rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k |
|---|---|---|
removeChangeListener(cl, null); | removeChangeListener(cl, ChangeType.UNKNOWN); | public void removeChangeListener(ChangeListener cl) { removeChangeListener(cl, null); } |
IExtension[] extensions = SchemeScriptPlugin.getDefault() .getDescriptor() .getExtensionPoint("interpreters") .getExtensions(); | IExtension[] extensions = Platform.getExtensionRegistry().getExtensionPoint(EXTENSION_POINT_ID).getExtensions(); | public static InterpreterType[] getTypes() { if (mCachedTypes != null) { return mCachedTypes; } IExtension[] extensions = SchemeScriptPlugin.getDefault() .getDescriptor() .getExtensi... |
parameters, | public CSourceMethod checkInterface(CClassContext context) throws PositionedError { try { if (returnType.isReference()) { returnType = returnType.checkType(context); } } catch (UnpositionedError e) { // FJTODO what to do with exception ... | |
parameters[i].getSignature(), | CaesarBcelWorld.getInstance().resolve(parameters[i]), | public void createAttribute( CContext context, CClass caller, JFormalParameter[] formalParameters, TokenReference tokenReference, int orderNr) { List formalBindings = new ArrayList(); //bind parameters for (int i = 0; i < parameters.length; i++) { if (!formalParameters[i].isGenerated()) { formalBind... |
if (Vm.getMegaVersion() > 1 && Vm.getMajorVersion() > 4) { | if (Vm.getMegaVersion() >= 1 && Vm.getMajorVersion() > 4) { | private void addJDK15InstrumentedSpec() { if (Vm.getMegaVersion() > 1 && Vm.getMajorVersion() > 4) { TransparencyClassSpec spec = getOrCreateSpec("java.util.concurrent.locks.ReentrantLock$ConditionObject"); spec.setCallConstructorOnLoad(true); spec.setHonorTransient(true); } } |
if (Vm.getMegaVersion() > 1 && Vm.getMajorVersion() > 4) { | if (Vm.getMegaVersion() >= 1 && Vm.getMajorVersion() > 4) { | private void addJDK15PreInstrumentedSpec() { if (Vm.getMegaVersion() > 1 && Vm.getMajorVersion() > 4) { TransparencyClassSpec spec = getOrCreateSpec("sun.misc.Unsafe"); addCustomAdapter("sun.misc.Unsafe", UnsafeAdapter.class); spec = getOrCreateSpec(DSOUnsafe.CLASS_DOTS); addCustomAdapter(DSOUn... |
} else if ("-list".equals(sw)) { | } else if ("-xff".equals(sw)) { format = "xff"; }else if ("-list".equals(sw)) { | public static void main(String[] args) throws Exception { String format = "fasta"; boolean all = false; int startArgs = 0; while (startArgs < args.length && args[startArgs].startsWith("-")) { String sw = args[startArgs]; if ("-fasta".equals(sw)) { format = "fasta"; } else if ("-gff".equals(sw... |
System.err.println("usage: rfetch [-fasta | -gff | -embl | -genbank | -agave] namespace id1 id2 ..."); | System.err.println("usage: rfetch [-fasta | -gff | -embl | -genbank | -agave | -xff] namespace id1 id2 ..."); | private static void printUsage() { System.err.println("usage: rfetch [-fasta | -gff | -embl | -genbank | -agave] namespace id1 id2 ..."); } |
} else if ("agave".equals(format)) { | } else if ("xff".equals(format)) { XFFWriter xffw = new XFFWriter(); PrintWriter pw = new PrintWriter(new OutputStreamWriter(System.out)); XMLWriter xw = new PrettyXMLWriter(pw); xffw.writeFeatureSet(seq, xw); pw.flush(); } else if ("agave".equals(format)) { | private static void writeSequence(Sequence seq, String format) throws Exception { if ("embl".equals(format)) { new EmblLikeFormat().writeSequence(seq, System.out); } else if ("genbank".equals(format)) { new GenbankFormat().writeSequence(seq, System.out); } else if ("fasta".equals(format)) { ne... |
public List selectAll(int startFrom, int count) throws Exception | public List selectAll(int startFrom, int count) | public List selectAll(int startFrom, int count) throws Exception { PreparedStatement p; if (count > 0) { p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("GenericModel.selectByLimit") + " " + count + " " + SystemGlobals.getSql("UserModel.selectAllByLimit")); p.... |
PreparedStatement p; | PreparedStatement p=null; ResultSet rs=null; | public List selectAll(int startFrom, int count) throws Exception { PreparedStatement p; if (count > 0) { p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("GenericModel.selectByLimit") + " " + count + " " + SystemGlobals.getSql("UserModel.selectAllByLimit")); p.... |
if (count > 0) { p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("GenericModel.selectByLimit") + " " + count + " " + SystemGlobals.getSql("UserModel.selectAllByLimit")); p.setInt(1, startFrom); p.setInt(2, count); } else { p = JForumExecutionContext.getConnection().prepareStatement(Syst... | try { if (count > 0) { p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("GenericModel.selectByLimit") + " " + count + " " + SystemGlobals.getSql("UserModel.selectAllByLimit")); p.setInt(1, startFrom); p.setInt(2, count); } else { p = JForumExecutionContext.getConnection().prepareStatemen... | public List selectAll(int startFrom, int count) throws Exception { PreparedStatement p; if (count > 0) { p = JForumExecutionContext.getConnection().prepareStatement(SystemGlobals.getSql("GenericModel.selectByLimit") + " " + count + " " + SystemGlobals.getSql("UserModel.selectAllByLimit")); p.... |
public List selectAllWithKarma(int startFrom, int count) throws Exception | public List selectAllWithKarma(int startFrom, int count) | public List selectAllWithKarma(int startFrom, int count) throws Exception { return super.loadKarma( this.selectAll(startFrom, count) ); } |
