rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k |
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public String asText(Map anyMap) { if (null == anyMap) return ""; | public String asText(HJBMessage aMessage) { if (null == aMessage) return ""; | public String asText(Map anyMap) { if (null == anyMap) return ""; StringWriter result = new StringWriter(); writeAsText(anyMap, result); return result.toString(); } |
writeAsText(anyMap, result); | writeAsText(aMessage, result); | public String asText(Map anyMap) { if (null == anyMap) return ""; StringWriter result = new StringWriter(); writeAsText(anyMap, result); return result.toString(); } |
public IdentityBuilder willReturn(Object returnValue) { return stub(new ReturnStub(returnValue)); | public IdentityBuilder willReturn(boolean returnValue) { return willReturn(new Boolean(returnValue)); | public IdentityBuilder willReturn(Object returnValue) { return stub(new ReturnStub(returnValue)); } |
throws HJBException, IOException { | throws IOException { | protected void handleCommandExecutionWasTimedOut(JMSCommandGenerator generator, HttpServletResponse response, Long commandTimeout, JMSCommand generatedCommand) ... |
} catch (HJBException e) { new RuntimeExceptionHandler().sendHJBFault(response, e); | protected void handleUsingMatchingGenerator(JMSCommandGenerator generators[], HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { try { for (int i =... | |
if (!generatedCommand.isExecutedOK()) { handleExecutionWasNotOk(generatedCommand); | if (! generatedCommand.isExecutedOK()) { getServletContext().log(generatedCommand.getStatusMessage(), generatedCommand.getFault()); | protected void handleUsingSelectedGenerator(JMSCommandGenerator generator, HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { Long commandTimeout = findComman... |
caesarClass.getMixinIfcDeclaration().join(ownerCtx); | public static void prepareForDynamicDeployment(JCompilationUnit cu) throws PositionedError { boolean bNewDelarations = false; CContext ownerCtx = cu.getContext(); for (JTypeDeclaration typeDecl : cu.getInners()) { if (typeDecl instanceof CjVirtualClassDeclaration) { CjVirtualClassDeclaration caesarClass ... | |
if (pos < raf.length()) atEOF = false; | public void seek(long pos) throws IOException { int p = (int) (raPtrPos - pos); // Check if we can seek within the buffer if (p >= 0 && p <= bufferEnd) { bufferPos = bufferEnd - p; } // Otherwise delegate to do a "real" seek and clean the // dirty buffe... | |
System.out.println("made SBSH for " + sym.hashCode() + " " + sym); | public SBSH(SimpleAtomicSymbol sym) { syms = sym.getSymbols(); ann = sym.getAnnotation(); System.out.println("made SBSH for " + sym.hashCode() + " " + sym); } | |
System.out.println("read SBSH for " + sym.hashCode() + " " + sym); | public Object readResolve() throws ObjectStreamException { try { Symbol sym = AlphabetManager.createSymbol(ann, syms, null); System.out.println("read SBSH for " + sym.hashCode() + " " + sym); return sym; } catch (IllegalSymbolException ex) { throw new InvalidObjec... | |
wrapper.setDeclaringType(mixinType); | wrapper.setTypePattern(mixinType); | private CaesarPointcutWrapper parseWithinPointcut() { parseIdentifier(); eat("("); TypePattern type = parseTypePattern(); eat(")"); // Creates the wrapper and register it WithinPointcut p = new WithinPointcut(type); CaesarPointcutWrapper wrapper = new CaesarPointcutWrapper(p); wrapper.setTypePattern(type); ... |
ITypedRegion partition = document.getPartition(command.offset); | ITypedRegion partition = SchemeTextUtilities.getPartition(document, command.offset); | public void customizeDocumentCommand(IDocument document, DocumentCommand command) { try { if (command.length == 1 && command.text.length() == 0) { ITypedRegion partition = document.getPartition(command.offset); if (partition.getType() == SchemePartitionScanner.SCHEME_... |
c.insets = new Insets(5, 5, 5, 5); | private JPanel getSpecificSettingsPanel() { if (specificSettingsPanel == null) { specificSettingsPanel = new JPanel(); specificSettingsPanel.setBorder( BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(), "Specific settings")); specificSettingsPanel.setLayout(new GridBagLayout()); GridBagC... | |
public List selectAllByTopicByLimit(int topicId, int startFrom, int count) throws Exception | public List selectAllByTopicByLimit(int topicId, int startFrom, int count) | public List selectAllByTopicByLimit(int topicId, int startFrom, int count) throws Exception { return super.selectAllByTopicByLimit(topicId, count, startFrom); } |
strings().getString(HJBStrings.NOT_APPLICAPLE)); | new Integer(getTheConnection().getConnectionIndex())); | public String getDescription() { return strings().getString(HJBStrings.DESCRIPTION_OF_CREATE_COMMANDS, Session.class.getName(), strings().getString(HJBStrings.NOT_APPLICAPLE)); // TODO remove not applicable once HJBConnection's know a... |
if (scope instanceof CaesarPointcutScope) { CaesarPointcutScope s = (CaesarPointcutScope) scope; CClass cclass = s.lookupClass(exactType.getName()); if (cclass != null && cclass.getAbstractType().isCaesarReference()) { return; } } | public void resolveBindings(IScope scope, Bindings bindings) { if (kind == Shadow.Initialization) {// scope.getMessageHandler().handleMessage(// MessageUtil.error(// "initialization unimplemented in 1.1beta1",// this.getSourceLocation())); } signature = signature.resolveBindings(scope, bindings); ... | |
