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String sessionProviderName) {
String sessionProviderName, boolean throwOnFailure) {
public Destination findRequiredDestination(Map decodedParameters, HJBRoot root, String sessionProviderName) { Object rawValue = decodedParameters.get(HJBServletConstants.DESTINATION_URL); assertIsValidDestinati...
assertIsValidDestinationURL(rawValue);
if (! assertIsValidDestinationURL(rawValue, throwOnFailure)) { return null; }
public Destination findRequiredDestination(Map decodedParameters, HJBRoot root, String sessionProviderName) { Object rawValue = decodedParameters.get(HJBServletConstants.DESTINATION_URL); assertIsValidDestinati...
assertIsSameProvider(sessionProviderName, destinationProviderName); HJBTreeWalker walker = new HJBTreeWalker(root, destinationURL);
assertIsSameProvider(sessionProviderName, destinationProviderName, throwOnFailure); HJBTreeWalker walker = new HJBTreeWalker(root, destinationURL, throwOnFailure);
public Destination findRequiredDestination(Map decodedParameters, HJBRoot root, String sessionProviderName) { Object rawValue = decodedParameters.get(HJBServletConstants.DESTINATION_URL); assertIsValidDestinati...
private ConnectionPool(String dbConfigFile) throws IOException, SQLException
private ConnectionPool() throws IOException, SQLException
private ConnectionPool(String dbConfigFile) throws IOException, SQLException { Properties driverProps = new Properties(); driverProps.load(new FileInputStream(dbConfigFile)); try { String driverName = driverProps.getProperty("driver.name"); Properties config = new Properties(); config.load(new FileInp...
Properties driverProps = new Properties(); driverProps.load(new FileInputStream(dbConfigFile));
SystemGlobals.loadAdditionalDefaults(SystemGlobals.getValue("database.driver.config")); String driver = SystemGlobals.getValue("database.connection.driver"); try { Class.forName(driver); this.minConnections = SystemGlobals.getIntValue("database.connection.pool.min"); this.maxConnections = SystemGlobals.getIntValue("d...
private ConnectionPool(String dbConfigFile) throws IOException, SQLException { Properties driverProps = new Properties(); driverProps.load(new FileInputStream(dbConfigFile)); try { String driverName = driverProps.getProperty("driver.name"); Properties config = new Properties(); config.load(new FileInp...
try { String driverName = driverProps.getProperty("driver.name"); Properties config = new Properties(); config.load(new FileInputStream(SystemGlobals.getApplicationResourceDir() + "/config/database/"+ driverName +"/"+ driverName +".properties"));
this.connectionString = SystemGlobals.getValue("database.connection.string");
private ConnectionPool(String dbConfigFile) throws IOException, SQLException { Properties driverProps = new Properties(); driverProps.load(new FileInputStream(dbConfigFile)); try { String driverName = driverProps.getProperty("driver.name"); Properties config = new Properties(); config.load(new FileInp...
SystemGlobals.setTransientValue(ConfigKeys.SQL_FILE, config.getProperty(ConfigKeys.SQL_FILE)); SystemGlobals.setTransientValue(ConfigKeys.DAO_DRIVER, config.getProperty(ConfigKeys.DAO_DRIVER)); Class.forName(config.getProperty("database.connection.driver")); this.minConnections = Integer.parseInt(config.getProperty("...
System.err.println("database.connection.string=" + this.connectionString);
private ConnectionPool(String dbConfigFile) throws IOException, SQLException { Properties driverProps = new Properties(); driverProps.load(new FileInputStream(dbConfigFile)); try { String driverName = driverProps.getProperty("driver.name"); Properties config = new Properties(); config.load(new FileInp...
System.err.println("database.connection.driver = "+ config.getProperty("database.connection.driver"));
System.err.println("database.connection.driver = "+ driver);
private ConnectionPool(String dbConfigFile) throws IOException, SQLException { Properties driverProps = new Properties(); driverProps.load(new FileInputStream(dbConfigFile)); try { String driverName = driverProps.getProperty("driver.name"); Properties config = new Properties(); config.load(new FileInp...
System.err.println(now.toString() + " openning connection "+ (i + 1));
System.err.println(now.toString() + " opening connection "+ (i + 1));
private ConnectionPool(String dbConfigFile) throws IOException, SQLException { Properties driverProps = new Properties(); driverProps.load(new FileInputStream(dbConfigFile)); try { String driverName = driverProps.getProperty("driver.name"); Properties config = new Properties(); config.load(new FileInp...
System.err.println("Ouch... Cannot find database driver: "+ driverProps.getProperty("driver.name"));
System.err.println("Ouch... Cannot find database driver: "+ driver);
private ConnectionPool(String dbConfigFile) throws IOException, SQLException { Properties driverProps = new Properties(); driverProps.load(new FileInputStream(dbConfigFile)); try { String driverName = driverProps.getProperty("driver.name"); Properties config = new Properties(); config.load(new FileInp...
if (pool == null)
if (pool == null) {
public static ConnectionPool getPool() throws SQLException { if (pool == null) throw new SQLException("ConnectionPool was not initialized yet. You need to call init() first."); return pool; }
}
public static ConnectionPool getPool() throws SQLException { if (pool == null) throw new SQLException("ConnectionPool was not initialized yet. You need to call init() first."); return pool; }
public static void init(String configFile) throws SQLException, IOException
public static void init() throws SQLException, IOException
public static void init(String configFile) throws SQLException, IOException { if (pool == null || !isDatabaseUp) { pool = new ConnectionPool(configFile); } }
pool = new ConnectionPool(configFile);
pool = new ConnectionPool();
public static void init(String configFile) throws SQLException, IOException { if (pool == null || !isDatabaseUp) { pool = new ConnectionPool(configFile); } }
compiler.get().reportTrouble( new CWarning( new TokenReference( location.getSourceFile().getPath(), location.getSourceFile(), location.getLine()), new Message( CaesarMessages.ASPECTJ_WARNING, message.getMessage())));
compiler.get().reportTrouble( new CWarning( new TokenReference( location.getSourceFile().getPath(), location.getSourceFile(), location.getLine()), new Message( CaesarMessages.ASPECTJ_WARNING, message.getMessage()))); } else { compiler.get().reportTrouble( new CWarning( TokenReference.NO_REF, new Message( CaesarMessage...
