).add(currentDB); } else { List fallbacks = new ArrayList(); fallbacks.add(currentDB); config.put(dbName, fallbacks); } | public static RegistryConfiguration parseRegistry(BufferedReader in, String locator) throws IOException, RegistryException { String line = ""; String dbName = ""; String key = ""; String value = ""; Map config = new HashM... |
FeatureFilter repeatID = FilterUtils.hasAnnotation(rpType); | FeatureFilter repeatID = FilterUtils.byAnnotationType(rpType); | public void testUseCases() { // schemas for our database features FeatureFilter transcript = FilterUtils.byType("transcript"); FeatureFilter exon = FilterUtils.byType("exon"); FeatureFilter repeat = FilterUtils.byType("repeat"); AnnotationType.Impl tsType = new AnnotationType.Impl(); ... |
optimizeExact(FilterUtils.and(exSchema, aTranscript), aTranscript); | optimizeExact(FilterUtils.and(exSchema, aTranscript), FilterUtils.none()); optimizeExact(FilterUtils.and(reSchema, aTranscript), FilterUtils.none()); optimizeEquals(dbFilter, dbFilter); | public void testUseCases() { // schemas for our database features FeatureFilter transcript = FilterUtils.byType("transcript"); FeatureFilter exon = FilterUtils.byType("exon"); FeatureFilter repeat = FilterUtils.byType("repeat"); AnnotationType.Impl tsType = new AnnotationType.Impl(); ... |
if (atEOF) return -1; | public final int read() throws IOException { if (bufferPos >= bufferEnd) if (fill() < 0) return -1; if (bufferEnd == 0) return -1; else return buffer[bufferPos++]; } | |
? "net.jforum.PooledConnection" : "net.jforum.SimpleConnection"; | ? POOLED_CONNECTION : SIMPLE_CONNECTION; | private Connection configureDatabase() { String database = this.getFromSession("database"); String connectionType = this.getFromSession("db_connection_type"); String implementation; boolean isDs = false; if ("JDBC".equals(connectionType)) { implementation = "yes".equals(this.getFromSession("usePool")) && !"... |
implementation = "net.jforum.DataSourceConnection"; | implementation = DATA_SOURCE_CONNECTION; | private Connection configureDatabase() { String database = this.getFromSession("database"); String connectionType = this.getFromSession("db_connection_type"); String implementation; boolean isDs = false; if ("JDBC".equals(connectionType)) { implementation = "yes".equals(this.getFromSession("usePool")) && !"... |
public String createRSS() throws Exception; | public String createRSS() ; | public String createRSS() throws Exception; |
type = new CDependentNameType(((CClassNameType)type).getQualifiedName()) .checkType(context); | if( type instanceof CClassNameType){ type = new CDependentNameType(((CClassNameType)type).getQualifiedName()) .checkType(context); } | public void analyse(CBodyContext context) throws PositionedError { TypeFactory factory = context.getTypeFactory(); try { type = type.checkType(context); } catch (UnpositionedError cue) { try { type = new CDependentNameType(((C... |
check(context, type.getCClass().isAccessible( context.getClassContext().getCClass()), KjcMessages.CLASS_NOACCESS, type); | public void analyse(CBodyContext context) throws PositionedError { TypeFactory factory = context.getTypeFactory(); try { type = type.checkType(context); } catch (UnpositionedError cue) { try { type = new CDependentNameType(((C... | |
return "250 <" + emailAddress + "> Sender ok."; | return "250 Ok"; | public String execute(String commandString, Session session) { if (session.getSender() != null) { return "503 Sender already specified."; } else { String args = getArgPredicate(commandString); if (!args.toUpperCase().startsWith("FROM:")) { return "501 Syntax: MAIL FROM: <address> Error in parameters: ... |
getClass().getClassLoader().getResource("bio/seq/tools/AlphabetManager.xml"); | getClass().getClassLoader().getResource("org/biojava/bio/seq/tools/AlphabetManager.xml"); | protected AlphabetManager() { try { URL alphabetURL = getClass().getClassLoader().getResource("bio/seq/tools/AlphabetManager.xml"); InputSource is = Resolver.createInputSource(alphabetURL, true); Document doc = XmlDocument.createXmlDocument(is, true); Map nameToResidue = new HashMap(); ... |
if ( inputStream != null ) { IoUtils.close( inputStream ); } | IoUtils.close( inputStream ); | public void transferCompleted( TransferEvent transferEvent ) { if ( digester == null ) { return; } Wagon wagon = transferEvent.getWagon(); actualChecksum = encode ( digester.digest() ); digester = null; InputStrea... |
HJBConnection result = new HJBConnection(connectionFactory.createConnection()); | public int createHJBConnection() { synchronized (activeConnections) { try { HJBConnection result = new HJBConnection(connectionFactory.createConnection()); Integer index = new Integer(connectionIndices.size()); connectionIndices.add(index); ... | |