public void deleteByTopic(int topicId) throws Exception; | public void deleteByTopic(int topicId) ; | public void deleteByTopic(int topicId) throws Exception; |
public List selectAllByTopic(int topicId) throws Exception; | public List selectAllByTopic(int topicId) ; | public List selectAllByTopic(int topicId) throws Exception; |
public List selectAllByTopicByLimit(int topicId, int startFrom, int count) throws Exception; | public List selectAllByTopicByLimit(int topicId, int startFrom, int count) ; | public List selectAllByTopicByLimit(int topicId, int startFrom, int count) throws Exception; |
try{ return AlphabetManager.alphabetForName(this.getName()); }catch(NoSuchElementException nse){ AlphabetManager.registerAlphabet(this.getName(), this); return this; } | if(AlphabetManager.registered(this.getName())){ return AlphabetManager.alphabetForName(this.getName()); }else{ if(this.registered){ AlphabetManager.registerAlphabet(this.getName(), this); } return this; } | protected Object readResolve() throws ObjectStreamException{ try{ return AlphabetManager.alphabetForName(this.getName()); }catch(NoSuchElementException nse){ //a custom alphabet has been sent to your VM, register it. AlphabetManager.registerAlphabet(this.getName(), this); return this; } ... |
Constants.LINK_TO_ALBUM_INDEX, "true" ).toLowerCase().equals( | Constants.SHOW_EXIF, "true" ).toLowerCase().equals( | private void loadOutputSettings() { Settings settings = Settings.getInstance(); setAlbumTitle( settings.getProperty( Constants.ALBUM_TITLE, "Photos" ) ); setAlbumDescription( settings.getProperty( Constants.ALBUM_DESCRIPTION, "" ) ); setOutputColumns( Integer.parseInt... |
if (idHeader != null && idHeader.length > 0) id = Long.parseLong(idHeader[0]); String contentType = null; try { contentType = archiver.getAttachmentContentType(id); } catch (PermissionException pex) { } catch (NotFoundException nfex) { } | if (idHeader != null && idHeader.length > 0) id = Long.parseLong(idHeader[0]); | public void onSend(SubEthaMessage msg, SendFilterContext ctx) throws MessagingException { try { for (Part p : msg.getParts()) { Long id = null; // Look for special header which means we must reattach. String[] idHeader = p.getHeader(SubEthaMessage.HDR_ATTACHMENT_REF); if (idHeader != null && idHead... |
p.setText("<a href=\"" + ctx.getList().getUrlBase() + "attachement/" + id + "\"> download attachement " + id + "/" + MailUtils.getNameFromContentType(contentType) + "</a>"); | String contentType = ""; try { contentType = archiver.getAttachmentContentType(id); } catch (PermissionException pex) { } catch (NotFoundException nfex) { } String name = MailUtils.getNameFromContentType(contentType); p.setText("<a href=\"" + ctx.getList().getUrlBase() + "attachment/" + id + "/" + name + "\"> downlo... | public void onSend(SubEthaMessage msg, SendFilterContext ctx) throws MessagingException { try { for (Part p : msg.getParts()) { Long id = null; // Look for special header which means we must reattach. String[] idHeader = p.getHeader(SubEthaMessage.HDR_ATTACHMENT_REF); if (idHeader != null && idHead... |
tagDelegator.setListener("REFERENCE", new Agregator(valueChanger, new Agregator.Observer() { | tagDelegator.setListener("REFERENCE", new MultiTagger(valueChanger, new BoundaryFinder() { | public ParserListener getParserListener(TagValueListener listener) { ChangeTable changeTable = new ChangeTable(); changeTable.setChanger("ENTRY", new ChangeTable.Changer() { public Object change(Object value) { String sv = (String) value; sv = sv.substring("EC ".length(), sv.lengt... |
public boolean setPassword(String oldPassword, String newPassword) | public void setPassword(String newPassword) | public boolean setPassword(String oldPassword, String newPassword) { log.debug("Setting password"); Person me = this.getMe(); // check the old password, current really. if (!me.checkPassword(oldPassword)) return false; me.setPassword(newPassword); return true; } |
if (!me.checkPassword(oldPassword)) return false; | public boolean setPassword(String oldPassword, String newPassword) { log.debug("Setting password"); Person me = this.getMe(); // check the old password, current really. if (!me.checkPassword(oldPassword)) return false; me.setPassword(newPassword); return true; } | |
return true; | public boolean setPassword(String oldPassword, String newPassword) { log.debug("Setting password"); Person me = this.getMe(); // check the old password, current really. if (!me.checkPassword(oldPassword)) return false; me.setPassword(newPassword); return true; } | |
String[] emailAddresses, | List<String> emailAddresses, | public Self(Long id, String name, String[] emailAddresses, boolean siteAdmin, List<SubscribedList> subscriptions) { super(id, name, emailAddresses); this.siteAdmin = siteAdmin; this.subscriptions = subscriptions; } |
public boolean setPassword(String oldPassword, String newPassword); | public void setPassword(String newPassword); | public boolean setPassword(String oldPassword, String newPassword); |