public boolean handleMessage(IMessage message) throws AbortException { if (isIgnoring(message.getKind())) { return true; } ISourceLocation location = message.getSourceLocation(); if (message.getKind() == IMessage.WARNING) { compiler.get().reportTrouble( new CWarning( new TokenReference( location.ge...
if(!isStatic()){ JFormalParameter paramThis = new JFormalParameter(TokenReference.NO_REF,JLocalVariable.DES_PARAMETER,this.getOwnerType(),"this",false); paramThis.setPosition(0); code.addLocalVarInfo(null, paramThis); }
private CodeInfo genByteCode(TypeFactory factory) { CodeSequence code = CodeSequence.getCodeSequence(); GenerationContext context = new GenerationContext(factory, code); LocalVariableScope scope = new LocalVariableScope(); code.pushLocalVariableScope(scope); // TODO [mef] : add "this" to loca...
setFault(e);
recordFault(e);
public void execute() { assertNotCompleted(); try { setMetaDataAsText(assistant.asText(getTheConnection().getMetaData())); } catch (RuntimeException e) { setFault(e); } catch (JMSException e) { LOG.error(e); setFault(new HJBException(e)); ...
LOG.error(e); setFault(new HJBException(e));
recordFault(new HJBException(e));
public void execute() { assertNotCompleted(); try { setMetaDataAsText(assistant.asText(getTheConnection().getMetaData())); } catch (RuntimeException e) { setFault(e); } catch (JMSException e) { LOG.error(e); setFault(new HJBException(e)); ...
}else{ ForumCommon.notifyUsers(forum, t, forumDao);
public void insertSave() throws Exception { int forumId = this.request.getIntParameter("forum_id"); boolean firstPost = false; if (!this.anonymousPost(forumId)) { SessionFacade.setAttribute(ConfigKeys.REQUEST_DUMP, this.request.dumpRequest()); return; } Topic t = new Topic(-1); t.setForumId(forumId); boo...
public static void saveCompressedImage(BufferedImage image, String toFileName, int type) throws IOException
public static void saveCompressedImage(BufferedImage image, String toFileName, int type)
public static void saveCompressedImage(BufferedImage image, String toFileName, int type) throws IOException { if (type == IMAGE_PNG) { throw new UnsupportedOperationException("PNG compression not implemented"); } ImageWriter writer = null; Iterator iter = ImageIO.getImageWritersByFormatName("jpg"); writer =...
if (type == IMAGE_PNG) { throw new UnsupportedOperationException("PNG compression not implemented"); } ImageWriter writer = null; Iterator iter = ImageIO.getImageWritersByFormatName("jpg"); writer = (ImageWriter)iter.next(); ImageOutputStream ios = ImageIO.createImageOutputStream(new File(toFileName)); writer.setOut...
try { if (type == IMAGE_PNG) { throw new UnsupportedOperationException("PNG compression not implemented"); } Iterator iter = ImageIO.getImageWritersByFormatName("jpg"); ImageWriter writer; writer = (ImageWriter)iter.next(); ImageOutputStream ios = ImageIO.createImageOutputStream(new File(toFileName)); writer.setOutpu...
public static void saveCompressedImage(BufferedImage image, String toFileName, int type) throws IOException { if (type == IMAGE_PNG) { throw new UnsupportedOperationException("PNG compression not implemented"); } ImageWriter writer = null; Iterator iter = ImageIO.getImageWritersByFormatName("jpg"); writer =...
if (GENENAME_TERM==null) GENENAME_TERM = RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene");
if (GENENAME_TERM==null) GENENAME_TERM = RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene_name");
public static ComparableTerm getGeneNameTerm() { if (GENENAME_TERM==null) GENENAME_TERM = RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene"); return GENENAME_TERM; }
String[] gs = ((String[])section.get(0))[1].split("(\\s+or\\s+|\\s+and\\s+|;)"); for (int i = 0; i < gs.length; i++) { String raw = gs[i].trim(); if (raw.length()==0) continue; String[] parts = raw.split("="); String[] moreparts = parts[1].split(","); for (int j = 0; j < moreparts.length; j++) rlistener.addSequenceProp...
String[] genes = ((String[])section.get(0))[1].split("\\s+(or|and)\\s+"); for (int geneID = 0; geneID < genes.length; geneID++) { String[] parts = genes[geneID].split(";"); for (int j = 0; j < parts.length; j++) { String[] moreparts = parts[j].split("="); String[] values = moreparts[1].split(","); if (moreparts[0].tri...
public boolean readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) throws IllegalSymbolException, IOException, ParseException { String line; boolean hasAnotherSequence = true; //bool...
Pattern rppat = Pattern.compile("\\(SEQUENCE OF (\\d+)-(\\d+).*\\)");
public boolean readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) throws IllegalSymbolException, IOException, ParseException { String line; boolean hasAnotherSequence = true; //bool...
if (key.equals(REFERENCE_POSITION_TAG)) {
if (key.equals(RP_LINE_TAG)) { remark = val;
public boolean readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) throws IllegalSymbolException, IOException, ParseException { String line; boolean hasAnotherSequence = true; //bool...
if (key.equals(REMARK_TAG)) remark = val;
if (key.equals(RC_LINE_TAG)) { String[] parts = val.split(";"); for (int j = 0; j < parts.length; j++) { String[] subparts = parts[j].split("="); String termName = subparts[0].trim(); Term t; if (termName.equals(Terms.SPECIES_KEY)) t = Terms.getSpeciesTerm(); else if (termName.equals(Terms.STRAIN_KEY)) t = Terms.getS...
public boolean readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) throws IllegalSymbolException, IOException, ParseException { String line; boolean hasAnotherSequence = true; //bool...
