rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k |
|---|---|---|
Template.readingFrame = FramedFeature.FRAME_2; | framed.readingFrame = FramedFeature.FRAME_2; | public Sequence annotate(Sequence seq) throws BioException, ChangeVetoException { Feature.Template plain = new Feature.Template(); StrandedFeature.Template stranded = new StrandedFeature.Template(); FramedFeature.Template framed = new FramedFeature.Template(); plain.annotation = Annota... |
public boolean isTerminal(){return children==null;} | abstract public boolean isTerminal(); | public boolean isTerminal(){return children==null;} |
root = new SuffixNode(); | root = new SimpleNode(); | public UkkonenSuffixTree(){ terminationChar = DEFAULT_TERM_CHAR; root = new SuffixNode(); e=0; sequences = ""; alpha=null; } |
SuffixNode leaf = new SuffixNode (parent, suffixStart); | SuffixNode leaf = new SimpleNode (parent, suffixStart); | private void doRule2(SuffixNode parent, int splittingPos, int suffixStart){ //int number = getAllNodes(root, null, false).size(); SuffixNode leaf = new SuffixNode (parent, suffixStart); parent.children.put(new Character(sequences.charAt(splittingPos)), leaf); //System.out.println("rule 2: "+sequences.char... |
SuffixNode middle= new SuffixNode(parent,suffixStart,splittingPos); | SuffixNode middle= new SimpleNode(parent,suffixStart,splittingPos); | private SuffixNode doRule3(SuffixNode child, int splittingPos, int suffixStart){ // return toBeSplit.splitEdge(endOfSubSeq, sequences.charAt(endOfSubSeq), // toBeSplit.getStart()+endOfSubSeq-rule3Position, // suffixStart); //int number = getAllNodes(root, null, false).size(); Suf... |
private void _writeWrappedLine(String key, int indent, String text, PrintStream os, String sep, String printSep) throws IOException { | private void _writeWrappedLine(String key, int indent, String text, PrintStream os, String sep) throws IOException { | private void _writeWrappedLine(String key, int indent, String text, PrintStream os, String sep, String printSep) throws IOException { text = text.trim(); StringBuffer b = new StringBuffer(); b.append(RichSequenceFormat.Tools.rightPad(key, indent)); String[] lines = RichSequenceFormat.Too... |
String[] lines = RichSequenceFormat.Tools.writeWordWrap(text, sep, printSep, this.getLineWidth()-indent); | String[] lines = RichSequenceFormat.Tools.writeWordWrap(text, sep, this.getLineWidth()-indent); | private void _writeWrappedLine(String key, int indent, String text, PrintStream os, String sep, String printSep) throws IOException { text = text.trim(); StringBuffer b = new StringBuffer(); b.append(RichSequenceFormat.Tools.rightPad(key, indent)); String[] lines = RichSequenceFormat.Too... |
templ.location = GenbankLocationParser.parseLocation(RichObjectFactory.getDefaultLocalNamespace(), accession, val); | String tidyLocStr = val.replaceAll("\\s+",""); templ.location = GenbankLocationParser.parseLocation(RichObjectFactory.getDefaultLocalNamespace(), accession, tidyLocStr); | public boolean readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener) throws IllegalSymbolException, IOException, ParseException { String line; boolean hasAnotherSequence = true; boolean hasInternalWhitespace = fals... |
String regex = "^(\\s{0,8}|\\s{21})(\\S+?)(\\s{1,7}|=)(.*)$"; | String regex = "^(\\s{0,8}(\\S+?)\\s{1,7}(.*)|\\s{21}(\\S+?)=(.*))$"; | private List readSection(BufferedReader br) throws ParseException { List section = new ArrayList(); String line; String currKey = null; StringBuffer currVal = new StringBuffer(); boolean done = false; int linecount = 0; String regex = "^(\\s{0,8}|\\s{21})(\\S+?)(\\s{... |
currKey = m.group(2); | currKey = m.group(2)==null?m.group(4):m.group(2); | private List readSection(BufferedReader br) throws ParseException { List section = new ArrayList(); String line; String currKey = null; StringBuffer currVal = new StringBuffer(); boolean done = false; int linecount = 0; String regex = "^(\\s{0,8}|\\s{21})(\\S+?)(\\s{... |