sb.append(Fkt.fix(Kn[kn].getX(), 2) +" "+ Fkt.fix(Kn[kn].getZ(), 2)); | sb.append(Fkt.nf(Kn[kn].getX(), 2) +" "+ Fkt.nf(Kn[kn].getZ(), 2)); | public int print(Graphics graphics, PageFormat pageformat, int pageIndex) throws PrinterException { if (pageIndex >= 1) return Printable.NO_SUCH_PAGE; /*if (schongedruckt) { paint(g); return Printable.PAGE_EXISTS; }*/ this.pf = pageformat; g = (Graphics2D) gr... |
sb.append(Fkt.fix(Kn[kn].getX(), 2) +" "+ Fkt.fix(Kn[kn].getZ(), 2) +" "+tr("WIDERSPRUCH")); | sb.append(Fkt.nf(Kn[kn].getX(), 2) +" "+ Fkt.nf(Kn[kn].getZ(), 2) +" "+tr("WIDERSPRUCH")); | public int print(Graphics graphics, PageFormat pageformat, int pageIndex) throws PrinterException { if (pageIndex >= 1) return Printable.NO_SUCH_PAGE; /*if (schongedruckt) { paint(g); return Printable.PAGE_EXISTS; }*/ this.pf = pageformat; g = (Graphics2D) gr... |
if (Kn[kn].getLx() != 0) sb.append(" Lx= " + Fkt.fix(Kn[kn].getLx(),1) + "kN"); if (Kn[kn].getLz() != 0) sb.append(" Lz= " + Fkt.fix(Kn[kn].getLz(),1) + "kN"); | if (Kn[kn].getLx() != 0) sb.append(" Lx= " + Fkt.nf(Kn[kn].getLx(),1) + "kN"); if (Kn[kn].getLz() != 0) sb.append(" Lz= " + Fkt.nf(Kn[kn].getLz(),1) + "kN"); | public int print(Graphics graphics, PageFormat pageformat, int pageIndex) throws PrinterException { if (pageIndex >= 1) return Printable.NO_SUCH_PAGE; /*if (schongedruckt) { paint(g); return Printable.PAGE_EXISTS; }*/ this.pf = pageformat; g = (Graphics2D) gr... |
sb.append("Rx = " + Fkt.fix(Kn[kn].getRx(),1) + "kN Rz= " + Fkt.fix(Kn[kn].getRz(),1) +"kN"); | sb.append("Rx = " + Fkt.nf(Kn[kn].getRx(),1) + "kN Rz= " + Fkt.nf(Kn[kn].getRz(),1) +"kN"); | public int print(Graphics graphics, PageFormat pageformat, int pageIndex) throws PrinterException { if (pageIndex >= 1) return Printable.NO_SUCH_PAGE; /*if (schongedruckt) { paint(g); return Printable.PAGE_EXISTS; }*/ this.pf = pageformat; g = (Graphics2D) gr... |
sb.append("Rx = " + Fkt.fix(Kn[kn].getRx(),1) + "kN Rz= " + Fkt.fix(Kn[kn].getRz(),1) | sb.append("Rx = " + Fkt.nf(Kn[kn].getRx(),1) + "kN Rz= " + Fkt.nf(Kn[kn].getRz(),1) | public int print(Graphics graphics, PageFormat pageformat, int pageIndex) throws PrinterException { if (pageIndex >= 1) return Printable.NO_SUCH_PAGE; /*if (schongedruckt) { paint(g); return Printable.PAGE_EXISTS; }*/ this.pf = pageformat; g = (Graphics2D) gr... |
sb.append("(" + '\u03B1' + "=" + Fkt.fix(Math.toDegrees(Kn[kn].getRalpha()),1)+"°) "); | sb.append("(" + '\u03B1' + "=" + Fkt.nf(Math.toDegrees(Kn[kn].getRalpha()),1)+"°) "); | public int print(Graphics graphics, PageFormat pageformat, int pageIndex) throws PrinterException { if (pageIndex >= 1) return Printable.NO_SUCH_PAGE; /*if (schongedruckt) { paint(g); return Printable.PAGE_EXISTS; }*/ this.pf = pageformat; g = (Graphics2D) gr... |
sb.append("Rx= " + Fkt.fix(Kn[kn].getRx(),1) + "kN Rz= " + Fkt.fix(Kn[kn].getRz(),1) + "kN "+tr("GESETZT")); | sb.append("Rx= " + Fkt.nf(Kn[kn].getRx(),1) + "kN Rz= " + Fkt.nf(Kn[kn].getRz(),1) + "kN "+tr("GESETZT")); | public int print(Graphics graphics, PageFormat pageformat, int pageIndex) throws PrinterException { if (pageIndex >= 1) return Printable.NO_SUCH_PAGE; /*if (schongedruckt) { paint(g); return Printable.PAGE_EXISTS; }*/ this.pf = pageformat; g = (Graphics2D) gr... |
sb.append(Fkt.fix(SummeLx,1) + "kN "); | sb.append(Fkt.nf(SummeLx,1) + "kN "); | private String[] summenkontrolle() { // Summe Lasten, Summe Auflagerkräfte String[] summentxtLR = new String[2]; StringBuffer sb = new StringBuffer(); double SummeLx = 0; double SummeLz = 0; double SummeML = 0; double SummeAx = 0; double SummeAz = 0; double SummeMA = 0; for... |
sb.append(Fkt.fix(SummeLz,1) + "kN "); | sb.append(Fkt.nf(SummeLz,1) + "kN "); | private String[] summenkontrolle() { // Summe Lasten, Summe Auflagerkräfte String[] summentxtLR = new String[2]; StringBuffer sb = new StringBuffer(); double SummeLx = 0; double SummeLz = 0; double SummeML = 0; double SummeAx = 0; double SummeAz = 0; double SummeMA = 0; for... |
sb.append(Fkt.fix(SummeML,1) + "kNm"); | sb.append(Fkt.nf(SummeML,1) + "kNm"); | private String[] summenkontrolle() { // Summe Lasten, Summe Auflagerkräfte String[] summentxtLR = new String[2]; StringBuffer sb = new StringBuffer(); double SummeLx = 0; double SummeLz = 0; double SummeML = 0; double SummeAx = 0; double SummeAz = 0; double SummeMA = 0; for... |
sb.append(Fkt.fix(SummeAx,1) + "kN "); | sb.append(Fkt.nf(SummeAx,1) + "kN "); | private String[] summenkontrolle() { // Summe Lasten, Summe Auflagerkräfte String[] summentxtLR = new String[2]; StringBuffer sb = new StringBuffer(); double SummeLx = 0; double SummeLz = 0; double SummeML = 0; double SummeAx = 0; double SummeAz = 0; double SummeMA = 0; for... |
sb.append(Fkt.fix(SummeAz,1) + "kN "); | sb.append(Fkt.nf(SummeAz,1) + "kN "); | private String[] summenkontrolle() { // Summe Lasten, Summe Auflagerkräfte String[] summentxtLR = new String[2]; StringBuffer sb = new StringBuffer(); double SummeLx = 0; double SummeLz = 0; double SummeML = 0; double SummeAx = 0; double SummeAz = 0; double SummeMA = 0; for... |
sb.append(Fkt.fix(SummeMA,1) + "kNm"); | sb.append(Fkt.nf(SummeMA,1) + "kNm"); | private String[] summenkontrolle() { // Summe Lasten, Summe Auflagerkräfte String[] summentxtLR = new String[2]; StringBuffer sb = new StringBuffer(); double SummeLx = 0; double SummeLz = 0; double SummeML = 0; double SummeAx = 0; double SummeAz = 0; double SummeMA = 0; for... |