HJBConnection result = new HJBConnection(connectionFactory.createConnection(), 0); | public int createHJBConnection() { synchronized (activeConnections) { try { HJBConnection result = new HJBConnection(connectionFactory.createConnection()); Integer index = new Integer(connectionIndices.size()); connectionIndices.add(index); ... | |
throw new UnsupportedOperationException("Security Manager does not allow creation through reflection"); | throw new UnsupportedOperationException("Security Manager exception: "+e.getMessage()); | public static ObjectInstantiator getInstantiator(Class instantiatorClass, Class type) { Constructor constructor; try { constructor = instantiatorClass.getDeclaredConstructor(new Class[] {Class.class}); return (ObjectInstantiator)constructor.newInstance(new Object[]{type}); } catch (SecurityException e) { thro... |
throw new RuntimeException("Problems creating instantiator", e); | throw new RuntimeException("InstantiationException creating instantiator of class "+type.getName()+": "+e.getMessage()); | public static ObjectInstantiator getInstantiator(Class instantiatorClass, Class type) { Constructor constructor; try { constructor = instantiatorClass.getDeclaredConstructor(new Class[] {Class.class}); return (ObjectInstantiator)constructor.newInstance(new Object[]{type}); } catch (SecurityException e) { thro... |
throw new RuntimeException("Problems creating instantiator", e); | throw new RuntimeException("IlleglAccessException creating instantiator of class "+type.getName()+": "+e.getMessage()); | public static ObjectInstantiator getInstantiator(Class instantiatorClass, Class type) { Constructor constructor; try { constructor = instantiatorClass.getDeclaredConstructor(new Class[] {Class.class}); return (ObjectInstantiator)constructor.newInstance(new Object[]{type}); } catch (SecurityException e) { thro... |
throw new RuntimeException("Problems creating instantiator", e); | throw new RuntimeException("InvocationTargetException creating instantiator of class "+type.getName()+": "+e.getMessage()); | public static ObjectInstantiator getInstantiator(Class instantiatorClass, Class type) { Constructor constructor; try { constructor = instantiatorClass.getDeclaredConstructor(new Class[] {Class.class}); return (ObjectInstantiator)constructor.newInstance(new Object[]{type}); } catch (SecurityException e) { thro... |
public int doModeration(String returnUrl) throws Exception | public int doModeration(String returnUrl) | public int doModeration(String returnUrl) throws Exception { int status = FAILURE; if (SecurityRepository.canAccess(SecurityConstants.PERM_MODERATION)) { // Deleting topics ActionServletRequest request = JForumExecutionContext.getRequest(); if (request.getParameter("topicRemove") != null) { if (SecurityR... |
private void lockUnlockTopics(int status) throws Exception | private void lockUnlockTopics(int status) | private void lockUnlockTopics(int status) throws Exception { String[] topics = JForumExecutionContext.getRequest().getParameterValues("topic_id"); if (topics != null && topics.length > 0) { int[] ids = new int[topics.length]; for (int i = 0; i < topics.length; i++) { ids[i] = Integer.parseInt(topics[i]); ... |
private void moveTopics() throws Exception | private void moveTopics() | private void moveTopics() throws Exception { SimpleHash context = JForumExecutionContext.getTemplateContext(); context.put("persistData", JForumExecutionContext.getRequest().getParameter("persistData")); context.put("allCategories", ForumCommon.getAllCategoriesAndForums(false)); String[] topics = JForumExecuti... |
public int moveTopicsSave(String successUrl) throws Exception | public int moveTopicsSave(String successUrl) | public int moveTopicsSave(String successUrl) throws Exception { int status = SUCCESS; if (!SecurityRepository.canAccess(SecurityConstants.PERM_MODERATION_TOPIC_MOVE)) { status = FAILURE; } else { ActionServletRequest request = JForumExecutionContext.getRequest(); String topics = request.getParameter("topic... |
private void removeTopics() throws Exception | private void removeTopics() | private void removeTopics() throws Exception { String[] topics = JForumExecutionContext.getRequest().getParameterValues("topic_id"); List forumsList = new ArrayList(); TopicDAO tm = DataAccessDriver.getInstance().newTopicDAO(); List topicsToDelete = new ArrayList(); if (topics != null && topics.length > 0) ... |
resource.setContentLength( file.length() ); resource.setLastModified( file.lastModified() ); | public void fillOutputData( OutputData outputData ) throws TransferFailedException { Resource resource = outputData.getResource(); File file = new File( getRepository().getBasedir(), resource.getName() ); File dir = file.getParentFile(); if ( dir != null && !dir.exists() ) ... | |