String name = new String(typeName);
CClass cclass = lookupClass(typeName); if (cclass != null && ! cclass.isClass()) {
public TypeX lookupType(String typeName, IHasPosition location) { // Primitive types are resolved directly if (context.getTypeFactory().isPrimitive(typeName)) return TypeX.forName(typeName); // Copies the name object String name = new String(typeName); // Check if the map has a pointcut for this location...
if (map.containsKey(location)) {
String name = new String(typeName);
public TypeX lookupType(String typeName, IHasPosition location) { // Primitive types are resolved directly if (context.getTypeFactory().isPrimitive(typeName)) return TypeX.forName(typeName); // Copies the name object String name = new String(typeName); // Check if the map has a pointcut for this location...
Pointcut p = (Pointcut) map.get(location);
if (map.containsKey(location)) { CaesarPointcutWrapper wrapper = map.get(location); Pointcut p = wrapper.getWrappee(); if (p instanceof CaesarKindedPointcut) {
public TypeX lookupType(String typeName, IHasPosition location) { // Primitive types are resolved directly if (context.getTypeFactory().isPrimitive(typeName)) return TypeX.forName(typeName); // Copies the name object String name = new String(typeName); // Check if the map has a pointcut for this location...
if (p instanceof CaesarKindedPointcut) { CaesarKindedPointcut kp = (CaesarKindedPointcut) p; if (Shadow.MethodCall.equals(kp.getKind())) {
CaesarKindedPointcut kp = (CaesarKindedPointcut) p; if (Shadow.MethodCall.equals(kp.getKind())) { if (hasStaticModifier(kp) || kp.wasConstructor()) { name = cclass.getImplQualifiedName(); } } if (Shadow.MethodExecution.equals(kp.getKind())) { if (hasStaticModifier(kp)) { name = cclass.getImplQualifiedName(); } } if (S...
public TypeX lookupType(String typeName, IHasPosition location) { // Primitive types are resolved directly if (context.getTypeFactory().isPrimitive(typeName)) return TypeX.forName(typeName); // Copies the name object String name = new String(typeName); // Check if the map has a pointcut for this location...
if (Shadow.MethodExecution.equals(kp.getKind())) {
if (p instanceof WithinPointcut) { name = cclass.getImplQualifiedName();
public TypeX lookupType(String typeName, IHasPosition location) { // Primitive types are resolved directly if (context.getTypeFactory().isPrimitive(typeName)) return TypeX.forName(typeName); // Copies the name object String name = new String(typeName); // Check if the map has a pointcut for this location...
if (Shadow.FieldGet.equals(kp.getKind())) { name = convertToImplName(name);
if (p instanceof WithincodePointcut) { name = cclass.getImplQualifiedName();
public TypeX lookupType(String typeName, IHasPosition location) { // Primitive types are resolved directly if (context.getTypeFactory().isPrimitive(typeName)) return TypeX.forName(typeName); // Copies the name object String name = new String(typeName); // Check if the map has a pointcut for this location...
if (Shadow.FieldSet.equals(kp.getKind())) { name = convertToImplName(name);
if (p instanceof ReferencePointcut) { ReferencePointcut kp = (ReferencePointcut) p; name = cclass.getImplQualifiedName()+ "$Registry";
public TypeX lookupType(String typeName, IHasPosition location) { // Primitive types are resolved directly if (context.getTypeFactory().isPrimitive(typeName)) return TypeX.forName(typeName); // Copies the name object String name = new String(typeName); // Check if the map has a pointcut for this location...
if (Shadow.ConstructorCall.equals(kp.getKind())) { System.out.println("!!Warning!!Constructors must be translated"); } if (Shadow.ConstructorExecution.equals(kp.getKind())) { System.out.println("!!Warning!!Constructors must be translated"); } if (Shadow.PreInitialization.equals(kp.getKind())) { name = convertToImplName...
if (p instanceof ThisOrTargetPointcut) { name = cclass.getImplQualifiedName();
public TypeX lookupType(String typeName, IHasPosition location) { // Primitive types are resolved directly if (context.getTypeFactory().isPrimitive(typeName)) return TypeX.forName(typeName); // Copies the name object String name = new String(typeName); // Check if the map has a pointcut for this location...
if (p instanceof WithinPointcut) { name = convertToImplName(name); } if (p instanceof WithincodePointcut) { WithincodePointcut kp = (WithincodePointcut) p; name = convertToImplName(name); } if (p instanceof ReferencePointcut) { ReferencePointcut kp = (ReferencePointcut) p; name = convertToImplName(name) + "$Regist...
public TypeX lookupType(String typeName, IHasPosition location) { // Primitive types are resolved directly if (context.getTypeFactory().isPrimitive(typeName)) return TypeX.forName(typeName); // Copies the name object String name = new String(typeName); // Check if the map has a pointcut for this location...
CClass cclass = lookupClass(name); if (cclass == null) { cclass = lookupClass(typeName);
cclass = lookupClass(name);
public TypeX lookupType(String typeName, IHasPosition location) { // Primitive types are resolved directly if (context.getTypeFactory().isPrimitive(typeName)) return TypeX.forName(typeName); // Copies the name object String name = new String(typeName); // Check if the map has a pointcut for this location...
public static void register(TypePattern type, Pointcut p) {
public static void register(TypePattern type, CaesarPointcutWrapper p) {
public static void register(TypePattern type, Pointcut p) { map.put(type, p); }
map = new IdentityHashMap();
map = new IdentityHashMap<TypePattern, CaesarPointcutWrapper>();
public static void resetRegister() { map = new IdentityHashMap(); }
public int addNew(Smilie smilie) throws Exception
public int addNew(Smilie smilie)
public int addNew(Smilie smilie) throws Exception { PreparedStatement p = this.getStatementForAutoKeys("SmiliesModel.addNew"); p.setString(1, smilie.getCode()); p.setString(2, smilie.getUrl()); p.setString(3, smilie.getDiskName()); this.setAutoGeneratedKeysQuery(SystemGlobals.getSql("SmiliesModel.lastGenerat...