try | while (searchReader.hasNext()) | public static void main (String [] args) { String queryFileName = args[0]; String subjectFileName = args[1]; String fastaOutputFileName = args[2]; File queryFile = new File(queryFileName); File queryIndex = new File(queryFileName + ".index"); File subjectFile = new File(subjectFileName); File sub... |
while (searchReader.hasNext()) | SeqSimilaritySearchResult result = (SeqSimilaritySearchResult) searchReader.next(); System.out.println("----------------------------------------"); System.out.println("Start of result: " + result.toString()); System.out.println("----------------------------------------"); System.out.println("Result has query sequence... | public static void main (String [] args) { String queryFileName = args[0]; String subjectFileName = args[1]; String fastaOutputFileName = args[2]; File queryFile = new File(queryFileName); File queryIndex = new File(queryFileName + ".index"); File subjectFile = new File(subjectFileName); File sub... |
SeqSimilaritySearchResult result = (SeqSimilaritySearchResult) searchReader.next(); | SeqSimilaritySearchHit hit = (SeqSimilaritySearchHit) hi.next(); | public static void main (String [] args) { String queryFileName = args[0]; String subjectFileName = args[1]; String fastaOutputFileName = args[2]; File queryFile = new File(queryFileName); File queryIndex = new File(queryFileName + ".index"); File subjectFile = new File(subjectFileName); File sub... |
System.out.println("----------------------------------------"); System.out.println("Start of result: " + result.toString()); System.out.println("----------------------------------------"); | System.out.println("\n-> Hit: " + hit); | public static void main (String [] args) { String queryFileName = args[0]; String subjectFileName = args[1]; String fastaOutputFileName = args[2]; File queryFile = new File(queryFileName); File queryIndex = new File(queryFileName + ".index"); File subjectFile = new File(subjectFileName); File sub... |
System.out.println("Result has query sequence: " + result.getQuerySequence().toString()); | List subHits = hit.getSubHits(); | public static void main (String [] args) { String queryFileName = args[0]; String subjectFileName = args[1]; String fastaOutputFileName = args[2]; File queryFile = new File(queryFileName); File queryIndex = new File(queryFileName + ".index"); File subjectFile = new File(subjectFileName); File sub... |
List hits = result.getHits(); | for (Iterator shi = subHits.iterator(); shi.hasNext();) { SeqSimilaritySearchSubHit subHit = (SeqSimilaritySearchSubHit) shi.next(); System.out.println("--> SubHit: " + subHit); System.out.println(" Query start: " + subHit.getQueryStart()); System.out.println(" Query end: " + subHit.getQueryEnd()); System.o... | public static void main (String [] args) { String queryFileName = args[0]; String subjectFileName = args[1]; String fastaOutputFileName = args[2]; File queryFile = new File(queryFileName); File queryIndex = new File(queryFileName + ".index"); File subjectFile = new File(subjectFileName); File sub... |
for (Iterator hi = hits.iterator(); hi.hasNext();) { SeqSimilaritySearchHit hit = (SeqSimilaritySearchHit) hi.next(); | Alignment al = subHit.getAlignment(); List labels = al.getLabels(); | public static void main (String [] args) { String queryFileName = args[0]; String subjectFileName = args[1]; String fastaOutputFileName = args[2]; File queryFile = new File(queryFileName); File queryIndex = new File(queryFileName + ".index"); File subjectFile = new File(subjectFileName); File sub... |
System.out.println("\n-> Hit: " + hit); List subHits = hit.getSubHits(); for (Iterator shi = subHits.iterator(); shi.hasNext();) | try | public static void main (String [] args) { String queryFileName = args[0]; String subjectFileName = args[1]; String fastaOutputFileName = args[2]; File queryFile = new File(queryFileName); File queryIndex = new File(queryFileName + ".index"); File subjectFile = new File(subjectFileName); File sub... |
SeqSimilaritySearchSubHit subHit = (SeqSimilaritySearchSubHit) shi.next(); System.out.println("--> SubHit: " + subHit); System.out.println(" Query start: " + subHit.getQueryStart()); System.out.println(" Query end: " + subHit.getQueryEnd()); System.out.println(" Query strand: " + subHit.getQueryStrand()... | for (Iterator li = labels.iterator(); li.hasNext();) | public static void main (String [] args) { String queryFileName = args[0]; String subjectFileName = args[1]; String fastaOutputFileName = args[2]; File queryFile = new File(queryFileName); File queryIndex = new File(queryFileName + ".index"); File subjectFile = new File(subjectFileName); File sub... |
for (Iterator li = labels.iterator(); li.hasNext();) { String label = (String) li.next(); System.out.println(label + ": " + al.symbolListForLabel(label).seqString()); } } catch (ClassCastException cce) { cce.printStackTrace(); } catch (NoSuchElementException nse) { nse.printStackTrace(); | String label = (String) li.next(); System.out.println(label + ": " + al.symbolListForLabel(label).seqString()); | public static void main (String [] args) { String queryFileName = args[0]; String subjectFileName = args[1]; String fastaOutputFileName = args[2]; File queryFile = new File(queryFileName); File queryIndex = new File(queryFileName + ".index"); File subjectFile = new File(subjectFileName); File sub... |