for (EnabledFilter enabled: list.getEnabledFilters()) | for (EnabledFilter enabled: list.getEnabledFilters().values()) | public void onInject(MimeMessage msg, MailingList list) throws IgnoreException, HoldException, MessagingException { if (log.isDebugEnabled()) log.debug("Running onInject filters for list '" + list.getName() + "' on message: " + msg.getSubject()); // TODO: factor in global plugins HoldException holdException = ... |
double maxwert = 1E-10; | final double startwert = 1E-10; double maxwert = startwert; | double[][] getVerschobeneLage() { assert fertigberechnet: "ERROR: Call clMechanismus.rechnen() first."; if (!INSTABIL_KEIN_GLGEW) { assert false; return null; } // Finden der Parameter (d.h. Freiheitsgrade), welche eine virt. Leistung verursachen, // d.h. das... |
} if (maxwert == startwert) { for (int unb = 1; unb < 1 + 2*anzKn; unb++) { if (Math.abs(unbek[unb]) > maxwert) maxwert = Math.abs(unbek[unb]); } | double[][] getVerschobeneLage() { assert fertigberechnet: "ERROR: Call clMechanismus.rechnen() first."; if (!INSTABIL_KEIN_GLGEW) { assert false; return null; } // Finden der Parameter (d.h. Freiheitsgrade), welche eine virt. Leistung verursachen, // d.h. das... | |
System.err.println("VORSICHT, neues UNGETESTETES Modul des Solvers im Einsatz."); | if (debug) System.err.println("VORSICHT, wenig GETESTETES Modul des Solvers im Einsatz."); | public final double[][] solve() throws ArithmeticException { // -------------------------------------------------------------------------- // EIGENTLICHER SOLVER für bestimmte Lösungsvariablen in unbestimmen Systemen // -------------------------------------------------------------------... |
if (distanceRemaining > 0) { | public void checkRobotCollision() { inCollision = false; for (int i = 0; i < battle.getRobots().size(); i++) { RobotPeer r = battle.getRobots().elementAt(i); if (!(r == null || r == this || r.isDead) && boundingBox.intersects(r.boundingBox)) { // Bounce back double angle = atan2(r.x - x, r.y - y); doubl... | |
} else { statistics.damagedByRamming(Rules.ROBOT_HIT_DAMAGE); } | public void checkRobotCollision() { inCollision = false; for (int i = 0; i < battle.getRobots().size(); i++) { RobotPeer r = battle.getRobots().elementAt(i); if (!(r == null || r == this || r.isDead) && boundingBox.intersects(r.boundingBox)) { // Bounce back double angle = atan2(r.x - x, r.y - y); doubl... | |
this.inCollision = true; | inCollision = true; | public void checkRobotCollision() { inCollision = false; for (int i = 0; i < battle.getRobots().size(); i++) { RobotPeer r = battle.getRobots().elementAt(i); if (!(r == null || r == this || r.isDead) && boundingBox.intersects(r.boundingBox)) { // Bounce back double angle = atan2(r.x - x, r.y - y); doubl... |
if (distanceRemaining < 0) { | public void checkRobotCollision() { inCollision = false; for (int i = 0; i < battle.getRobots().size(); i++) { RobotPeer r = battle.getRobots().elementAt(i); if (!(r == null || r == this || r.isDead) && boundingBox.intersects(r.boundingBox)) { // Bounce back double angle = atan2(r.x - x, r.y - y); doubl... | |
public Set<EnabledFilter> getEnabledFilters() { return this.enabledFilters; } | public Map<String, EnabledFilter> getEnabledFilters() { return this.enabledFilters; } | public Set<EnabledFilter> getEnabledFilters() { return this.enabledFilters; } |
public boolean equals(Location l) { return getMin() == l.getMin() && getMax() == l.getMax() && l.isContiguous(); | public boolean equals(Object o) { if(o instanceof Location) { Location l = (Location) o; return getMin() == l.getMin() && getMax() == l.getMax() && l.isContiguous(); } else { return false; } | public boolean equals(Location l) { return getMin() == l.getMin() && getMax() == l.getMax() && l.isContiguous(); } |
double hydroxMass = 0.0; if(isotopicType.equals(SymbolPropertyTable.AVG_MASS)){ hydroxMass = Havg + Oavg; } else if(isotopicType.equals(SymbolPropertyTable.MONO_MASS)){ hydroxMass = Hmono + Omono; } if (pepMass != 0.0) { if (MH_PLUS) { pepMass = pepMass + 3 * hydroxMass; } else { pepMass = pepMass + 2 * hydroxMass; } | double termMass = calcTermMass(isotopicType,MH_PLUS); if (pepMass != 0.0){ pepMass += termMass; | public static final double getMass(SymbolList proteinSeq, String isotopicType, boolean MH_PLUS) throws IllegalSymbolException { if(!proteinSeq.getAlphabet().getName().equals("PROTEIN")){ //thr... |
Integer timeout = getFinder().findTimeout(decodedParameters); | Long timeout = getFinder().findTimeout(decodedParameters); | protected void constructCommandFrom(HttpServletRequest request, HJBRoot root) throws HJBException { String pathInfo = request.getPathInfo(); Matcher m = getPathPattern().matcher(pathInfo); m.matches(); String providerName = m.group(1); String factoryName = applyURLDecod... |