return super.loadKarma( this.selectAll(startFrom, count) ); } | try { return super.loadKarma( this.selectAll(startFrom, count) ); } catch (SQLException e) { String es = "Erorr selectAllWithKarma()"; log.error(es, e); throw new RuntimeException(es, e); } } | public List selectAllWithKarma(int startFrom, int count) throws Exception { return super.loadKarma( this.selectAll(startFrom, count) ); } |
public static String[] writeWordWrap(String input, String sepRegex, String separator, int width) { width--; if (input.length()<=width) return new String[]{input}; String[] parts = input.split(sepRegex); StringBuffer currentLine = new StringBuffer(); List lines = new ArrayList(); for (int i = 0; i < parts.length; i++) {... | public static String[] writeWordWrap(String input, String sepRegex, int width) { List lines = new ArrayList(); Pattern p = Pattern.compile(sepRegex); int start = 0; while (start < input.length()) { if (input.charAt(start)=='\n') start++; int splitPoint = start+width; if (splitPoint > input.length()) splitPoint=input.... | public static String[] writeWordWrap(String input, String sepRegex, String separator, int width) { width--; // because of some weird start-at-zero thingy - if you pass 60, we must work with 59. if (input.length()<=width) return new String[]{input}; String... |
currentLine.append(word); | public static String[] writeWordWrap(String input, String sepRegex, String separator, int width) { width--; // because of some weird start-at-zero thingy - if you pass 60, we must work with 59. if (input.length()<=width) return new String[]{input}; String... | |
if (currentLine.length()>0) lines.add(currentLine.toString()); | public static String[] writeWordWrap(String input, String sepRegex, String separator, int width) { width--; // because of some weird start-at-zero thingy - if you pass 60, we must work with 59. if (input.length()<=width) return new String[]{input}; String... | |
public List getPosts(int start, int count, int minPostId, int maxPostId, Connection conn) throws Exception | public List getPosts(int start, int count, int minPostId, int maxPostId, Connection conn) | public List getPosts(int start, int count, int minPostId, int maxPostId, Connection conn) throws Exception { return dao.getPosts(minPostId, maxPostId, start, count, conn); } |
boolean a = false; boolean b = false; int i = 1; if(super.isContiguous()) return true; if(getWrapped() instanceof CompoundLocation){ CompoundLocation l = (CompoundLocation)getWrapped(); for(Iterator iter = l.blockIterator(); iter.hasNext(); i++){ if(i > 2) return false; Location block = (Location)iter.next(); if(bloc... | return getWrapped().isContiguous(); | public boolean isContiguous() { boolean a = false; boolean b = false; int i = 1; if(super.isContiguous()) return true; if(getWrapped() instanceof CompoundLocation){ CompoundLocation l = (CompoundLocation)getWrapped(); for(Iterator iter = l.blockIterator(); iter.hasNext(); i++){ if(i > ... |
gopher.l = l; CrossProductResidue r = (CrossProductResidue) ourResidues.get(gopher); | CrossProductResidue r; synchronized(gopher) { gopher.l = l; r = (CrossProductResidue) ourResidues.get(gopher); } | public CrossProductResidue getResidue(List l) throws IllegalAlphabetException { gopher.l = l; CrossProductResidue r = (CrossProductResidue) ourResidues.get(gopher); if (r == null) { throw new IllegalAlphabetException( "Unable to find CrossProduct residue for " + l + " in alphabet " + getNa... |
l + " in alphabet " + getName() | new SimpleCrossProductResidue(l, '?').getName() + " in alphabet " + getName() | public CrossProductResidue getResidue(List l) throws IllegalAlphabetException { gopher.l = l; CrossProductResidue r = (CrossProductResidue) ourResidues.get(gopher); if (r == null) { throw new IllegalAlphabetException( "Unable to find CrossProduct residue for " + l + " in alphabet " + getNa... |
public SimpleResidueList(Alphabet alpha, List rList) { | public SimpleResidueList(Alphabet alpha) { | public SimpleResidueList(Alphabet alpha, List rList) { this.alphabet = alpha; this.residues = rList; } |
this.residues = rList; | residues = new ArrayList(); | public SimpleResidueList(Alphabet alpha, List rList) { this.alphabet = alpha; this.residues = rList; } |
protected Mail getMailFor(Long mailId, Permission check, Person me) throws NotFoundException, PermissionException | protected Mail getMailFor(Long mailId, Permission check) throws NotFoundException, PermissionException | protected Mail getMailFor(Long mailId, Permission check, Person me) throws NotFoundException, PermissionException { Mail mail = this.dao.findMail(mailId); Role role = mail.getList().getRoleFor(me); if (! role.getPermissions().contains(check)) throw new PermissionException(check); return mail; } |
Mail mail = this.dao.findMail(mailId); Role role = mail.getList().getRoleFor(me); if (! role.getPermissions().contains(check)) throw new PermissionException(check); return mail; | return this.getMailFor(mailId, check, this.getMe()); | protected Mail getMailFor(Long mailId, Permission check, Person me) throws NotFoundException, PermissionException { Mail mail = this.dao.findMail(mailId); Role role = mail.getList().getRoleFor(me); if (! role.getPermissions().contains(check)) throw new PermissionException(check); return mail; } |