PreparedStatement p = this.getStatementForAutoKeys("SmiliesModel.addNew"); p.setString(1, smilie.getCode()); p.setString(2, smilie.getUrl()); p.setString(3, smilie.getDiskName()); this.setAutoGeneratedKeysQuery(SystemGlobals.getSql("SmiliesModel.lastGeneratedSmilieId")); int id = this.executeAutoKeysQuery(p);
PreparedStatement p=null; try { p = this.getStatementForAutoKeys("SmiliesModel.addNew");
public int addNew(Smilie smilie) throws Exception { PreparedStatement p = this.getStatementForAutoKeys("SmiliesModel.addNew"); p.setString(1, smilie.getCode()); p.setString(2, smilie.getUrl()); p.setString(3, smilie.getDiskName()); this.setAutoGeneratedKeysQuery(SystemGlobals.getSql("SmiliesModel.lastGenerat...
p.close(); return id; }
p.setString(1, smilie.getCode()); p.setString(2, smilie.getUrl()); p.setString(3, smilie.getDiskName()); this.setAutoGeneratedKeysQuery(SystemGlobals.getSql("SmiliesModel.lastGeneratedSmilieId")); return this.executeAutoKeysQuery(p); } catch (SQLException e) { String es = "Erorr addNew()"; log.error(es, e); throw new...
public int addNew(Smilie smilie) throws Exception { PreparedStatement p = this.getStatementForAutoKeys("SmiliesModel.addNew"); p.setString(1, smilie.getCode()); p.setString(2, smilie.getUrl()); p.setString(3, smilie.getDiskName()); this.setAutoGeneratedKeysQuery(SystemGlobals.getSql("SmiliesModel.lastGenerat...
public void delete(int id) throws Exception
public void delete(int id)
public void delete(int id) throws Exception { PreparedStatement p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("SmiliesModel.delete")); p.setInt(1, id); p.executeUpdate(); p.close(); }
PreparedStatement p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("SmiliesModel.delete")); p.setInt(1, id); p.executeUpdate(); p.close(); }
PreparedStatement p=null; try { p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("SmiliesModel.delete")); p.setInt(1, id); p.executeUpdate(); } catch (SQLException e) { String es = "Erorr delete()"; log.error(es, e); throw new RuntimeException(es, e); } finally { DbUtils.close( p); } }
public void delete(int id) throws Exception { PreparedStatement p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("SmiliesModel.delete")); p.setInt(1, id); p.executeUpdate(); p.close(); }
public List selectAll() throws Exception
public List selectAll()
public List selectAll() throws Exception { List l = new ArrayList(); PreparedStatement p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("SmiliesModel.selectAll")); ResultSet rs = p.executeQuery(); while (rs.next()) { l.add(this.getSmilie(rs)); } rs.close(); p.close(); r...
PreparedStatement p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("SmiliesModel.selectAll")); ResultSet rs = p.executeQuery(); while (rs.next()) { l.add(this.getSmilie(rs)); } rs.close(); p.close(); return l; }
PreparedStatement p=null; ResultSet rs=null; try { p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("SmiliesModel.selectAll")); rs = p.executeQuery(); while (rs.next()) { l.add(this.getSmilie(rs)); } return l; } catch (SQLException e) { String es = "Erorr selectAll()"; log.error(es, e);...
public List selectAll() throws Exception { List l = new ArrayList(); PreparedStatement p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("SmiliesModel.selectAll")); ResultSet rs = p.executeQuery(); while (rs.next()) { l.add(this.getSmilie(rs)); } rs.close(); p.close(); r...
public Smilie selectById(int id) throws Exception
public Smilie selectById(int id)
public Smilie selectById(int id) throws Exception { PreparedStatement p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("SmiliesModel.selectById")); p.setInt(1, id); Smilie s = new Smilie(); ResultSet rs = p.executeQuery(); if (rs.next()) { s = this.getSmilie(rs); } rs.cl...
PreparedStatement p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("SmiliesModel.selectById")); p.setInt(1, id); Smilie s = new Smilie(); ResultSet rs = p.executeQuery(); if (rs.next()) { s = this.getSmilie(rs); } rs.close(); p.close(); return s; }
PreparedStatement p=null; ResultSet rs=null; try { p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("SmiliesModel.selectById")); p.setInt(1, id); Smilie s = new Smilie(); rs = p.executeQuery(); if (rs.next()) { s = this.getSmilie(rs); } return s; } catch (SQLException e) { String es =...
public Smilie selectById(int id) throws Exception { PreparedStatement p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("SmiliesModel.selectById")); p.setInt(1, id); Smilie s = new Smilie(); ResultSet rs = p.executeQuery(); if (rs.next()) { s = this.getSmilie(rs); } rs.cl...
public void update(Smilie smilie) throws Exception
public void update(Smilie smilie)
public void update(Smilie smilie) throws Exception { PreparedStatement p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("SmiliesModel.update")); p.setString(1, smilie.getCode()); p.setString(2, smilie.getUrl()); p.setString(3, smilie.getDiskName()); p.setInt(4, smilie.getId()); ...
PreparedStatement p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("SmiliesModel.update")); p.setString(1, smilie.getCode()); p.setString(2, smilie.getUrl()); p.setString(3, smilie.getDiskName()); p.setInt(4, smilie.getId()); p.executeUpdate(); p.close(); }
PreparedStatement p=null; try { p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("SmiliesModel.update")); p.setString(1, smilie.getCode()); p.setString(2, smilie.getUrl()); p.setString(3, smilie.getDiskName()); p.setInt(4, smilie.getId()); p.executeUpdate(); } catch (SQLException e) { S...
public void update(Smilie smilie) throws Exception { PreparedStatement p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("SmiliesModel.update")); p.setString(1, smilie.getCode()); p.setString(2, smilie.getUrl()); p.setString(3, smilie.getDiskName()); p.setInt(4, smilie.getId()); ...