timeout.intValue()); | timeout.longValue()); | protected void constructCommandFrom(HttpServletRequest request, HJBRoot root) throws HJBException { String pathInfo = request.getPathInfo(); Matcher m = getPathPattern().matcher(pathInfo); m.matches(); String providerName = m.group(1); String factoryName = applyURLDecod... |
Date firstTime = new Date(rs.getTimestamp(1).getTime()); | Timestamp firstTime = rs.getTimestamp(1); if (rs.wasNull()) { firstTime = null; } | public ForumStats getBoardStatus() { ForumStats fs = new ForumStats(); fs.setPosts(this.getTotalMessages()); Connection c = JForumExecutionContext.getConnection(); // Total Users Statement s=null; ResultSet rs=null; try { s = c.createStatement(); rs = s.executeQuery(Sy... |
rs.next(); firstTime = new Date(rs.getTimestamp(1).getTime()); | if (rs.next()) { firstTime = rs.getTimestamp(1); if (rs.wasNull()) { firstTime = null; } } | public ForumStats getBoardStatus() { ForumStats fs = new ForumStats(); fs.setPosts(this.getTotalMessages()); Connection c = JForumExecutionContext.getConnection(); // Total Users Statement s=null; ResultSet rs=null; try { s = c.createStatement(); rs = s.executeQuery(Sy... |
userPerDay = fs.getUsers() / this.daysUntilToday(today, firstTime); | userPerDay = firstTime != null ? fs.getUsers() / this.daysUntilToday(today, firstTime) : 0; | public ForumStats getBoardStatus() { ForumStats fs = new ForumStats(); fs.setPosts(this.getTotalMessages()); Connection c = JForumExecutionContext.getConnection(); // Total Users Statement s=null; ResultSet rs=null; try { s = c.createStatement(); rs = s.executeQuery(Sy... |
locator0 = "<locator1>"; locator0 = "<locator2>"; | locator1 = "<locator1>"; locator2 = "<locator2>"; | protected void setUp() { confParams0 = new HashMap(); confParams0.put("protocol", "<protocol-type 0>"); confParams0.put("location", "<location-string 0>"); confParams0.put("parameter-x", "<value 0>"); confParams1 = new HashMap(); confParams1.put("protocol", "<protocol-ty... |
try { if (mPosition >= 0) { mCurrentPartition = mDocument.getPartition(mPosition); mType = mCurrentPartition.getType(); while (mType == SchemePartitionScanner.SCHEME_COMMENT) { mPosition = mCurrentPartition.getOffset() - 1; mCurrentPartition = mDocument.getPartition(mPosition); mType = mCurrentPartition.getType(); } mS... | if (mPosition >= 0) { mCurrentPartition = getCurrentPartition(); mType = mCurrentPartition.getType(); while (mType == SchemePartitionScanner.SCHEME_COMMENT) { mPosition = mCurrentPartition.getOffset() - 1; ITypedRegion partition = getCurrentPartition(); if (partition == null) break; mCurrentPartition = partition; mType... | private void fetchPreviousPartition() { mPosition--; try { if (mPosition >= 0) { mCurrentPartition = mDocument.getPartition(mPosition); mType = mCurrentPartition.getType(); while (mType == SchemePartitionScanner.SCHEME_COMMENT) { ... |
try { mPosition = position; mCurrentPartition = mDocument.getPartition(position); mType = mCurrentPartition.getType(); mStart = mCurrentPartition.getOffset(); if (mType == SchemePartitionScanner.SCHEME_COMMENT) { mPosition = mStart; } else if (SchemePartitionScanner.isStringPartition(mType)) { mPosition = mStart + mCur... | mPosition = position; mCurrentPartition = getCurrentPartition(); mType = mCurrentPartition.getType(); mStart = mCurrentPartition.getOffset(); if (mType == SchemePartitionScanner.SCHEME_COMMENT) { mPosition = mStart; } else if (SchemePartitionScanner.isStringPartition(mType)) { mPosition = mStart + mCurrentPartition.get... | public void setPosition(int position) { try { mPosition = position; mCurrentPartition = mDocument.getPartition(position); mType = mCurrentPartition.getType(); mStart = mCurrentPartition.getOffset(); if (mType == SchemePartitionScanner.SCHEME_COMMENT) { ... |
aList.add(alphabetForName(name.substring(i, j).trim())); | if(i != j){ aList.add(alphabetForName(name.substring(i, j).trim())); } | static public Alphabet generateCrossProductAlphaFromName( String name ) { if(!name.startsWith("(") || !name.endsWith(")")) { throw new BioError( "Can't parse " + name + " into a cross-product alphabet as it is not bracketed" ); } name = name.substring(1, name.length()-1).trim(); ... |
int atomicSyms = alpha.size(); int totalSyms = 1 << atomicSyms; for (int cnt = 0; cnt < totalSyms; ++cnt) { Set matchSet = new HashSet(); for (int atom = 0; atom < atomicSyms; ++atom) { if ((cnt & (1 << atom)) != 0) { matchSet.add(orderedAlpha.get(atom)); } } | int atomicSyms = alpha.size(); int totalSyms = 1 << atomicSyms; | public static Set getAllSymbols(FiniteAlphabet alpha) { Set allSymbols = new HashSet(); List orderedAlpha = new ArrayList(alpha.size()); for (Iterator i = alpha.iterator(); i.hasNext(); ) { orderedAlpha.add(i.next()); } int atomicSyms = alpha.size(); int totalSyms = 1 << atomicSyms; for (int cnt = 0; cnt < tot... |