protected MailingList getListFor(Long listId, Permission check, Person me) throws NotFoundException, PermissionException | protected MailingList getListFor(Long listId, Permission check) throws NotFoundException, PermissionException | protected MailingList getListFor(Long listId, Permission check, Person me) throws NotFoundException, PermissionException { MailingList list = this.dao.findMailingList(listId); Role role = list.getRoleFor(me); if (! role.getPermissions().contains(check)) throw new PermissionException(check); return list; } |
MailingList list = this.dao.findMailingList(listId); Role role = list.getRoleFor(me); if (! role.getPermissions().contains(check)) throw new PermissionException(check); return list; | return this.getListFor(listId, check, this.getMe()); | protected MailingList getListFor(Long listId, Permission check, Person me) throws NotFoundException, PermissionException { MailingList list = this.dao.findMailingList(listId); Role role = list.getRoleFor(me); if (! role.getPermissions().contains(check)) throw new PermissionException(check); return list; } |
params, | public CCjAdvice( CClass owner, int modifiers, String ident, CType returnType, CType[] paramTypes, CReferenceType[] exceptions, JBlock body, CaesarPointcut pointcut, CaesarAdviceKind kind, int extraArgumentFlags) { super( owner, modifiers | ACC_FINAL, ident, returnType, paramTypes, exceptions, ... | |
public CaesarFormalBinding(String signature, String name, int index, int start, int end, String fileName) | public CaesarFormalBinding(ResolvedTypeX type, String name, int index, int start, int end, String fileName) | public CaesarFormalBinding(String signature, String name, int index, int start, int end, String fileName) { binding = new FormalBinding( TypeX.forSignature(signature), name, index, start, end, fileName); } |
TypeX.forSignature(signature), | type, | public CaesarFormalBinding(String signature, String name, int index, int start, int end, String fileName) { binding = new FormalBinding( TypeX.forSignature(signature), name, index, start, end, fileName); } |
prepareForDynamicDeployment(environment); | new DeploymentPreparation(currentInnerInner).prepareForDynamicDeployment(environment); | public void prepareForDynamicDeployment(KjcEnvironment environment) { List newInners = new ArrayList(); for (int i = 0; i < cd.getInners().length; i++) { newInners.add(cd.getInners()[i]); if (cd.getInners()[i] instanceof FjClassDeclaration) { //create support classes for each crosscutting inner class Fj... |
if(found.length == 0) fail("No errors found : "+getId()+" : "+getDescription()); if(expected.length != found.length) fail("More ("+errors.size()+") errors found than expected: "+getId()+" : "+getDescription()); for (int i = 0; i < found.length; i++) { if(!(expected[i] == found[i].getFormattedMessage().getDescription(... | else { if(found.length == 0) fail("No errors found : "+getId()+" : "+getDescription()); if(expected.length != found.length) fail("More ("+errors.size()+") errors found than expected: "+getId()+" : "+getDescription()); for (int i = 0; i < found.length; i++) { if(!(expected[i] == found[i].getFormattedMessage().getDescr... | private void checkErrors(MessageDescription[] expected){ List errors = new LinkedList(); for (Iterator iter = positionedErrorList.iterator(); iter.hasNext();) { Object o = iter.next(); // ignore warnings which are a subtype of PositionedError if (!(o instanceof CWarnin... |
setFault(e); | recordFault(e); | public void execute() { assertNotCompleted(); try { createConsumerAndSaveItsIndex(); } catch (RuntimeException e) { setFault(e); } completed(); } |
numRoundsTextField.setPreferredSize(new Dimension(50, 16)); numRoundsTextField.setMaximumSize(new Dimension(50, 16)); numRoundsTextField.setMinimumSize(new Dimension(50, 16)); | private JTextField getNumRoundsTextField() { if (numRoundsTextField == null) { numRoundsTextField = new JTextField(); numRoundsTextField.setAutoscrolls(false); numRoundsTextField.setPreferredSize(new Dimension(50, 16)); numRoundsTextField.setMaximumSize(new Dimension(50, 16)); numRoundsTextField.setMinimumS... | |
FileSpecification robotSpecification = (FileSpecification) robotList.elementAt(i); | FileSpecification robotSpecification = robotList.elementAt(i); | public void setRobotList(Vector<FileSpecification> robotListVector) { AvailableRobotsPanel.this.robotList = robotListVector; SwingUtilities.invokeLater( new Runnable() { public void run() { availablePackages.clear(); availableRobots.clear(); if (AvailableRobotsPanel.this.robotList == null) { Avail... |
String[] tags = SystemGlobals.getValue(s).toUpperCase().split(","); | String s1 = SystemGlobals.getValue(s); if (s1==null) { return; } String[] tags = s1.toUpperCase().split(","); | private static void splitAndTrim(String s, Set data) { String[] tags = SystemGlobals.getValue(s).toUpperCase().split(","); for (int i = 0; i < tags.length; i++) { data.add(tags[i].trim()); } } |
cache = new HashMap(); | public DiagonalCachingKernel() { cache = new HashMap(); } | |
public void setString(String key, String value) { setString(DEFAULT_SESSION_ID, key, value); | public void setString(SessionID sessionID, String key, String value) { getOrCreateSessionProperties(sessionID).setProperty(key, value.trim()); | public void setString(String key, String value) { setString(DEFAULT_SESSION_ID, key, value); } |