System.out.println("----------------------------------------"); System.out.println("End of result: " + result.toString()); System.out.println("----------------------------------------"); | public static void main (String [] args) { String queryFileName = args[0]; String subjectFileName = args[1]; String fastaOutputFileName = args[2]; File queryFile = new File(queryFileName); File queryIndex = new File(queryFileName + ".index"); File subjectFile = new File(subjectFileName); File sub... | |
} catch (Exception e) { e.printStackTrace(); | System.out.println("----------------------------------------"); System.out.println("End of result: " + result.toString()); System.out.println("----------------------------------------"); | public static void main (String [] args) { String queryFileName = args[0]; String subjectFileName = args[1]; String fastaOutputFileName = args[2]; File queryFile = new File(queryFileName); File queryIndex = new File(queryFileName + ".index"); File subjectFile = new File(subjectFileName); File sub... |
catch (Exception e) | catch (IOException e) | public static void main (String [] args) { String queryFileName = args[0]; String subjectFileName = args[1]; String fastaOutputFileName = args[2]; File queryFile = new File(queryFileName); File queryIndex = new File(queryFileName + ".index"); File subjectFile = new File(subjectFileName); File sub... |
private IndexedSequenceDB( String name, File indexFile, SequenceFormat format, SequenceFactory sFact, SymbolParser symParser, IDMaker idMaker ) | private IndexedSequenceDB(String name, File indexFile, SequenceFormat format, SequenceBuilderFactory sbFact, SymbolParser symParser, IDMaker idMaker) | private IndexedSequenceDB( String name, File indexFile, SequenceFormat format, SequenceFactory sFact, SymbolParser symParser, IDMaker idMaker ) { this.name = name; this.indexFile = indexFile; this.format = format; this.sFact = sFact; this.symParser = symParser; this.idMaker = idMaker; this.file... |
this.sFact = sFact; | this.sbFact = sbFact; | private IndexedSequenceDB( String name, File indexFile, SequenceFormat format, SequenceFactory sFact, SymbolParser symParser, IDMaker idMaker ) { this.name = name; this.indexFile = indexFile; this.format = format; this.sFact = sFact; this.symParser = symParser; this.idMaker = idMaker; this.file... |
throw new BioError("[FIXME] broken after newio"); | private IndexedSequenceDB( String name, File indexFile, SequenceFormat format, SequenceFactory sFact, SymbolParser symParser, IDMaker idMaker ) { this.name = name; this.indexFile = indexFile; this.format = format; this.sFact = sFact; this.symParser = symParser; this.idMaker = idMaker; this.file... | |
public synchronized void addSequenceDB(String name, Set otherIdentifiers) { Contract.pre(name != null, "name not null"); | public synchronized void addSequenceDB(String name, Set otherIdentifiers) { Contract.pre(name != null, "name was null"); | public synchronized void addSequenceDB(String name, Set otherIdentifiers) { Contract.pre(name != null, "name not null"); // otherIdentifiers may only contain String objects - but this is checked later // create set of all identifiers for the to-be-created SequenceDB Set allIdentifiers = new HashSet(); ... |
Set currentIdentifiers = this.sequenceDBByIdentifier.keySet(); for (Iterator i = allIdentifiers.iterator(); i.hasNext(); ) { Object o = i.next(); Contract.pre(o instanceof String, "otherIdentifiers must be a set of String objects"); Contract.pre(!(currentIdentifiers.contains(o)), "name and otherIdentifiers must not alr... | Set currentIdentifiers = this.sequenceDBByIdentifier.keySet(); for (Iterator i = allIdentifiers.iterator(); i.hasNext();) { Object o = i.next(); Contract.pre(o instanceof String, "otherIdentifiers must be a Set of String objects"); Contract.pre(! (currentIdentifiers.contains(o)), "name and otherIdentifiers must not alr... | public synchronized void addSequenceDB(String name, Set otherIdentifiers) { Contract.pre(name != null, "name not null"); // otherIdentifiers may only contain String objects - but this is checked later // create set of all identifiers for the to-be-created SequenceDB Set allIdentifiers = new HashSet(); ... |
SequenceDB db = new HashSequenceDB(name); for (Iterator i = allIdentifiers.iterator(); i.hasNext(); ) { String identifier = (String) i.next(); this.sequenceDBByIdentifier.put(identifier, db); } } | public synchronized void addSequenceDB(String name, Set otherIdentifiers) { Contract.pre(name != null, "name not null"); // otherIdentifiers may only contain String objects - but this is checked later // create set of all identifiers for the to-be-created SequenceDB Set allIdentifiers = new HashSet(); ... | |
public void editSave() throws Exception | public void editSave() | public void editSave() throws Exception { this.updateData(this.getConfig()); this.list(); } |
public void list() throws Exception { | public void list() { | public void list() throws Exception { Properties p = new Properties(); Iterator iter = SystemGlobals.fetchConfigKeyIterator(); while (iter.hasNext()) { String key = (String) iter.next(); String value = SystemGlobals.getValue(key); p.put(key, value); } Properties locales = new Properties(); locales.load(new... |