try { allSymbols.add(alpha.getAmbiguity(matchSet)); } catch (IllegalSymbolException ex) { throw new BioError(ex, "Assertion failed: couldn't get ambiguity symbol"); } } | for (int cnt = 0; cnt < totalSyms; ++cnt) { Set matchSet = new HashSet(); for (int atom = 0; atom < atomicSyms; ++atom) { if ((cnt & (1 << atom)) != 0) { matchSet.add(orderedAlpha.get(atom)); } } | public static Set getAllSymbols(FiniteAlphabet alpha) { Set allSymbols = new HashSet(); List orderedAlpha = new ArrayList(alpha.size()); for (Iterator i = alpha.iterator(); i.hasNext(); ) { orderedAlpha.add(i.next()); } int atomicSyms = alpha.size(); int totalSyms = 1 << atomicSyms; for (int cnt = 0; cnt < tot... |
return allSymbols; | try { allSymbols.add(alpha.getAmbiguity(matchSet)); } catch (IllegalSymbolException ex) { throw new BioError(ex, "Assertion failed: couldn't get ambiguity symbol"); } } return allSymbols; | public static Set getAllSymbols(FiniteAlphabet alpha) { Set allSymbols = new HashSet(); List orderedAlpha = new ArrayList(alpha.size()); for (Iterator i = alpha.iterator(); i.hasNext(); ) { orderedAlpha.add(i.next()); } int atomicSyms = alpha.size(); int totalSyms = 1 << atomicSyms; for (int cnt = 0; cnt < tot... |
URL heapUrl = SchemeScriptPlugin.getDefault().find(new Path("/lib/sisc.shp")); | URL heapUrl = SchemeScriptPlugin.findFile(new Path("/lib/sisc.shp")); | public SiscStreamsProxy() { try { PipedInputStream inputStream = new PipedInputStream(); PipedOutputStream outputStream = new PipedOutputStream(inputStream); mSiscInputStream = outputStream; final AppContext appContext = new AppContext(); Context.setDefaultAppContext(appContext); URL heapUrl = Sch... |
public List selectAllByGroup(int groupId, int start, int count) throws Exception | public List selectAllByGroup(int groupId, int start, int count) | public List selectAllByGroup(int groupId, int start, int count) throws Exception { return super.selectAllByGroup(start, count, groupId); } |
public BlastOutputHandler(ContentHandler handler) | public BlastOutputHandler(StAXFeatureHandler staxenv) | public BlastOutputHandler(ContentHandler handler) { super(); staxenv = this; listener = handler; // initialise delegation initDelegation(); } |
super(); staxenv = this; listener = handler; | super(staxenv); | public BlastOutputHandler(ContentHandler handler) { super(); staxenv = this; listener = handler; // initialise delegation initDelegation(); } |
listener.endElement(biojavaUri, "BlastLikeDataSet", biojavaUri + ":BlastLikeDataSet"); if (wrap) listener.endElement(biojavaUri, "BlastLikeDataSetCollection", biojavaUri + ":BlastLikeDataSetCollection"); | staxenv.listener.endElement(biojavaUri, "BlastLikeDataSet", biojavaUri + ":BlastLikeDataSet"); | void endElementHandler( String nsURI, String localName, String qName, StAXContentHandler handler) throws SAXException { // generate end of <biojava:BlastLikeDataSet> listener.endElement(biojavaUri, "BlastLikeDataSet", biojavaUri + ":BlastLikeD... |
System.out.println("program, version " + program + " " + version); | private void initDelegation() { // delegate handling of <BlastOutput_param>// super.addHandler(new ElementRecognizer.ByLocalName("BlastOutput_param"),// BlastOutputParamHandler.BLAST_OUTPUT_PARAM_HANDLER_FACTORY); // delegate handling of <BlastOutput_program> super.addHandl... | |
ContentHandler listener = getListener(); | private void initDelegation() { // delegate handling of <BlastOutput_param>// super.addHandler(new ElementRecognizer.ByLocalName("BlastOutput_param"),// BlastOutputParamHandler.BLAST_OUTPUT_PARAM_HANDLER_FACTORY); // delegate handling of <BlastOutput_program> super.addHandl... | |
ContentHandler listener = getListener(); | public StAXContentHandler getHandler(StAXFeatureHandler staxenv) { return new BlastOutputIterationsHandler(staxenv) { public void startElementHandler( String nsURI, String localName, ... | |
ContentHandler listener = getListener(); | public void startElementHandler( String nsURI, String localName, String qName, Attributes attrs) throws SAXException { ... | |
System.out.println("program, version " + program + " " + version); | public StAXContentHandler getHandler(StAXFeatureHandler staxenv) { return new StringElementHandlerBase() { public void setStringValue(String s) throws SAXException { version = s.trim(); } ... | |
System.out.println("program, version " + program + " " + version); | public void endElement( String nsURI, String localName, String qName, StAXContentHandler handler) throws SAXException { ... | |