for(int j = 0; localVariables != null && j < localVariables.length; j++){ while(!((InstructionHandle)localVariables[j].getEnd()).isReached()) { localVariables[j].setEnd(((InstructionHandle)localVariables[j].getEnd()).getPrevious()); } } | private boolean cleanCode() { boolean codeRemoved = false; for (int i = 0; i < handlers.length; i++) { while (!((InstructionHandle)handlers[i].getEnd()).isReached()) { handlers[i].setEnd(((InstructionHandle)handlers[i].getEnd()).getPrevious()); } // !!!if (start > end) remove handler } Ins... | |
while (level-- > 0 && codeChanged) { | while ( codeChanged) { | public static CodeInfo optimize(CodeInfo code, int level) { Optimizer opt = new Optimizer(code); // do work at specified level boolean codeChanged = true; while (level-- > 0 && codeChanged) { codeChanged = opt.optimizeCodeSequence(); } code = opt.getCodeInfo(); return code; } |
HJBConnection result = findConnectionFactory(providerName, factoryName).getConnection(connectionIndex); if (null == result) { | try { HJBConnection result = findConnectionFactory(providerName, factoryName).getConnection(connectionIndex); if (null == result) { handleMissingComponent("" + PathNaming.CONNECTION + "" + connectionIndex); } return result; } catch (IndexOutOfBoundsException e) { | public HJBConnection findConnection(String providerName, String factoryName, int connectionIndex) { HJBConnection result = findConnectionFactory(providerName, factoryName).getConnection(connectionIndex); if (null == result) ... |
return result; | public HJBConnection findConnection(String providerName, String factoryName, int connectionIndex) { HJBConnection result = findConnectionFactory(providerName, factoryName).getConnection(connectionIndex); if (null == result) ... | |
public static PermissionControl load(int userId, boolean force) throws Exception | public static PermissionControl load(int userId, boolean force) | public static PermissionControl load(int userId, boolean force) throws Exception { if (force || cache.get(FQN, Integer.toString(userId)) == null) { UserDAO um = DataAccessDriver.getInstance().newUserDAO(); return SecurityRepository.load(um.selectById(userId), force); } return SecurityRepository.get(userId)... |
public RoleCollection loadRolesByUserGroups(User user) throws Exception; | public RoleCollection loadRolesByUserGroups(User user) ; | public RoleCollection loadRolesByUserGroups(User user) throws Exception; |
else if (paramsList.get(i) instanceof Map) types[i] = Map.class; | public Object buildObject(Class clazz, List paramsList) { // Create the Hibernate query to look it up with String queryText; String queryType; List queryParamsList = new ArrayList(paramsList); if (SimpleNamespace.class.isAssignableFrom(clazz)) { queryText = "from Namesp... | |
try | Principal p = this.sessionContext.getCallerPrincipal(); String name = p.getName(); if (name == null || name.equals(SubEthaLoginModule.UNAUTHENTICATED_IDENTITY)) | protected EmailAddress getMyAddress() { try { Principal p = this.sessionContext.getCallerPrincipal(); String name = p.getName(); if (name == null) { return null; } else { try { return this.dao.findEmailAddress(name); } catch (NotFoundException ex) { return null; } ... |
Principal p = this.sessionContext.getCallerPrincipal(); String name = p.getName(); if (name == null) | return null; } else { try { return this.dao.findEmailAddress(name); } catch (NotFoundException ex) | protected EmailAddress getMyAddress() { try { Principal p = this.sessionContext.getCallerPrincipal(); String name = p.getName(); if (name == null) { return null; } else { try { return this.dao.findEmailAddress(name); } catch (NotFoundException ex) { return null; } ... |
else { try { return this.dao.findEmailAddress(name); } catch (NotFoundException ex) { return null; } } } catch (IllegalStateException ex) { return null; | protected EmailAddress getMyAddress() { try { Principal p = this.sessionContext.getCallerPrincipal(); String name = p.getName(); if (name == null) { return null; } else { try { return this.dao.findEmailAddress(name); } catch (NotFoundException ex) { return null; } ... | |
btnRefresh.setMnemonic('r'); | btnRefresh.setMnemonic(java.util.ResourceBundle.getBundle("com/javaimagealbum/resources/MnemonicResource").getString("Refresh_Folder").charAt(0)); | private void initComponents() { java.awt.GridBagConstraints gridBagConstraints; lblTitle = new javax.swing.JLabel(); pnlContents = new javax.swing.JPanel(); tpInstructions = new javax.swing.JTextPane(); pnlCenter = new javax.swing.JPanel(); spScroll = new javax.swing.JScrol... |
btnBrowse.setMnemonic('w'); | btnBrowse.setMnemonic(java.util.ResourceBundle.getBundle("com/javaimagealbum/resources/MnemonicResource").getString("Browse").charAt(0)); | private void initComponents() { java.awt.GridBagConstraints gridBagConstraints; lblTitle = new javax.swing.JLabel(); pnlContents = new javax.swing.JPanel(); tpInstructions = new javax.swing.JTextPane(); pnlCenter = new javax.swing.JPanel(); spScroll = new javax.swing.JScrol... |
if( found != null ) { | if( found == null ) { break; } else { | public void setSelectedFile( File f ) { Stack composition = new Stack(); do { File parent = f.getParentFile(); String name = f.getName(); if( parent == null ) { // If this is a root filename, use toString instead of getName. name = f.toStr... |
} else { break; | public void setSelectedFile( File f ) { Stack composition = new Stack(); do { File parent = f.getParentFile(); String name = f.getName(); if( parent == null ) { // If this is a root filename, use toString instead of getName. name = f.toStr... | |