locales.load(new FileInputStream(SystemGlobals.getValue(ConfigKeys.CONFIG_DIR) + "/languages/locales.properties")); List localesList = new ArrayList(); | try { locales.load(new FileInputStream(SystemGlobals.getValue(ConfigKeys.CONFIG_DIR) + "/languages/locales.properties")); } catch (IOException e) { String es = "Erorr list()"; log.error(es, e); throw new RuntimeException(es, e); } List localesList = new ArrayList(); | public void list() throws Exception { Properties p = new Properties(); Iterator iter = SystemGlobals.fetchConfigKeyIterator(); while (iter.hasNext()) { String key = (String) iter.next(); String value = SystemGlobals.getValue(key); p.put(key, value); } Properties locales = new Properties(); locales.load(new... |
this.prefix = prefix; this.ident = ident.intern(); this.args = args; | expr = new JMethodCallExpression(getTokenReference(), prefix, ident, args); | public CjMethodCallExpression( TokenReference where, JExpression prefix, String ident, JExpression[] args ) { super(where); this.prefix = prefix; this.ident = ident.intern(); this.args = args; } |
out.print("220-" + serverContext.getHostname() + " SubEthaMail SMTP Server " + serverContext.getServerVersion() + "; " + new Date() + "\r\n"); try { out.print("220 You are " + serverContext .resolveHost(session.getRemoteHostname()) + "\r\n"); } catch (IOException e) { session.quit(); out.print("221 " + serverContext.ge... | out.print("220 " + serverContext.getHostname() + " ESMTP SubethaMail" + "\r\n"); | public void run() { // TODO(imf): Refactor try { out.print("220-" + serverContext.getHostname() + " SubEthaMail SMTP Server " + serverContext.getServerVersion() + "; " + new Date() + "\r\n"); try { out.print("220 You are " + serverContext .resolveHost(session.getRemoteHostname()) ... |
catch (ServerRejectedException e) | catch (Exception e) | public void run() { // TODO(imf): Refactor try { out.print("220-" + serverContext.getHostname() + " SubEthaMail SMTP Server " + serverContext.getServerVersion() + "; " + new Date() + "\r\n"); try { out.print("220 You are " + serverContext .resolveHost(session.getRemoteHostname()) ... |
protected void createDirectory( Wagon wagon, String resourceToCreate, String[] resourcesPresent, String dirName ) | protected void createDirectory( Wagon wagon, String resourceToCreate, String dirName ) | protected void createDirectory( Wagon wagon, String resourceToCreate, String[] resourcesPresent, String dirName ) throws Exception { writeTestFile( resourceToCreate ); wagon.connect( testRepository, getAuthInfo() ); wagon.putDirectory( sourceFile, dirName ); for ( int i = 0; i ... |
for ( int i = 0; i < resourcesPresent.length; i++ ) { String resourceName = dirName + "/" + resourcesPresent[i]; File destFile = FileTestUtils.createUniqueFile( getName(), resourceName ); destFile.deleteOnExit(); wagon.get( resourceName, destFile ); } | protected void createDirectory( Wagon wagon, String resourceToCreate, String[] resourcesPresent, String dirName ) throws Exception { writeTestFile( resourceToCreate ); wagon.connect( testRepository, getAuthInfo() ); wagon.putDirectory( sourceFile, dirName ); for ( int i = 0; i ... | |
createDirectory( wagon, resourceToCreate, resources, dirName ); wagon.connect( testRepository, getAuthInfo() ); | createDirectory( wagon, resourceToCreate, dirName ); | public void testWagonPutDirectoryWhenDirectoryAlreadyExists() throws Exception { final String dirName = "directory-copy-existing"; final String resourceToCreate = "test-resource-1.txt"; final String[] resources = {"a/test-resource-2.txt", "a/b/test-resource-3.txt", "c/test-resource-4.... |
SubEthaMessage msg = new SubEthaMessage(this.mailSession, mail.getContent()); this.filterRunner.onSend(msg, mail); this.detacher.attach(msg); msg.writeTo(stream); | writeMessage(mail, stream); | public void writeMessage(Long mailId, OutputStream stream) throws NotFoundException, PermissionException { Mail mail = this.getMailFor(mailId, Permission.VIEW_ARCHIVES); try { SubEthaMessage msg = new SubEthaMessage(this.mailSession, mail.getContent()); this.filterRunner.onSend(msg, mail); this.detacher.a... |
if (log.isDebugEnabled()) log.debug("error getting exception getting mail#" + mailId + "\n" + e.toString()); | if (log.isDebugEnabled()) log.debug("exception getting mail#" + mailId + "\n" + e.toString()); | public void writeMessage(Long mailId, OutputStream stream) throws NotFoundException, PermissionException { Mail mail = this.getMailFor(mailId, Permission.VIEW_ARCHIVES); try { SubEthaMessage msg = new SubEthaMessage(this.mailSession, mail.getContent()); this.filterRunner.onSend(msg, mail); this.detacher.a... |
logger.warn("Error while sending notification emails: " + e); | public void insertSave() throws Exception { Topic t = new Topic(); t.setForumId(Integer.parseInt(JForum.getRequest().getParameter("forum_id"))); if (!this.shallProceed(t.getForumId()) || this.isForumReadonly(t.getForumId(), JForum.getRequest() .getParameter... | |
if (document.getChar(command.offset - 1) == '\\') { command.offset -= 1; } | public void customizeDocumentCommand(IDocument document, DocumentCommand command) { try { if (command.length == 1 && command.text.length() == 0) { ITypedRegion partition = document.getPartition(command.offset); if (partition.getType() == SchemePartitionScanner.SCHEME_... | |