model.url = data.getUrl(); model.email = data.getEmail(); | public void execute() throws Exception { Model model = new Model(); ListData data = Backend.instance().getListMgr().getList(this.listId); model.listId = data.getId(); model.name = data.getName(); model.description = data.getDescription(); model.holdSubs = data.isSubscriptionHeld(); this.getCtx().setModel(... | |
listener.endElement(biojavaUri, "HSPCollection", biojavaUri + ":HSPCollection"); | staxenv.listener.endElement(biojavaUri, "HSPCollection", biojavaUri + ":HSPCollection"); | public void endElementHandler( String nsURI, String localName, String qName, StAXContentHandler handler) throws SAXException { // generate end of <biojava:HSPCollection> listener.endElement(biojavaUri, "HSPCollection", biojavaUri + ":HSPCollec... |
CType returnType, | CType returnType, JFormalParameter[] params, | public CCjSourceAccessorMethod( JAccessorMethod decl, CClass owner, int modifiers, String ident, CType returnType, CType[] paramTypes, CReferenceType[] exceptions, boolean deprecated, boolean synthetic, JBlock body ) { super(owner... |
super(owner, modifiers, ident, returnType, paramTypes, exceptions, | super(owner, modifiers, ident, returnType, params, paramTypes, exceptions, | public CCjSourceAccessorMethod( JAccessorMethod decl, CClass owner, int modifiers, String ident, CType returnType, CType[] paramTypes, CReferenceType[] exceptions, boolean deprecated, boolean synthetic, JBlock body ) { super(owner... |
setFault(e); | recordFault(e); | public void execute() { assertNotCompleted(); try { getTheConnection().start(); } catch (RuntimeException e) { setFault(e); } catch (JMSException e) { LOG.error(e); setFault(new HJBException(e)); } completed(); } |
LOG.error(e); setFault(new HJBException(e)); | recordFault(new HJBException(e)); | public void execute() { assertNotCompleted(); try { getTheConnection().start(); } catch (RuntimeException e) { setFault(e); } catch (JMSException e) { LOG.error(e); setFault(new HJBException(e)); } completed(); } |
public int addNew(Forum forum) throws Exception; | public int addNew(Forum forum) ; | public int addNew(Forum forum) throws Exception; |
public List checkUnreadTopics(int forumId, long lastVisit) throws Exception; | public List checkUnreadTopics(int forumId, long lastVisit) ; | public List checkUnreadTopics(int forumId, long lastVisit) throws Exception; |
public void decrementTotalTopics(int forumId, int count) throws Exception; | public void decrementTotalTopics(int forumId, int count) ; | public void decrementTotalTopics(int forumId, int count) throws Exception; |
public void delete(int forumId) throws Exception; | public void delete(int forumId) ; | public void delete(int forumId) throws Exception; |
public ForumStats getBoardStatus() throws Exception; | public ForumStats getBoardStatus() ; | public ForumStats getBoardStatus() throws Exception; |
public LastPostInfo getLastPostInfo(int forumId) throws Exception; | public LastPostInfo getLastPostInfo(int forumId) ; | public LastPostInfo getLastPostInfo(int forumId) throws Exception; |
public int getMaxPostId(int forumId) throws Exception; | public int getMaxPostId(int forumId) ; | public int getMaxPostId(int forumId) throws Exception; |
public List getModeratorList(int forumId) throws Exception; | public List getModeratorList(int forumId) ; | public List getModeratorList(int forumId) throws Exception; |
public int getTotalMessages() throws Exception; | public int getTotalMessages() ; | public int getTotalMessages() throws Exception; |
public int getTotalTopics(int forumId) throws Exception; | public int getTotalTopics(int forumId) ; | public int getTotalTopics(int forumId) throws Exception; |
public void incrementTotalTopics(int forumId, int count) throws Exception; | public void incrementTotalTopics(int forumId, int count) ; | public void incrementTotalTopics(int forumId, int count) throws Exception; |
public boolean isUserSubscribed(int forumId, int userId) throws Exception; | public boolean isUserSubscribed(int forumId, int userId) ; | public boolean isUserSubscribed(int forumId, int userId) throws Exception; |
public void moveTopics(String[] topics, int fromForumId, int toForumId) throws Exception; | public void moveTopics(String[] topics, int fromForumId, int toForumId) ; | public void moveTopics(String[] topics, int fromForumId, int toForumId) throws Exception; |
public List notifyUsers(Forum forum) throws Exception; | public List notifyUsers(Forum forum) ; | public List notifyUsers(Forum forum) throws Exception; |
public void removeSubscription(int forumId, int userId) throws Exception; | public void removeSubscription(int forumId, int userId) ; | public void removeSubscription(int forumId, int userId) throws Exception; |