super(); | public CannotChangePanelException() { } | |
wrapper.setProperty(mrd.getAttributeName(i), mrd.getAttributeValue(i)); | wrapper.setProperty(name, mrd.getAttributeValue(i)); } else if (name.equals("__id_")) { wrapper.addStaticArgument("id", mrd.getAttributeValue(i)); } else if (name.equals("id")) { continue; | protected void setProperties(FlowElement wrapper, HierarchicalStreamReader rd, UnmarshallingContext context) { MXppReader mrd = (MXppReader) rd; for (int i = 0; i < mrd.getAttributeCount(); i++) { String name = mrd.getAttributeName(i).toLowerCase().intern(); if (name.equalsIgnoreCase(FlowElement.UID)) { Int... |
if( local.isMixin() ) { if(local.getDepth() == field.getOwner().getDepth()) { | if( local.isMixin() ) { if (field.isStatic()) { prefix = new JTypeNameExpression( getTokenReference(), new CClassNameType(field.getOwnerType().getQualifiedName()) ); } else if(local.getDepth() == field.getOwner().getDepth()) { | public JExpression analyse(CExpressionContext context) throws PositionedError { TypeFactory factory = context.getTypeFactory(); if (analysed) { return this; } JExpression origPrefix = prefix; CClass local = context.getClassContext().getCClass(); //findPrefix(local, new CExpressionContex... |
if(!field.isStatic()) { prefix = new JOwnerExpression(getTokenReference(), local); } else { prefix = new JTypeNameExpression( getTokenReference(), new CClassNameType(field.getOwnerType().getQualifiedName()) ); } | prefix = new JOwnerExpression(getTokenReference(), local); | public JExpression analyse(CExpressionContext context) throws PositionedError { TypeFactory factory = context.getTypeFactory(); if (analysed) { return this; } JExpression origPrefix = prefix; CClass local = context.getClassContext().getCClass(); //findPrefix(local, new CExpressionContex... |
check(context, !context.isLeftSide(), CaesarMessages.READ_ONLY_ACCESS_TO_CCLASS_FIELDS); return new CjAccessorCallExpression( getTokenReference(), prefix, field ).analyse(context); | return new CjAccessorCallExpression( getTokenReference(), prefix, field ).analyse(context); | public JExpression analyse(CExpressionContext context) throws PositionedError { TypeFactory factory = context.getTypeFactory(); if (analysed) { return this; } JExpression origPrefix = prefix; CClass local = context.getClassContext().getCClass(); //findPrefix(local, new CExpressionContex... |
aspectClass.getPointcuts(), | new PointcutDeclaration[0], | public FjClassDeclaration createSingletonAspect() { AdviceDeclaration[] advices = aspectClass.getAdvices(); JMethodDeclaration[] methods = aspectClass.getMethods(); List fields = new ArrayList(); List singletonAspectMethods = new ArrayList(); JMethodDeclaration[] aspectClassMethods = new JMethodDeclaration[meth... |
public MockExpectation(boolean matches, boolean needsMoreInvocations, boolean allowsMoreInvocations) { this.matches = matches; this.needsMoreInvocations = needsMoreInvocations; this.allowsMoreInvocations = allowsMoreInvocations; } | public MockExpectation() { this(false, false, false); } | public MockExpectation(boolean matches, boolean needsMoreInvocations, boolean allowsMoreInvocations) { this.matches = matches; this.needsMoreInvocations = needsMoreInvocations; this.allowsMoreInvocations = allowsMoreInvocations; } |
if (DebugUtil.DEBUG) { System.err.println("In FutureTask innerGet: -- Client id: " + ManagerUtil.getClientID() + ", state: " + state + ", proxyRunner: " + proxyRunner); } | Object innerGet() throws InterruptedException, ExecutionException { lock.lock(); try { while (tryAcquireShared() < 0) { ran.await(); } } finally { lock.unlock(); } if (getSynchronizedState() == CANCELLED) throw new CancellationException(); if (exception !=... | |
if (start < 0 || end > length()) { | if (start < 1 || end > length()) { | public SymbolList subList(int start, int end) { if (start < 0 || end > length()) { throw new IndexOutOfBoundsException( "Sublist index out of bounds " + length() + ":" + start + "," + end ); } if (end < start) { throw new IndexOutOfBoundsException( ... |
throw new IndexOutOfBoundsException( "send must not be lower than sstart: start=" + start + ", end=" + end | throw new IllegalArgumentException( "end must not be lower than start: start=" + start + ", end=" + end | public SymbolList subList(int start, int end) { if (start < 0 || end > length()) { throw new IndexOutOfBoundsException( "Sublist index out of bounds " + length() + ":" + start + "," + end ); } if (end < start) { throw new IndexOutOfBoundsException( ... |
PreparedStatement ps = conn.prepareStatement("select residue_serial, serial, residue_id,code_3_letter, CHEM_ATOM_NAME_PDB_LS, chem_atom_name, element_symbol,alt_code, CHAIN_CODE_1_LETTER, chain_code, chain_pdb_code, OCCUPANCY, PDB_CHARGE,PDB_Group, x,y,z, CHEM_COMP_CODE, CHEM_ATOM_ID,U_ISO_OR_EQUIV, RESIDUE_P... | PreparedStatement ps = conn.prepareStatement("select residue_serial, serial, residue_id,code_3_letter, CHEM_ATOM_NAME_PDB_LS, chem_atom_name, element_symbol,alt_code, CHAIN_CODE_1_LETTER, chain_code, chain_pdb_code, OCCUPANCY, PDB_CHARGE,PDB_Group, x,y,z, CHEM_COMP_CODE, CHEM_ATOM_ID,U_ISO_OR_EQUIV, RESIDUE_P... | public Structure getStructureById(String pdbId) throws IOException { // open connection to database Connection conn ; Structure structure = new StructureImpl(); try { conn = dataSource.getConnection(); // create Structure object from MSD database query. } catch (SQLException e) { e.printStackTrace(); ... |