String nextToken = lineTokens.nextToken(); if(nextToken.startsWith(GenbankFormat.GI_TAG)) { this.saveSeqAnno(); headerTag = GenbankFormat.GI_TAG; headerTagText = new StringBuffer(nextToken.substring(3));
if (lineTokens.hasMoreTokens()) { String nextToken = lineTokens.nextToken(); if(nextToken.startsWith(GenbankFormat.GI_TAG)) { this.saveSeqAnno(); headerTag = GenbankFormat.GI_TAG; headerTagText = new StringBuffer(nextToken.substring(3)); }
private void processHeaderLine(String line) throws ParseException { if(line.startsWith(GenbankFormat.LOCUS_TAG)) { // the LOCUS line is a special case because it contains the // locus, size, molecule type, GenBank division, and the date // of last modification. this.saveSeqAnno(); StringToken...
id = line.substring(0, a);
if(a != -1) { id = line.substring(0, a); } else { id = line; }
public void addSequenceProperty(Object key, Object value) { if(key.equals(FastaFormat.PROPERTY_DESCRIPTIONLINE)) { String line = (String) value; /* 2nd word int a = line.indexOf(" ") + 1; int b = line.indexOf(" ", a); id = line.substring(a, b); ...
;
public void run() { try { while(true) { Object task = take(); if(task == null) { break; } if(task instanceof Task) { try { ((Task)task).execute(); } catch(Exception e ) { ;// I don't care } } else { SimpleResult sr = (SimpleResult)task; try { O...
r1 = LocationTools.makeCircularLocation(1, 100, 200); r2 = LocationTools.makeCircularLocation(1, 200, 200); r3 = LocationTools.makeCircularLocation(105, 300, 200); r4 = LocationTools.makeCircularLocation(-50, 20, 200); r5 = LocationTools.makeCircularLocation(90, 110, 200);
r1 = LocationTools.makeCircularLocation(1, 100, 200); r2 = LocationTools.makeCircularLocation(1, 200, 200); r3 = LocationTools.makeCircularLocation(105, 300, 200); r4 = LocationTools.makeCircularLocation(-50, 20, 200); r5 = LocationTools.makeCircularLocation(90, 110, 200); r6 = LocationTools.makeCircularLocation(18,24...
protected void setUp() throws Exception { r1 = LocationTools.makeCircularLocation(1, 100, 200); r2 = LocationTools.makeCircularLocation(1, 200, 200); r3 = LocationTools.makeCircularLocation(105, 300, 200); r4 = LocationTools.makeCircularLocation(-50, 20, 200); r5 = LocationTools.makeCircularLocation(90, 110, 200...
assertTrue(LocationTools.contains(r2, r1)); assertTrue(LocationTools.contains(r2, r3)); assertTrue(LocationTools.contains(r2, r4)); assertTrue(LocationTools.contains(r2, r5)); assertTrue(LocationTools.contains(r3, r4)); assertTrue(! LocationTools.contains(r4, r5)); assertTrue(! LocationTools.contains(r4, r3)); assertT...
assertTrue(LocationTools.contains(r2, r1)); assertTrue(LocationTools.contains(r2, r3)); assertTrue(LocationTools.contains(r2, r4)); assertTrue(LocationTools.contains(r2, r5)); assertTrue(LocationTools.contains(r3, r4));
public void testContains() { assertTrue(LocationTools.contains(r2, r1)); assertTrue(LocationTools.contains(r2, r3)); assertTrue(LocationTools.contains(r2, r4)); assertTrue(LocationTools.contains(r2, r5)); assertTrue(LocationTools.contains(r3, r4)); assertTrue(! LocationTools.contains(r4, r5)); assertTrue(! Loca...
assertTrue(r1.contains(1)); assertTrue(r1.contains(100)); assertTrue(r1.contains(202)); assertTrue(! r1.contains(101));
assertTrue(! LocationTools.contains(r4, r5)); assertTrue(! LocationTools.contains(r4, r3)); assertTrue(! LocationTools.contains(r1, r2)); assertTrue(r1.contains(1)); assertTrue(r1.contains(100)); assertTrue(r1.contains(202)); assertTrue(! r1.contains(101));
public void testContains() { assertTrue(LocationTools.contains(r2, r1)); assertTrue(LocationTools.contains(r2, r3)); assertTrue(LocationTools.contains(r2, r4)); assertTrue(LocationTools.contains(r2, r5)); assertTrue(LocationTools.contains(r3, r4)); assertTrue(! LocationTools.contains(r4, r5)); assertTrue(! Loca...
assertTrue(r1.isContiguous()); assertTrue(r2.isContiguous()); assertTrue(r3.isContiguous()); assertTrue(r4.isContiguous()); assertTrue(r5.isContiguous()); Location l = LocationTools.union(new RangeLocation(1,4),new RangeLocation(7,10));
assertTrue(r1.isContiguous()); assertTrue(r2.isContiguous()); assertTrue(! r3.isContiguous()); assertTrue(! r4.isContiguous()); assertTrue(r5.isContiguous()); Location l = LocationTools.union(new RangeLocation(1,4),new RangeLocation(7,10));
public void testIsContiguous() { assertTrue(r1.isContiguous()); assertTrue(r2.isContiguous()); assertTrue(r3.isContiguous()); assertTrue(r4.isContiguous()); assertTrue(r5.isContiguous()); Location l = LocationTools.union(new RangeLocation(1,4),new RangeLocation(7,10)); CircularLocation cl = new CircularL...
assertTrue(LocationTools.overlaps(r1, r1)); assertTrue(LocationTools.overlaps(r2, r2)); assertTrue(LocationTools.overlaps(r1, r2)); assertTrue(LocationTools.overlaps(r2, r1)); assertTrue(LocationTools.overlaps(r4, r2)); assertTrue(LocationTools.overlaps(r2, r4)); assertTrue(LocationTools.overlaps(r5, r3)); assertTrue(...
assertTrue(LocationTools.overlaps(r1, r1)); assertTrue(LocationTools.overlaps(r2, r2)); assertTrue(LocationTools.overlaps(r1, r2)); assertTrue(LocationTools.overlaps(r2, r1)); assertTrue(LocationTools.overlaps(r4, r2)); assertTrue(LocationTools.overlaps(r2, r4)); assertTrue(LocationTools.overlaps(r5, r3)); assertTrue(L...