public void removeSubscriptionByForum(int forumId) throws Exception; | public void removeSubscriptionByForum(int forumId) ; | public void removeSubscriptionByForum(int forumId) throws Exception; |
public Forum selectById(int forumId) throws Exception; | public Forum selectById(int forumId) ; | public Forum selectById(int forumId) throws Exception; |
public void setLastPost(int forumId, int postId) throws Exception; | public void setLastPost(int forumId, int postId) ; | public void setLastPost(int forumId, int postId) throws Exception; |
public void setModerated(int categoryId, boolean status) throws Exception; | public void setModerated(int categoryId, boolean status) ; | public void setModerated(int categoryId, boolean status) throws Exception; |
public Forum setOrderDown(Forum forum, Forum related) throws Exception; | public Forum setOrderDown(Forum forum, Forum related) ; | public Forum setOrderDown(Forum forum, Forum related) throws Exception; |
public Forum setOrderUp(Forum forum, Forum related) throws Exception; | public Forum setOrderUp(Forum forum, Forum related) ; | public Forum setOrderUp(Forum forum, Forum related) throws Exception; |
public void subscribeUser(int forumId, int userId) throws Exception; | public void subscribeUser(int forumId, int userId) ; | public void subscribeUser(int forumId, int userId) throws Exception; |
public void update(Forum forum) throws Exception; | public void update(Forum forum) ; | public void update(Forum forum) throws Exception; |
System.err.println("*** Constructing DistributedSequence: " + id); | DistributedSequence(String id, DistributedSequenceDB db, DistDataSource seqSource, Set featureSources) { this.id = id; this.seqSource = seqSource; this.featureSources = featureSources; this.db = db; } | |
+ HJBConstants.CREATION_TIME + "=" + defaultClockTimeAsHJBEncodedLong() + CR + "message-selector=testSelector"; | + '\t' + HJBConstants.CREATION_TIME + "=" + defaultClockTimeAsHJBEncodedLong() + ", message-selector=testSelector"; | public void testLongDescriptionOutputsAllValues() { Mock mockConsumer = mock(MessageConsumer.class); mockConsumer.stubs() .method("getMessageSelector") .will(returnValue("testSelector")); MessageConsumer testConsumer = (MessageConsumer) mockConsumer.proxy(); Consume... |
public SimpleSeqSimilaritySearchResult(SeqSimilaritySearcher searcher, SymbolList querySequence, SequenceDB sequenceDB, Map searchParameters, List hits) { Contract.pre(searcher != null, "searcher not null"); Contract.pre(querySequence != null, "querySequence not null"); Contract.pre(sequenceDB != null, "sequenceDB not ... | public SimpleSeqSimilaritySearchResult(SymbolList querySequence, SequenceDB sequenceDB, Map searchParameters, List hits) { Contract.pre(querySequence != null, "querySequence was null"); Contract.pre(sequenceDB != null, "sequenceDB was null"); Contract.pre(hits != null, "hits was null"); | public SimpleSeqSimilaritySearchResult(SeqSimilaritySearcher searcher, SymbolList querySequence, SequenceDB sequenceDB, Map searchParameters, List hits) { Contract.pre(searcher != null, "searcher not null"); Contract.pre(querySequence != null, "querySequence not null"); Contract.pre(sequenceDB != null, ... |
this.searcher = searcher; this.querySequence = querySequence; this.sequenceDB = sequenceDB; this.searchParameters = searchParameters; this.hits = hits; } | this.querySequence = querySequence; this.sequenceDB = sequenceDB; this.searchParameters = searchParameters; this.hits = hits; } | public SimpleSeqSimilaritySearchResult(SeqSimilaritySearcher searcher, SymbolList querySequence, SequenceDB sequenceDB, Map searchParameters, List hits) { Contract.pre(searcher != null, "searcher not null"); Contract.pre(querySequence != null, "querySequence not null"); Contract.pre(sequenceDB != null, ... |
if (!ObjectUtil.equals(this.searcher, that.searcher)) return false; if (!ObjectUtil.equals(this.querySequence, that.querySequence)) return false; if (!ObjectUtil.equals(this.sequenceDB, that.sequenceDB)) return false; if (!ObjectUtil.equals(this.searchParameters, that.searchParameters)) return false; if (!ObjectUtil.eq... | if (! ObjectUtil.equals(this.querySequence, that.querySequence)) return false; if (! ObjectUtil.equals(this.sequenceDB, that.sequenceDB)) return false; if (! ObjectUtil.equals(this.searchParameters, that.searchParameters)) return false; if (! ObjectUtil.equals(this.hits, that.hits)) return false; | public boolean equals(Object o) { if (o == this) return true; // if this class is a direct sub-class of Object: if (o == null) return false; if (!o.getClass().equals(this.getClass())) return false; SimpleSeqSimilaritySearchResult that = (SimpleSeqSimilaritySearchResult) o; // only compar... |