defaults.load(input); | installation.load(input); | private void loadInstallationImpl() throws IOException { try { FileInputStream input = new FileInputStream(installationConfig); defaults.load(input); input.close(); expander.clearCache(); } catch (IOException e) { System.err.println("*WARNING* cannot load installation specific properties: "+ installationC... |
return Math.abs(mInstallOffset - offset) < 5; | return Math.abs(mInstallOffset - offset) == 0; | public boolean isContextInformationValid(int offset) { return Math.abs(mInstallOffset - offset) < 5; } |
try { String symbol = SchemeTextUtilities.findSymbolAroundPoint(viewer.getDocument(), offset); if (symbol != null) { List informations = new LinkedList(); SymbolEntry[] matchingEntries = getEditor().getSymbolDictionary().findSymbol(symbol); for (int index = 0; index < matchingEntries.length; index++) { informations.add... | String symbol = null; SexpNavigator navigator = new SexpNavigator(viewer.getDocument()); if (navigator.upSexpression(offset)) { navigator.downSexpression(navigator.getSexpStart()); if (navigator.forwardSexpression(navigator.getSexpEnd()) && navigator.getSexpType() == SexpNavigator.TYPE_SYMBOL) { symbol = navigator.get... | public IContextInformation[] computeContextInformation(ITextViewer viewer, int offset) { IContextInformation[] result = null; try { String symbol = SchemeTextUtilities.findSymbolAroundPoint(viewer.getDocument(), offset); if (symbol != null) { List informations = ne... |
catch (BadLocationException exception) { | if (symbol != null) { List informations = new LinkedList(); SymbolEntry[] matchingEntries = getEditor().getSymbolDictionary().findSymbol(symbol); for (int index = 0; index < matchingEntries.length; index++) { informations.add(makeContextInfo(matchingEntries[index])); } if (informations.size() != 0) { result = (IContex... | public IContextInformation[] computeContextInformation(ITextViewer viewer, int offset) { IContextInformation[] result = null; try { String symbol = SchemeTextUtilities.findSymbolAroundPoint(viewer.getDocument(), offset); if (symbol != null) { List informations = ne... |
return new char[] { ' ' }; | return new char[] { }; | public char[] getContextInformationAutoActivationCharacters() { return new char[] { ' ' }; } |
SymbolParser symParser = seqAlpha.getParser("symbol"); | SymbolParser symParser = seqAlpha.getParser("token"); | public static WeightMatrix readMatrix(Element root) throws IllegalSymbolException, IllegalAlphabetException, BioException { Element alphaE = (Element) root.getElementsByTagName("alphabet").item(0); Alphabet sa = AlphabetManager.instance().alphabetForName( alphaE.getAttribute("name")); if(! (sa instance... |
symbolParser = seqAlpha.getParser("symbol"); | symbolParser = seqAlpha.getParser("token"); | public static MarkovModel readModel(Element root) throws BioException, IllegalSymbolException, IllegalAlphabetException { if(root.getTagName().equals("WeightMatrix")) { return new WMAsMM(readMatrix(root)); } int heads = Integer.parseInt(root.getAttribute("heads")); Element alphaE = (Element) roo... |
public SimpleMarkovModel(int heads, Alphabet emissionAlpha) { this.emissionAlpha = emissionAlpha; this.stateAlpha = new SimpleAlphabet(); this.magicalState = MagicalState.getMagicalState(emissionAlpha, heads); try { addState(magicalState); } catch (IllegalSymbolException ise) { throw new BioError(ise, "Assertion failu... | public SimpleMarkovModel(int heads, Alphabet emissionAlpha, String name) { this(heads, emissionAlpha); ((SimpleAlphabet) stateAlpha).setName(name); | public SimpleMarkovModel(int heads, Alphabet emissionAlpha) { this.emissionAlpha = emissionAlpha; this.stateAlpha = new SimpleAlphabet(); this.magicalState = MagicalState.getMagicalState(emissionAlpha, heads); try { addState(magicalState); } catch (IllegalSymbolException ise) { throw new ... |
synchronized(changeSupport) { changeSupport.firePreChangeEvent(ce); | if (changeSupport == null) { f.addSymbol(to); t.addSymbol(from); } else { synchronized(changeSupport) { changeSupport.firePreChangeEvent(ce); | public void createTransition(State from, State to) throws IllegalSymbolException, ChangeVetoException { stateAlphabet().validate(from); stateAlphabet().validate(to); ChangeEvent ce = new ChangeEvent( this, MarkovModel.ARCHITECTURE, new Object[] { from, to }, null ); FiniteAlphabet f... |
changeSupport.firePostChangeEvent(ce); | changeSupport.firePostChangeEvent(ce); } | public void createTransition(State from, State to) throws IllegalSymbolException, ChangeVetoException { stateAlphabet().validate(from); stateAlphabet().validate(to); ChangeEvent ce = new ChangeEvent( this, MarkovModel.ARCHITECTURE, new Object[] { from, to }, null ); FiniteAlphabet f... |
String stylesheet = request.getParam("stylesheet"); | String stylesheet = request.getParam("stylesheet", null); | public String handleHTTPGet(HTTPRequest request) throws PluginHTTPException { StringBuffer out = new StringBuffer(); //int page = request.getIntParam("page", 1); String indexuri = request.getParam("index", DEFAULT_INDEX_URI); String search = request.getParam("search"); String stylesheet = request.getParam("styles... |