if ( chain_pdb_code == null ) { | if ( insertionCode == null ) insertionCode = ""; if ( chain_pdb_code == null ) | public Structure getStructureById(String pdbId) throws IOException { // open connection to database Connection conn ; Structure structure = new StructureImpl(); try { conn = dataSource.getConnection(); // create Structure object from MSD database query. } catch (SQLException e) { e.printStackTrace(); ... |
} if (! prevChain.equals(chain_pdb_code)) { | if (! prevChain.equals(chain_pdb_code)) | public Structure getStructureById(String pdbId) throws IOException { // open connection to database Connection conn ; Structure structure = new StructureImpl(); try { conn = dataSource.getConnection(); // create Structure object from MSD database query. } catch (SQLException e) { e.printStackTrace(); ... |
} if ( CHEM_ATOM_NAME_LS == null) { | if ( CHEM_ATOM_NAME_LS == null) | public Structure getStructureById(String pdbId) throws IOException { // open connection to database Connection conn ; Structure structure = new StructureImpl(); try { conn = dataSource.getConnection(); // create Structure object from MSD database query. } catch (SQLException e) { e.printStackTrace(); ... |
} | public Structure getStructureById(String pdbId) throws IOException { // open connection to database Connection conn ; Structure structure = new StructureImpl(); try { conn = dataSource.getConnection(); // create Structure object from MSD database query. } catch (SQLException e) { e.printStackTrace(); ... | |
g.setPDBCode(residue_pdb_seq+""); | g.setPDBCode(residue_pdb_seq+insertionCode); | public Structure getStructureById(String pdbId) throws IOException { // open connection to database Connection conn ; Structure structure = new StructureImpl(); try { conn = dataSource.getConnection(); // create Structure object from MSD database query. } catch (SQLException e) { e.printStackTrace(); ... |
altLoc = new Character(' '); | public AtomImpl () { name = null ; fullName = null ; coords = new double[3]; pdbline = "" ; occupancy = 0.0 ; tempfactor = 0.0 ; } | |
public static String readBlobUTF16BinaryStream(ResultSet rs, String fieldName) throws IOException, SQLException | public static String readBlobUTF16BinaryStream(ResultSet rs, String fieldName) throws SQLException | public static String readBlobUTF16BinaryStream(ResultSet rs, String fieldName) throws IOException, SQLException { Blob clob = rs.getBlob(fieldName); InputStream is = clob.getBinaryStream(); StringBuffer sb = new StringBuffer(); int readedBytes = 0; int bufferSize = 4096; do { byte[] bytes = new byte[bufferSize... |
Blob clob = rs.getBlob(fieldName); | try { Blob clob = rs.getBlob(fieldName); | public static String readBlobUTF16BinaryStream(ResultSet rs, String fieldName) throws IOException, SQLException { Blob clob = rs.getBlob(fieldName); InputStream is = clob.getBinaryStream(); StringBuffer sb = new StringBuffer(); int readedBytes = 0; int bufferSize = 4096; do { byte[] bytes = new byte[bufferSize... |
InputStream is = clob.getBinaryStream(); StringBuffer sb = new StringBuffer(); int readedBytes = 0; int bufferSize = 4096; | InputStream is = clob.getBinaryStream(); StringBuffer sb = new StringBuffer(); int readedBytes; int bufferSize = 4096; do { byte[] bytes = new byte[bufferSize]; readedBytes = is.read(bytes); if (readedBytes > 0) { String readed = new String(bytes, 0, readedBytes, "UTF-16"); sb.append(readed); } } while (readedBytes == ... | public static String readBlobUTF16BinaryStream(ResultSet rs, String fieldName) throws IOException, SQLException { Blob clob = rs.getBlob(fieldName); InputStream is = clob.getBinaryStream(); StringBuffer sb = new StringBuffer(); int readedBytes = 0; int bufferSize = 4096; do { byte[] bytes = new byte[bufferSize... |
do { byte[] bytes = new byte[bufferSize]; readedBytes = is.read(bytes); if (readedBytes > 0) { String readed = new String(bytes, 0, readedBytes, "UTF-16"); sb.append(readed); } } while (readedBytes == bufferSize); | is.close(); return sb.toString(); } catch (IOException e) { String es = "Erorr readBlobUTF16BinaryStream()"; log.error(es, e); throw new RuntimeException(es, e); } | public static String readBlobUTF16BinaryStream(ResultSet rs, String fieldName) throws IOException, SQLException { Blob clob = rs.getBlob(fieldName); InputStream is = clob.getBinaryStream(); StringBuffer sb = new StringBuffer(); int readedBytes = 0; int bufferSize = 4096; do { byte[] bytes = new byte[bufferSize... |
is.close(); return sb.toString(); | public static String readBlobUTF16BinaryStream(ResultSet rs, String fieldName) throws IOException, SQLException { Blob clob = rs.getBlob(fieldName); InputStream is = clob.getBinaryStream(); StringBuffer sb = new StringBuffer(); int readedBytes = 0; int bufferSize = 4096; do { byte[] bytes = new byte[bufferSize... | |
public static void writeBlobUTF16BinaryStream(String query, int idForQuery, String value) throws IOException, SQLException | public static void writeBlobUTF16BinaryStream(String query, int idForQuery, String value) throws SQLException | public static void writeBlobUTF16BinaryStream(String query, int idForQuery, String value) throws IOException, SQLException { PreparedStatement p = JForumExecutionContext.getConnection().prepareStatement(query); p.setInt(1, idForQuery); ResultSet rs = p.executeQuery(); rs.next(); Blob postText = rs.getBlob(1); ... |