hc = ObjectUtil.hashCode(hc, searcher); hc = ObjectUtil.hashCode(hc, querySequence); hc = ObjectUtil.hashCode(hc, sequenceDB); hc = ObjectUtil.hashCode(hc, searchParameters); hc = ObjectUtil.hashCode(hc, hits); | hc = ObjectUtil.hashCode(hc, querySequence); hc = ObjectUtil.hashCode(hc, sequenceDB); hc = ObjectUtil.hashCode(hc, searchParameters); hc = ObjectUtil.hashCode(hc, hits); | public int hashCode() { // if this class is a direct sub-class of Object: int hc = 0; // only take into account fields of this class (not of super-class): hc = ObjectUtil.hashCode(hc, searcher); hc = ObjectUtil.hashCode(hc, querySequence); hc = ObjectUtil.hashCode(hc, sequenceDB); hc = ObjectUtil... |
if (mExplorer == null || mExplorer.getDocument() != part.getDocument()) { if (mExplorer != null) mExplorer.dispose(); mExplorer = new SexpNavigator(part.getDocument()); | if (mExpressionNavigator == null || mExpressionNavigator.getDocument() != part.getDocument()) { if (mExpressionNavigator != null) mExpressionNavigator.dispose(); mExpressionNavigator = new SexpNavigator(part.getDocument()); | private void createExplorer(ITextViewer part) { if (mExplorer == null || mExplorer.getDocument() != part.getDocument()) { if (mExplorer != null) mExplorer.dispose(); mExplorer = new SexpNavigator(part.getDocument()); } } |
boolean done = selectComment(pos) || selectString(pos) || selectSpaces(pos) || selectSExpression(pos); | if (! (selectComment(pos) || selectString(pos) || selectSpaces(pos))) { selectSExpression(pos); } | public void doubleClicked(ITextViewer part) { mText = part; createExplorer(part); int pos = part.getSelectedRange().x; if (pos < 0) return; boolean done = selectComment(pos) || selectString(pos) || selectSpaces(pos) || selectSExpression(pos); } |
try { ITypedRegion partition = mExplorer.getDocument().getPartition(caretPos); if (partition.getType() == SchemePartitionScanner.SCHEME_COMMENT) { selectRange(partition.getOffset(), partition.getOffset() + partition.getLength()); return true; } } catch (BadLocationException exception) { } | ITypedRegion partition = SchemeTextUtilities.getPartition(mExpressionNavigator.getDocument(), caretPos); if (partition.getType() == SchemePartitionScanner.SCHEME_COMMENT) { selectRange(partition.getOffset(), partition.getOffset() + partition.getLength()); return true; } | protected boolean selectComment(int caretPos) { try { ITypedRegion partition = mExplorer.getDocument().getPartition(caretPos); if (partition.getType() == SchemePartitionScanner.SCHEME_COMMENT) { selectRange(partition.getOffset(), partition.getOffset() + partition.getLengt... |
IDocument document = mExplorer.getDocument(); | IDocument document = mExpressionNavigator.getDocument(); | protected boolean selectSExpression(int caretPos) { try { IDocument document = mExplorer.getDocument(); char ch = document.getChar(caretPos); if (ch == '(') { if (mExplorer.forwardSexpression(caretPos)) { selectRange(mExplorer.getSexpStart(),... |
if (mExplorer.forwardSexpression(caretPos)) { selectRange(mExplorer.getSexpStart(), mExplorer.getSexpEnd()); | if (mExpressionNavigator.forwardSexpression(caretPos)) { selectRange(mExpressionNavigator.getSexpStart(), mExpressionNavigator.getSexpEnd()); | protected boolean selectSExpression(int caretPos) { try { IDocument document = mExplorer.getDocument(); char ch = document.getChar(caretPos); if (ch == '(') { if (mExplorer.forwardSexpression(caretPos)) { selectRange(mExplorer.getSexpStart(),... |
if (mExplorer.forwardSexpression(caretPos)) { mExplorer.backwardSexpression(mExplorer.getSexpEnd()); selectRange(mExplorer.getSexpStart(), mExplorer.getSexpEnd()); | if (mExpressionNavigator.forwardSexpression(caretPos)) { mExpressionNavigator.backwardSexpression(mExpressionNavigator.getSexpEnd()); selectRange(mExpressionNavigator.getSexpStart(), mExpressionNavigator.getSexpEnd()); | protected boolean selectSExpression(int caretPos) { try { IDocument document = mExplorer.getDocument(); char ch = document.getChar(caretPos); if (ch == '(') { if (mExplorer.forwardSexpression(caretPos)) { selectRange(mExplorer.getSexpStart(),... |
if (mExplorer.backwardSexpression(caretPos)) { selectRange(mExplorer.getSexpStart(), mExplorer.getSexpEnd()); | if (mExpressionNavigator.backwardSexpression(caretPos)) { selectRange(mExpressionNavigator.getSexpStart(), mExpressionNavigator.getSexpEnd()); | protected boolean selectSExpression(int caretPos) { try { IDocument document = mExplorer.getDocument(); char ch = document.getChar(caretPos); if (ch == '(') { if (mExplorer.forwardSexpression(caretPos)) { selectRange(mExplorer.getSexpStart(),... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.