return "Invalid stylesheet"; | return "Invalid stylesheet: "+e.getMessage(); | public String handleHTTPGet(HTTPRequest request) throws PluginHTTPException { StringBuffer out = new StringBuffer(); //int page = request.getIntParam("page", 1); String indexuri = request.getParam("index", DEFAULT_INDEX_URI); String search = request.getParam("search"); String stylesheet = request.getParam("styles... |
public SmallCursor(State [] states, int length, ResidueList resList, Iterator resIterator) { | public SmallCursor(State [] states, ResidueList resList, Iterator resIterator) { | public SmallCursor(State [] states, int length, ResidueList resList, Iterator resIterator) { super(resIterator); this.length = length; this.currentC = new double[states.length]; this.lastC = new double[states.length]; } |
this.length = length; | this.resList = resList; | public SmallCursor(State [] states, int length, ResidueList resList, Iterator resIterator) { super(resIterator); this.length = length; this.currentC = new double[states.length]; this.lastC = new double[states.length]; } |
return length; | return resList.length(); | public int length() { return length; } |
if (errorFound) { return false; } | if (errorFound) return false; | public boolean run(String[] args) { errorFound = false; if (!parseArguments(args)) { return false; } KjcEnvironment environment = createEnvironment(options); setSourceVersion(environment.getSourceVersion()); initialize(environment); if (infiles.size() == 0... |
if (errorFound) { return false; } | if (errorFound) return false; System.out.println("checkAllInterfaces"); | public boolean run(String[] args) { errorFound = false; if (!parseArguments(args)) { return false; } KjcEnvironment environment = createEnvironment(options); setSourceVersion(environment.getSourceVersion()); initialize(environment); if (infiles.size() == 0... |
if (errorFound) { return false; } | if (errorFound) return false; System.out.println("checkAllInitializers"); | public boolean run(String[] args) { errorFound = false; if (!parseArguments(args)) { return false; } KjcEnvironment environment = createEnvironment(options); setSourceVersion(environment.getSourceVersion()); initialize(environment); if (infiles.size() == 0... |
if (errorFound) { return false; } | if (errorFound) return false; System.out.println("checkAllBodies"); | public boolean run(String[] args) { errorFound = false; if (!parseArguments(args)) { return false; } KjcEnvironment environment = createEnvironment(options); setSourceVersion(environment.getSourceVersion()); initialize(environment); if (infiles.size() == 0... |
((Main) compiler).reJoin( unit ); | ((Main) compiler).join( unit ); | protected void _override( FjOverrideable instance, CompilerBase compiler ) { FjOverrideClassDeclaration.setOverridingSuperClass( instance, compiler ); JCompilationUnit unit = (JCompilationUnit) compilationUnitMap.get( instance ); ((Main) compiler).reJoin( unit ); } |
GappedSymbolList gl = new GappedSymbolList(res); | SimpleGappedSymbolList gl = new SimpleGappedSymbolList(res); | public static void main(String [] args) { try { SymbolList res = Tools.createSymbolList(10); final int trials = 10; System.out.println("Starting with:\n" + res.seqString()); GappedSymbolList gl = new GappedSymbolList(res); System.out.println("Gapped version:\n" + gl.seqString()); gl.dumpBlock... |
System.err.println("Trying canBeEncoded with " + orderedCopiers[i]); | if (LOG.isDebugEnabled()) { LOG.debug("Checking if " + name + " can be encoded using " + orderedCopiers[i]); } | public boolean canBeEncoded(String name, Message message) throws HJBException { EncodedValueCopier[] orderedCopiers = getOrderedValueCopiers(); for (int i = 0; i < orderedCopiers.length; i++) { System.err.println("Trying canBeEncoded with " + orderedCopiers[i]); if (or... |
System.err.println("Trying getAsEncodedValue with " + orderedCopiers[i]); | if (LOG.isDebugEnabled()) { LOG.debug("Checking to get value for " + name + " using " + orderedCopiers[i]); } | public String getAsEncodedValue(String name, Message message) throws HJBException { EncodedValueCopier[] orderedCopiers = getOrderedValueCopiers(); for (int i = 0; i < orderedCopiers.length; i++) { System.err.println("Trying getAsEncodedValue with " + orderedCopiers[i]); ... |
private void addForum() throws Exception | private void addForum() | private void addForum() throws Exception { Forum f = ForumRepository.getForum(this.request.getIntParameter("relation_id")); String title = f.getName(); String description = f.getDescription(); Bookmark b = DataAccessDriver.getInstance().newBookmarkDAO().selectForUpdate( f.getId(), BookmarkType.FORUM, SessionF... |
private void addTopic() throws Exception | private void addTopic() | private void addTopic() throws Exception { Topic t = DataAccessDriver.getInstance().newTopicDAO().selectById( this.request.getIntParameter("relation_id")); String title = t.getTitle(); Bookmark b = DataAccessDriver.getInstance().newBookmarkDAO().selectForUpdate( t.getId(), BookmarkType.TOPIC, SessionFacade.... |
private void addUser() throws Exception | private void addUser() | private void addUser() throws Exception { User u = DataAccessDriver.getInstance().newUserDAO().selectById( this.request.getIntParameter("relation_id")); String title = u.getUsername(); Bookmark b = DataAccessDriver.getInstance().newBookmarkDAO().selectForUpdate( u.getId(), BookmarkType.USER, SessionFacade.g... |
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