PreparedStatement p = JForumExecutionContext.getConnection().prepareStatement(query); p.setInt(1, idForQuery); | PreparedStatement p=null; ResultSet rs=null; try { p = JForumExecutionContext.getConnection().prepareStatement(query); p.setInt(1, idForQuery); | public static void writeBlobUTF16BinaryStream(String query, int idForQuery, String value) throws IOException, SQLException { PreparedStatement p = JForumExecutionContext.getConnection().prepareStatement(query); p.setInt(1, idForQuery); ResultSet rs = p.executeQuery(); rs.next(); Blob postText = rs.getBlob(1); ... |
ResultSet rs = p.executeQuery(); rs.next(); Blob postText = rs.getBlob(1); | rs = p.executeQuery(); rs.next(); Blob postText = rs.getBlob(1); | public static void writeBlobUTF16BinaryStream(String query, int idForQuery, String value) throws IOException, SQLException { PreparedStatement p = JForumExecutionContext.getConnection().prepareStatement(query); p.setInt(1, idForQuery); ResultSet rs = p.executeQuery(); rs.next(); Blob postText = rs.getBlob(1); ... |
OutputStream blobWriter = null; if (postText instanceof BLOB) { blobWriter = ((BLOB)postText).getBinaryOutputStream(); } else { blobWriter = postText.setBinaryStream(0); } | OutputStream blobWriter; if (postText instanceof BLOB) { blobWriter = ((BLOB)postText).getBinaryOutputStream(); } else { blobWriter = postText.setBinaryStream(0); } | public static void writeBlobUTF16BinaryStream(String query, int idForQuery, String value) throws IOException, SQLException { PreparedStatement p = JForumExecutionContext.getConnection().prepareStatement(query); p.setInt(1, idForQuery); ResultSet rs = p.executeQuery(); rs.next(); Blob postText = rs.getBlob(1); ... |
blobWriter.close(); rs.close(); p.close(); } | blobWriter.close(); } catch (IOException e) { String es = "Erorr writeBlobUTF16BinaryStream()"; log.error(es, e); throw new RuntimeException(es, e); } finally { DbUtils.close(rs, p); } } | public static void writeBlobUTF16BinaryStream(String query, int idForQuery, String value) throws IOException, SQLException { PreparedStatement p = JForumExecutionContext.getConnection().prepareStatement(query); p.setInt(1, idForQuery); ResultSet rs = p.executeQuery(); rs.next(); Blob postText = rs.getBlob(1); ... |
Boolean value = (Boolean)cfg.getValue(); | String value = (String)cfg.getValue(); | public void start() throws Exception { // If we haven't been bootstrapped, we need to run. try { Config cfg = this.dao.findConfig(BOOTSTRAPPED_CONFIG_ID); // Might as well sanity check it Boolean value = (Boolean)cfg.getValue(); if (value == null || value == false) { this.bootstrap(); cfg.setV... |
if (value == null || value == false) | if (value == null || value.length() == 0) | public void start() throws Exception { // If we haven't been bootstrapped, we need to run. try { Config cfg = this.dao.findConfig(BOOTSTRAPPED_CONFIG_ID); // Might as well sanity check it Boolean value = (Boolean)cfg.getValue(); if (value == null || value == false) { this.bootstrap(); cfg.setV... |
cfg.setValue(Boolean.TRUE); | cfg.setValue("1.0"); | public void start() throws Exception { // If we haven't been bootstrapped, we need to run. try { Config cfg = this.dao.findConfig(BOOTSTRAPPED_CONFIG_ID); // Might as well sanity check it Boolean value = (Boolean)cfg.getValue(); if (value == null || value == false) { this.bootstrap(); cfg.setV... |
Config cfg = new Config(BOOTSTRAPPED_CONFIG_ID, Boolean.TRUE); | Config cfg = new Config(BOOTSTRAPPED_CONFIG_ID, "1.0"); | public void start() throws Exception { // If we haven't been bootstrapped, we need to run. try { Config cfg = this.dao.findConfig(BOOTSTRAPPED_CONFIG_ID); // Might as well sanity check it Boolean value = (Boolean)cfg.getValue(); if (value == null || value == false) { this.bootstrap(); cfg.setV... |
public Config(String id, Object value) { if (log.isDebugEnabled()) log.debug("Creating new Config: " + id); this.id = id; this.value = value; } | public Config() {} | public Config(String id, Object value) { if (log.isDebugEnabled()) log.debug("Creating new Config: " + id); this.id = id; this.value = value; } |
pnlAlbumTitleOption = new javax.swing.JPanel(); lblAlbumTitle = new javax.swing.JLabel(); tfAlbumTitle = new javax.swing.JTextField(); lblAlbumDescription = new javax.swing.JLabel(); tfAlbumDescription = new javax.swing.JTextField(); | private void initComponents() { java.awt.GridBagConstraints gridBagConstraints; lblTitle = new javax.swing.JLabel(); pnlContents = new javax.swing.JPanel(); tpInstructions = new javax.swing.JTextPane(); pnlAlbumTitleOption = new javax.swing.JPanel(); lblAlbumTitle = new jav... | |
pnlLinkToAlbumIndex = new javax.swing.JPanel(); cbLinkToAlbumIndex = new javax.swing.JCheckBox(); | pnShowExif = new javax.swing.JPanel(); cbShowExif = new javax.swing.JCheckBox(); | private void initComponents() { java.awt.GridBagConstraints gridBagConstraints; lblTitle = new javax.swing.JLabel(); pnlContents = new javax.swing.JPanel(); tpInstructions = new javax.swing.JTextPane(); pnlAlbumTitleOption = new javax.swing.JPanel(); lblAlbumTitle = new jav... |
cbShowExif = new javax.swing.JCheckBox(); | private void initComponents() { java.awt.GridBagConstraints gridBagConstraints; lblTitle = new javax.swing.JLabel(); pnlContents = new javax.swing.JPanel(); tpInstructions = new javax.swing.JTextPane(); pnlAlbumTitleOption = new javax.swing.JPanel(); lblAlbumTitle = new jav... | |