currVal.append(m.group(4).trim()); | currVal.append((m.group(2)==null?m.group(5):m.group(3)).trim()); | private List readSection(BufferedReader br) throws ParseException { List section = new ArrayList(); String line; String currKey = null; StringBuffer currVal = new StringBuffer(); boolean done = false; int linecount = 0; String regex = "^(\\s{0,8}|\\s{21})(\\S+?)(\\s{... |
currVal.append(" "); | currVal.append("\n"); | private List readSection(BufferedReader br) throws ParseException { List section = new ArrayList(); String line; String currKey = null; StringBuffer currVal = new StringBuffer(); boolean done = false; int linecount = 0; String regex = "^(\\s{0,8}|\\s{21})(\\S+?)(\\s{... |
this._writeWrappedLine(key,indent,text,os,"\\s+"," "); | this._writeWrappedLine(key,indent,text,os,"\\s"); | private void writeWrappedLine(String key, int indent, String text, PrintStream os) throws IOException { this._writeWrappedLine(key,indent,text,os,"\\s+"," "); } |
this._writeWrappedLine(key,indent,text,os,",",","); | this._writeWrappedLine(key,indent,text,os,","); | private void writeWrappedLocationLine(String key, int indent, String text, PrintStream os) throws IOException { this._writeWrappedLine(key,indent,text,os,",",","); } |
public static boolean equals(double d1, double d2) { return ((Double.isNaN(d1) && Double.isNaN(d2)) || (d1 == d2)); | public static boolean equals(boolean b1, boolean b2) { return b1 == b2; | public static boolean equals(double d1, double d2) { return ((Double.isNaN(d1) && Double.isNaN(d2)) || (d1 == d2)); } |
public static int hashCode(int currentHashCodeValue, double d) { return hashCode(currentHashCodeValue, d == 0.0 ? 0L : Double.doubleToLongBits(d)); | public static int hashCode(int currentHashCodeValue, boolean b) { return PRIME*currentHashCodeValue + (b ? 1 : 0); | public static int hashCode(int currentHashCodeValue, double d) { return hashCode(currentHashCodeValue, d == 0.0 ? 0L : Double.doubleToLongBits(d)); } |
this.annotation = new SimpleAnnotation(template.annotation); | this.annotation = (template.annotation == Annotation.EMPTY_ANNOTATION) ? new SimpleAnnotation() : template.annotation; | public SimpleFeature(Sequence sourceSeq, FeatureHolder parent, Feature.Template template) throws IllegalArgumentException { if(template.location == null) { throw new IllegalArgumentException( "Location can not be null. Did you mean Location.EMPTY_LOCATION?" ); } if(!(parent inst... |
if (null == root) { throw new IllegalArgumentException(strings().needsANonNull(HJBRoot.class)); } if (null == requestPath) { throw new IllegalArgumentException(strings().needsANonNull("request path")); } this.root = root; this.requestPath = requestPath; | this(root, requestPath, true); | public HJBTreeWalker(HJBRoot root, String requestPath) { if (null == root) { throw new IllegalArgumentException(strings().needsANonNull(HJBRoot.class)); } if (null == requestPath) { throw new IllegalArgumentException(strings().needsANonNull("request path")); } ... |
String message = strings().getString(HJBStrings.ALLOWED_PATH_NOT_FOUND, getRequestPath(), component); LOG.error(message); throw new HJBNotFoundException(message); | if (failsOnMissingComponent()) { String message = strings().getString(HJBStrings.ALLOWED_PATH_NOT_FOUND, getRequestPath(), component); LOG.error(message); throw new HJBNotFoundException(message); } else { if (LOG.isDebugEnabled()) { String message = strings().getString(HJBStrings.ALLOWED_PATH_NOT_FOUND, getRequestPath(... | protected void handleMissingComponent(String component) throws HJBException { String message = strings().getString(HJBStrings.ALLOWED_PATH_NOT_FOUND, getRequestPath(), component); LOG.error(message); throw n... |