public void testOverlaps() { assertTrue(LocationTools.overlaps(r1, r1)); assertTrue(LocationTools.overlaps(r2, r2)); assertTrue(LocationTools.overlaps(r1, r2)); assertTrue(LocationTools.overlaps(r2, r1)); assertTrue(LocationTools.overlaps(r4, r2)); assertTrue(LocationTools.overlaps(r2, r4)); assertTrue(LocationT...
public void add(UserSession us, Connection conn) throws Exception
public void add(UserSession us, Connection conn)
public void add(UserSession us, Connection conn) throws Exception { this.add(us, conn, false); }
public UserSession selectById(UserSession us, Connection conn) throws Exception
public UserSession selectById(UserSession us, Connection conn)
public UserSession selectById(UserSession us, Connection conn) throws Exception { PreparedStatement p = conn.prepareStatement(SystemGlobals.getSql("UserSessionModel.selectById")); p.setInt(1, us.getUserId()); ResultSet rs = p.executeQuery(); boolean found = false; UserSession returnUs = new UserSession(us); ...
PreparedStatement p = conn.prepareStatement(SystemGlobals.getSql("UserSessionModel.selectById")); p.setInt(1, us.getUserId()); ResultSet rs = p.executeQuery(); boolean found = false; UserSession returnUs = new UserSession(us); if (rs.next()) { returnUs.setSessionTime(rs.getLong("session_time")); returnUs.setStartTim...
PreparedStatement p=null; ResultSet rs=null; try { p = conn.prepareStatement(SystemGlobals.getSql("UserSessionModel.selectById")); p.setInt(1, us.getUserId()); rs = p.executeQuery(); boolean found = false; UserSession returnUs = new UserSession(us); if (rs.next()) { returnUs.setSessionTime(rs.getLong("session_time")...
public UserSession selectById(UserSession us, Connection conn) throws Exception { PreparedStatement p = conn.prepareStatement(SystemGlobals.getSql("UserSessionModel.selectById")); p.setInt(1, us.getUserId()); ResultSet rs = p.executeQuery(); boolean found = false; UserSession returnUs = new UserSession(us); ...
public void update(UserSession us, Connection conn) throws Exception
public void update(UserSession us, Connection conn)
public void update(UserSession us, Connection conn) throws Exception { if (this.selectById(us, conn) == null) { this.add(us, conn, true); return; } PreparedStatement p = conn.prepareStatement(SystemGlobals.getSql("UserSessionModel.update")); p.setTimestamp(1, new Timestamp(us.getStartTime().getTime())); p.s...
PreparedStatement p = conn.prepareStatement(SystemGlobals.getSql("UserSessionModel.update")); p.setTimestamp(1, new Timestamp(us.getStartTime().getTime())); p.setLong(2, us.getSessionTime()); p.setString(3, us.getSessionId()); p.setInt(4, us.getUserId()); p.executeUpdate(); p.close();
PreparedStatement p=null; try { p = conn.prepareStatement(SystemGlobals.getSql("UserSessionModel.update")); p.setTimestamp(1, new Timestamp(us.getStartTime().getTime())); p.setLong(2, us.getSessionTime()); p.setString(3, us.getSessionId()); p.setInt(4, us.getUserId()); p.executeUpdate(); } catch (SQLException e) { Str...
public void update(UserSession us, Connection conn) throws Exception { if (this.selectById(us, conn) == null) { this.add(us, conn, true); return; } PreparedStatement p = conn.prepareStatement(SystemGlobals.getSql("UserSessionModel.update")); p.setTimestamp(1, new Timestamp(us.getStartTime().getTime())); p.s...
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...
Integer.valueOf(max), Integer.valueOf(this.max)
new Integer(max), new Integer(this.max)
public void setMax(int max) throws ChangeVetoException { if(!this.hasListeners(RichLocation.MAX)) { this.max = max; } else { ChangeEvent ce = new ChangeEvent( this, RichLocation.MAX, Integer.valueOf(max), ...
Integer.valueOf(min), Integer.valueOf(this.min)
new Integer(min), new Integer(this.min)
public void setMin(int min) throws ChangeVetoException { if(!this.hasListeners(RichLocation.MIN)) { this.min = min; } else { ChangeEvent ce = new ChangeEvent( this, RichLocation.MIN, Integer.valueOf(min), ...
Integer.valueOf(rank), Integer.valueOf(this.rank)
new Integer(rank), new Integer(this.rank)
public void setRank(int rank) throws ChangeVetoException { if(!this.hasListeners(RichLocation.RANK)) { this.rank = rank; } else { ChangeEvent ce = new ChangeEvent( this, RichLocation.RANK, Integer.valueOf(rank), ...
setFault(e);
recordFault(e);
public void execute() { assertNotCompleted(); try { getProvider().deleteDestination(getName()); } catch (RuntimeException e) { setFault(e); } completed(); }
if (email == null)
if (email == null || email.length() == 0)
public static boolean validEmail(String email) { if (email == null) return false; if (email.length() > MAX_EMAIL_ADDRESS){ if (log.isDebugEnabled()) log.debug("Email too long: " + email); return false; } int indexOfAt = email.indexOf('@'); if (indexOfAt < 1){ // must have @ and must not be 1st char if...
if (site.charAt(site.length() - 2) == '.'){
if (site.length() - 2 > 0 && site.charAt(site.length() - 2) == '.'){
public static boolean validEmail(String email) { if (email == null) return false; if (email.length() > MAX_EMAIL_ADDRESS){ if (log.isDebugEnabled()) log.debug("Email too long: " + email); return false; } int indexOfAt = email.indexOf('@'); if (indexOfAt < 1){ // must have @ and must not be 1st char if...