pnlAlbumTitleOption.setLayout(new java.awt.GridBagLayout()); pnlAlbumTitleOption.setBackground(java.awt.Color.white); lblAlbumTitle.setDisplayedMnemonic('t'); lblAlbumTitle.setFont(new java.awt.Font("SansSerif", 0, 12)); lblAlbumTitle.setLabelFor(tfAlbumTitle); lblAlbumTitle.setText("Album Title:"); gridBagConstraints... | private void initComponents() { java.awt.GridBagConstraints gridBagConstraints; lblTitle = new javax.swing.JLabel(); pnlContents = new javax.swing.JPanel(); tpInstructions = new javax.swing.JTextPane(); pnlAlbumTitleOption = new javax.swing.JPanel(); lblAlbumTitle = new jav... | |
pnlLinkToAlbumIndex.setLayout(new java.awt.FlowLayout(java.awt.FlowLayout.LEFT)); pnlLinkToAlbumIndex.setBackground(java.awt.Color.white); cbLinkToAlbumIndex.setBackground(java.awt.Color.white); cbLinkToAlbumIndex.setFont(new java.awt.Font("SansSerif", 0, 12)); cbLinkToAlbumIndex.setMnemonic('i'); cbLinkToAlbumIndex.s... | pnShowExif.setLayout(new java.awt.FlowLayout(java.awt.FlowLayout.LEFT)); pnShowExif.setBackground(java.awt.Color.white); | private void initComponents() { java.awt.GridBagConstraints gridBagConstraints; lblTitle = new javax.swing.JLabel(); pnlContents = new javax.swing.JPanel(); tpInstructions = new javax.swing.JTextPane(); pnlAlbumTitleOption = new javax.swing.JPanel(); lblAlbumTitle = new jav... |
pnlContents.add(cbShowExif, new java.awt.GridBagConstraints()); | pnShowExif.add(cbShowExif); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.gridwidth = java.awt.GridBagConstraints.REMAINDER; gridBagConstraints.gridheight = java.awt.GridBagConstraints.REMAINDER; gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL; gridBagConstraints.anchor = ... | private void initComponents() { java.awt.GridBagConstraints gridBagConstraints; lblTitle = new javax.swing.JLabel(); pnlContents = new javax.swing.JPanel(); tpInstructions = new javax.swing.JTextPane(); pnlAlbumTitleOption = new javax.swing.JPanel(); lblAlbumTitle = new jav... |
cbLinkToAlbumIndexActionPerformed(evt); | cbShowExifActionPerformed(evt); | public void actionPerformed(java.awt.event.ActionEvent evt) { cbLinkToAlbumIndexActionPerformed(evt); } |
publishManager.setAlbumTitle( tfAlbumTitle.getText() ); publishManager.setAlbumDescription( tfAlbumDescription.getText() ); | private void scanAndPersistOptions() { publishManager.setAlbumTitle( tfAlbumTitle.getText() ); publishManager.setAlbumDescription( tfAlbumDescription.getText() ); publishManager.setOutputColumns( Integer.parseInt( tfColumns.getText() ) ); publishManager.setThumbnailsPerPage( ... | |
publishManager.setLinkToAlbumIndex( cbLinkToAlbumIndex.isSelected() ); | private void scanAndPersistOptions() { publishManager.setAlbumTitle( tfAlbumTitle.getText() ); publishManager.setAlbumDescription( tfAlbumDescription.getText() ); publishManager.setOutputColumns( Integer.parseInt( tfColumns.getText() ) ); publishManager.setThumbnailsPerPage( ... | |
tfAlbumTitle.setText( publishManager.getAlbumTitle() ); | public void showPanel() { tfAlbumTitle.setText( publishManager.getAlbumTitle() ); tfColumns.setText( "" + publishManager.getOutputColumns() ); coThumbnailsPerPage.setSelectedItem( publishManager.getThumbnailsPerPage() ); cbResizeAll.setSelected( publishManager.getResizeAll() ... | |
cbLinkToAlbumIndex.setSelected( publishManager.getLinkToAlbumIndex() ); | public void showPanel() { tfAlbumTitle.setText( publishManager.getAlbumTitle() ); tfColumns.setText( "" + publishManager.getOutputColumns() ); coThumbnailsPerPage.setSelectedItem( publishManager.getThumbnailsPerPage() ); cbResizeAll.setSelected( publishManager.getResizeAll() ... | |
SequenceFactory sFact = new SimpleSequenceFactory(); | SequenceBuilderFactory sFact = new FastaDescriptionLineParser.Factory(SimpleSequenceBuilder.FACTORY); | public static final void main(String [] args) throws Exception { if(args.length != 2) { throw new Exception("Use: CorbaDBServer sequences.fa type"); } // work out what to load File seqDBFile = new File(args[0]); Alphabet alpha = AlphabetManager.alphabetForName(args[1]); if(alpha == null) { ... |
System.out.println("Loading fasta database: " + seqDBFile); | System.err.println("Loading fasta database: " + seqDBFile); | public static final void main(String [] args) throws Exception { if(args.length != 2) { throw new Exception("Use: CorbaDBServer sequences.fa type"); } // work out what to load File seqDBFile = new File(args[0]); Alphabet alpha = AlphabetManager.alphabetForName(args[1]); if(alpha == null) { ... |
throw new IllegalStateException("Already running"); | throw new IllegalStateException("SMTPServer already running"); | public void setHostName(String hostname) { if (this.smtpServer != null) throw new IllegalStateException("Already running"); this.hostName = hostname; } |
throw new IllegalStateException("Already running"); | throw new IllegalStateException("SMTPServer already running"); | public void setPort(int port) { if (this.smtpServer != null) throw new IllegalStateException("Already running"); this.port = port; } |
throw new IllegalStateException("Already running"); | throw new IllegalStateException("SMTPServer already running"); | public void start() throws IOException { if (this.smtpServer != null) throw new IllegalStateException("Already running"); if (this.hostName == null) { try { this.hostName = InetAddress.getLocalHost().getCanonicalHostName(); } catch (UnknownHostException e) { this.hostName = "localhost"; } } ... |
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