showMapInDebug(result, "Decoded"); | public Map decode(Map parameterMap) { Map result = new HashMap(); if (null == parameterMap) return Collections.unmodifiableMap(result); List toBeDecoded = getCompulsoryDecodings(); for (Iterator i = parameterMap.keySet().iterator(); i.hasNext();) { Object next = i.next(); ... | |
return new StaticMemberPlaceHolder(SimpleFeatureRealizer.class.getField("DEFAULT")); | return new StaticMemberPlaceHolder(FeatureImpl.class.getField("DEFAULT")); | public Object writeReplace() { try { return new StaticMemberPlaceHolder(SimpleFeatureRealizer.class.getField("DEFAULT")); } catch (NoSuchFieldException ex) { throw new BioError(ex); } } |
public ImageIOReader(String name, String[] suffixes) { super(name, suffixes); } | public ImageIOReader(String name, String suffix) { super(name, suffix); } | public ImageIOReader(String name, String[] suffixes) { super(name, suffixes); } |
System.out.println(prop + " -> " + val); | private void writeFileIDs() throws BioException, IOException, ChangeVetoException { for(int i = 0; i < fileCount; i++) { RAF file = fileIDToRAF[i]; long length = file.length(); String prop = "fileid_" + i; String val = file.getFile().toString() + "\t" + length; metaData.setProperty(prop, ... | |
comandLineBox.addItem(""); | private void readHistory(){ BufferedReader f; String line; if(comandLineBox == null) comandLineBox = new JComboBox(); try{ f = new BufferedReader(new FileReader("/home/seyrich/cimsql.hst")); while((line = f.readLine()) != null) comandLineBox.addItem(line); f.close(); } catch (IOException e) { // TOD... | |
if (num < (numMappings - 1)) { System.arraycopy(mappings, num + 1, mappings, num, (numMappings - num - 1) * 2); } | if (num < numMappings) { System.arraycopy(mappings, num * 2, mappings, (num - 1) * 2, (numMappings - num) * 2); } mappings[numMappings * 2 - 1] = null; mappings[numMappings * 2 - 2] = null; | private void removeMapping(int num) { if (num < (numMappings - 1)) { System.arraycopy(mappings, num + 1, mappings, num, (numMappings - num - 1) * 2); } numMappings--; } |
store = getPreferenceStore(); | store = EditorsUI.getPreferenceStore(); | private void setupBackgroundColor() { IPreferenceStore store = SchemeScriptPlugin.getDefault().getPreferenceStore(); Color color = null; if (!store.getBoolean(ColorPreferences.SYSTEM_BACKGROUND)) { color = new Color(null, PreferenceConverter.getColor(store, ColorPreferences.BACKGROU... |
public ArrayList getGroups( String type) { ArrayList tmp = new ArrayList() ; for (int i=0;i<groups.size();i++){ Group g = (Group)groups.get(i); if (g.getType().equals(type)){ tmp.add(g); } } return tmp ; | public List getGroups( String type) { List tmp = new ArrayList() ; for (int i=0;i<groups.size();i++){ Group g = (Group)groups.get(i); if (g.getType().equals(type)){ tmp.add(g); } } return tmp ; | public ArrayList getGroups( String type) { ArrayList tmp = new ArrayList() ; for (int i=0;i<groups.size();i++){ Group g = (Group)groups.get(i); if (g.getType().equals(type)){ tmp.add(g); } } //Group[] g = (Group[])tmp.toArray(new Group[tmp.size()]); return tmp ; } |
ArrayList g = getGroups("amino"); return g.size() ; | List g = getGroups("amino"); return g.size() ; | public int getLengthAminos() { ArrayList g = getGroups("amino"); return g.size() ; } |
List aminos = getGroups("amino"); StringBuffer sequence = new StringBuffer() ; for ( int i=0 ; i< aminos.size(); i++){ AminoAcid a = (AminoAcid)aminos.get(i); sequence.append( a.getAminoType()); } String s = sequence.toString(); return s ; | List aminos = getGroups("amino"); StringBuffer sequence = new StringBuffer() ; for ( int i=0 ; i< aminos.size(); i++){ AminoAcid a = (AminoAcid)aminos.get(i); sequence.append( a.getAminoType()); | public String getSequence(){ List aminos = getGroups("amino"); StringBuffer sequence = new StringBuffer() ; for ( int i=0 ; i< aminos.size(); i++){ AminoAcid a = (AminoAcid)aminos.get(i); sequence.append( a.getAminoType()); } String s = sequen... |