ValidationUtils.rejectIfEmptyOrWhitespace(errors, "description", "required", "Field is required."); ValidationUtils.rejectIfEmptyOrWhitespace(errors, "source", "required", "Field is required."); ValidationUtils.rejectIfEmptyOrWhitespace(errors, "info", "required", "Field is required.");
ValidationUtils.rejectIfEmptyOrWhitespace(errors, "description", "required", "Description is required."); ValidationUtils.rejectIfEmptyOrWhitespace(errors, "source", "required", "Source is required."); ValidationUtils.rejectIfEmptyOrWhitespace(errors, "info", "required", "Info is required."); Recording recording = (Rec...
public void validate(Object target, Errors errors) { ValidationUtils.rejectIfEmptyOrWhitespace(errors, "description", "required", "Field is required."); ValidationUtils.rejectIfEmptyOrWhitespace(errors, "source", "required", "Field is required."); ValidationUtils.rejectIfEmptyOrWhitespace(er...
String commandArgs = getArgs( getRepository().getAnnotations() );
String args = getSshArgs( getRepository().getAnnotations() );
public void executeCommand( String command ) throws TransferFailedException { AuthenticationInfo authenticationInfo = getRepository().getAuthenticationInfo(); String commandArgs = getArgs( getRepository().getAnnotations() ); String commandExecutable = getExectutable( getRepository().g...
String commandExecutable = getExectutable( getRepository().getAnnotations() );
String executable = getSshExecutable( getRepository().getAnnotations() );
public void executeCommand( String command ) throws TransferFailedException { AuthenticationInfo authenticationInfo = getRepository().getAuthenticationInfo(); String commandArgs = getArgs( getRepository().getAnnotations() ); String commandExecutable = getExectutable( getRepository().g...
cl.setExecutable( commandExecutable );
cl.setExecutable( executable );
public void executeCommand( String command ) throws TransferFailedException { AuthenticationInfo authenticationInfo = getRepository().getAuthenticationInfo(); String commandArgs = getArgs( getRepository().getAnnotations() ); String commandExecutable = getExectutable( getRepository().g...
if ( commandArgs != null )
if ( args != null )
public void executeCommand( String command ) throws TransferFailedException { AuthenticationInfo authenticationInfo = getRepository().getAuthenticationInfo(); String commandArgs = getArgs( getRepository().getAnnotations() ); String commandExecutable = getExectutable( getRepository().g...
cl.createArgument().setLine( commandArgs );
cl.createArgument().setLine( args );
public void executeCommand( String command ) throws TransferFailedException { AuthenticationInfo authenticationInfo = getRepository().getAuthenticationInfo(); String commandArgs = getArgs( getRepository().getAnnotations() ); String commandExecutable = getExectutable( getRepository().g...
String scpArgs = getArgs( getRepository().getAnnotations() );
String args = getScpArgs( getRepository().getAnnotations() );
private void executeScpCommand( File localFile, String remoteFile, boolean put ) throws TransferFailedException { AuthenticationInfo authenticationInfo = getRepository().getAuthenticationInfo(); String scpArgs = getArgs( getRepository().getAnnotations() ); String spcExecutable = getEx...
String spcExecutable = getExectutable( getRepository().getAnnotations() );
String executable = getScpExecutable( getRepository().getAnnotations() );
private void executeScpCommand( File localFile, String remoteFile, boolean put ) throws TransferFailedException { AuthenticationInfo authenticationInfo = getRepository().getAuthenticationInfo(); String scpArgs = getArgs( getRepository().getAnnotations() ); String spcExecutable = getEx...
cl.setExecutable( scpExecutable );
cl.setExecutable( executable );
private void executeScpCommand( File localFile, String remoteFile, boolean put ) throws TransferFailedException { AuthenticationInfo authenticationInfo = getRepository().getAuthenticationInfo(); String scpArgs = getArgs( getRepository().getAnnotations() ); String spcExecutable = getEx...
if ( scpArgs != null )
if ( args != null )
private void executeScpCommand( File localFile, String remoteFile, boolean put ) throws TransferFailedException { AuthenticationInfo authenticationInfo = getRepository().getAuthenticationInfo(); String scpArgs = getArgs( getRepository().getAnnotations() ); String spcExecutable = getEx...
public SimpleFeature(Sequence sourceSeq, Feature.Template template) {
public SimpleFeature(Sequence sourceSeq, Feature.Template template) throws IllegalArgumentException{ if(template.location == null) { throw new IllegalArgumentException( "Location can not be null. Did you mean Location.EMPTY_LOCATION?" ); }
public SimpleFeature(Sequence sourceSeq, Feature.Template template) { this.sourceSeq = sourceSeq; this.loc = template.location; this.type = template.type; this.source = template.source; this.annotation = new SimpleAnnotation(template.annotation); }
mMonitor = new OutputStreamMonitor(is);
SocketExceptionHandler listener = new SocketExceptionHandler() { public void exceptionOccurred(SocketException exception) { try { mInstance.terminate(); } catch (DebugException e) { } } }; mMonitor = new OutputStreamMonitor(is, listener);
public StreamsProxy(InputStream is, OutputStream os) { mMonitor = new OutputStreamMonitor(is); mMonitor.startMonitoring(); mReplInput = new PrintStream(os); }
InetAddress binding = null;
public void start() throws IOException { if (this.smtpServer != null) throw new IllegalStateException("SMTPServer already running"); InetAddress binding = null; String bindAddress = System.getProperty("jboss.bind.address"); if (bindAddress != null && !"0.0.0.0".equals(bindAddress)) binding = InetAddress.ge...
if (document.getChar(command.offset - 1) == '"') {
if (command.offset > 0 && document.getChar(command.offset - 1) == '"') {
public void customizeDocumentCommand(IDocument document, DocumentCommand command) { try { if (command.text.length() != 1) return; char insertedChar = command.text.charAt(0); switch (insertedChar) { case '"': if (document.getCha...
setFault(e);
recordFault(e);
public void execute() { assertNotCompleted(); try { setProducerIndex(getProducers().createProducer(getSessionIndex(), getDestination(), getProducerArguments())); } catc...
"strand was not POSITIVE or NEGATIVE but " + strand
"strand was not POSITIVE or NEGATIVE but " + template.strand
public SimpleStrandedFeature(Sequence sourceSeq, StrandedFeature.Template template) throws IllegalArgumentException, IllegalAlphabetException { super(sourceSeq, template); if(template.strand != POSITIVE && template.strand != NEGATIVE) { throw new IllegalArgumentException( ...
this.strand = strand;
this.strand = template.strand;
public SimpleStrandedFeature(Sequence sourceSeq, StrandedFeature.Template template) throws IllegalArgumentException, IllegalAlphabetException { super(sourceSeq, template); if(template.strand != POSITIVE && template.strand != NEGATIVE) { throw new IllegalArgumentException( ...
public CannotCreateFromFieldSetException(String msg, NumberFormatException e) { super(msg+" : "+e, e);
public CannotCreateFromFieldSetException(String msg) { super(msg);
public CannotCreateFromFieldSetException(String msg, NumberFormatException e) { super(msg+" : "+e, e); }
public PaddedEphemerallyEncryptedBucket(Bucket bucket, int minSize, long knownSize, byte[] key, RandomSource origRandom) throws IOException { if(bucket.size() < knownSize) throw new IOException("Bucket is too small on disk - knownSize="+knownSize+" but bucket.size="+bucket.size()+" for "+bucket); this.dataLength = know...
public PaddedEphemerallyEncryptedBucket(Bucket bucket, int minSize, RandomSource origRandom, boolean forgetKey) {
public PaddedEphemerallyEncryptedBucket(Bucket bucket, int minSize, long knownSize, byte[] key, RandomSource origRandom) throws IOException { if(bucket.size() < knownSize) throw new IOException("Bucket is too small on disk - knownSize="+knownSize+" but bucket.size="+bucket.size()+" for "+bucket); this.dataLength =...
aes.initialize(key); this.key = key;
byte[] tempKey = new byte[32]; origRandom.nextBytes(tempKey); aes.initialize(tempKey); if(forgetKey) { for(int i=0;i<tempKey.length;i++) tempKey[i] = 0; this.key = null; } else { this.key = tempKey; }
public PaddedEphemerallyEncryptedBucket(Bucket bucket, int minSize, long knownSize, byte[] key, RandomSource origRandom) throws IOException { if(bucket.size() < knownSize) throw new IOException("Bucket is too small on disk - knownSize="+knownSize+" but bucket.size="+bucket.size()+" for "+bucket); this.dataLength =...
value = getCreateDate().compareTo(pollsQuestion.getCreateDate());
value = DateUtil.compareTo(getCreateDate(), pollsQuestion.getCreateDate());
public int compareTo(Object obj) { if (obj == null) { return -1; } PollsQuestion pollsQuestion = (PollsQuestion)obj; int value = 0; value = getCreateDate().compareTo(pollsQuestion.getCreateDate()); value = value * -1; if (value != 0) { return value; } return 0; }
sb.append(StringPool.SPACE); Properties extraSettingsProps = fileEntry.getExtraSettingsProperties(); Iterator itr = (Iterator)extraSettingsProps.entrySet().iterator(); while (itr.hasNext()) { Map.Entry entry = (Map.Entry)itr.next(); String value = GetterUtil.getString( (String)entry.getValue()); sb.append(value); ...
public static void addFile( String companyId, String portletId, String groupId, String repositoryId, String fileName) throws IOException { synchronized (IndexWriter.class) { if (_log.isDebugEnabled()) { _log.debug( "Indexing document " + companyId + " " + portletId + " " + groupId + " " + repositor...
public static String getUID( String portletId, String field1, String field2) { return getUID(portletId, field1, field2, null);
public static String getUID(String portletId, String field1) { return getUID(portletId, field1, null);
public static String getUID( String portletId, String field1, String field2) { return getUID(portletId, field1, field2, null); }
fieldObj.setBoost(0);
public static Field getKeyword(String field, String keyword) { //keyword = KeywordsUtil.escape(keyword); Field fieldObj = new Field( field, keyword, Field.Store.YES, Field.Index.UN_TOKENIZED); fieldObj.setBoost(0); return fieldObj; }
ABContact c = new ABContact(null);
ABContact c = new ABContact();
private ABContact _createContact(String[] values, Map defs, DateFormat df) { ABContact c = new ABContact(null); c.setFirstName(getValue(values, defs, "First Name")); c.setLastName(getValue(values, defs, "Last Name")); c.setEmailAddress(getValue(values, defs, "E-mail Address")); c.setHomeStreet(getValue(values, de...
super();
public ABContact() { super(); }
sb.append("if (_" + col.getName() + " == null) {"); sb.append("_" + col.getName() + " = new HashSet();"); sb.append("}");
private void _createHBM(Entity entity) throws IOException { List pkList = entity.getPKList(); List columnList = entity.getColumnList(); StringBuffer sb = new StringBuffer(); // Package sb.append("package " + _packagePath + ".service.persistence;"); // Imports sb.append("import " + _packagePath + ".model." + ent...
public static void write(File file, String s) throws IOException { write(file, s, false);
public static void write(String fileName, String s) throws IOException { write(new File(fileName), s);
public static void write(File file, String s) throws IOException { write(file, s, false); }
public static String read(File file) throws IOException { BufferedReader br = new BufferedReader(new FileReader(file)); StringBuffer sb = new StringBuffer(); String line = null; while ((line = br.readLine()) != null) { sb.append(line).append('\n'); } br.close(); return sb.toString().trim();
public static String read(String fileName) throws IOException { return read(new File(fileName));
public static String read(File file) throws IOException { BufferedReader br = new BufferedReader(new FileReader(file)); StringBuffer sb = new StringBuffer(); String line = null; while ((line = br.readLine()) != null) { sb.append(line).append('\n'); } br.close(); return sb.toString().trim(); }
fileEl.setAttribute("desc", _getLayoutName(layout));
private void _getFiles(CommandArgument arg, Node root, Document doc) throws Exception { if (!arg.getCurrentFolder().equals("/")) { Element filesEl = doc.createElement("Files"); root.appendChild(filesEl); String groupName = _getGroupName(arg.getCurrentFolder()); Group group = GroupServiceUtil.getGroup( arg...