String s = sequence.toString(); return s ; } | public String getSequence(){ List aminos = getGroups("amino"); StringBuffer sequence = new StringBuffer() ; for ( int i=0 ; i< aminos.size(); i++){ AminoAcid a = (AminoAcid)aminos.get(i); sequence.append( a.getAminoType()); } String s = sequen... | |
String str = "Chain >"+getName() + "< total length:" + getLength() + " residues"; int i = 0 ; do { Group gr = (Group)groups.get(i); str += gr.toString() + "\n" ; i++ ; } while ( i< groups.size()) ; return str ; } | String str = "Chain >"+getName() + "< total length:" + getLength() + " residues"; for ( int i = 0 ; i < groups.size();i++){ Group gr = (Group) groups.get(i); str += gr.toString() + "\n" ; } return str ; } | public String toString(){ String str = "Chain >"+getName() + "< total length:" + getLength() + " residues"; // loop over the residues int i = 0 ; do { Group gr = (Group)groups.get(i); str += gr.toString() + "\n" ; i++ ; } while ( i< groups.size()) ; return str ; } |
File currentDir = new File ( dir, path); System.out.println( "Processing dir: " + currentDir ); | File currentDir = new File ( dir, path ); | public static void putDirectory( File dir, Wagon wagon, boolean includeBasdir ) throws ResourceDoesNotExistException, TransferFailedException, AuthorizationException { LinkedList queue = new LinkedList(); if ( includeBasdir ) { queue.add( dir.getName() ); } ... |
System.out.println( "Processing file: " + file ); | public static void putDirectory( File dir, Wagon wagon, boolean includeBasdir ) throws ResourceDoesNotExistException, TransferFailedException, AuthorizationException { LinkedList queue = new LinkedList(); if ( includeBasdir ) { queue.add( dir.getName() ); } ... | |
Object ob = null; if (staxenv.featureTemplate.annotation.containsProperty("qualifier")) { ob = staxenv.featureTemplate.annotation.getProperty("qualifier"); } | String propType = prop.getPropType(); String value = prop.getValue(); | public void addProperty(AGAVEProperty prop) { try{ Object ob = null; if (staxenv.featureTemplate.annotation.containsProperty("qualifier")) { ob = staxenv.featureTemplate.annotation.getProperty("qualifier"); } if( ob != null ) ((List)ob).add( prop ) ; else { ... |
if( ob != null ) ((List)ob).add( prop ) ; | Object ob = null; if (staxenv.featureTemplate.annotation.containsProperty(propType)) { ob = staxenv.featureTemplate.annotation.getProperty(propType); } if( ob != null && ob instanceof Collection) ((Collection)ob).add( value ) ; | public void addProperty(AGAVEProperty prop) { try{ Object ob = null; if (staxenv.featureTemplate.annotation.containsProperty("qualifier")) { ob = staxenv.featureTemplate.annotation.getProperty("qualifier"); } if( ob != null ) ((List)ob).add( prop ) ; else { ... |
props.add( prop ) ; staxenv.featureTemplate.annotation.setProperty("qualifier", props) ; | props.add( value ) ; staxenv.featureTemplate.annotation.setProperty(propType, props) ; | public void addProperty(AGAVEProperty prop) { try{ Object ob = null; if (staxenv.featureTemplate.annotation.containsProperty("qualifier")) { ob = staxenv.featureTemplate.annotation.getProperty("qualifier"); } if( ob != null ) ((List)ob).add( prop ) ; else { ... |
CType exprType = expr.getType(context.getTypeFactory()); if( ((CReferenceType)exprType).getDeclContext().getInitializerContext() != null && context.getMethodContext() == null ) { ((ContextExpression)rFam.getHead()).adaptK(-3); | if(rFam != Path.NULL && context.getInitializerContext() != null) { ((ContextExpression)rFam.getHead()).adaptK(-3); | public void analyse(CBodyContext context) throws PositionedError { TypeFactory factory = context.getTypeFactory(); try { type = type.checkType(context); } catch (UnpositionedError cue) { try { type = new CDependentNameType(((C... |
fudgeAcross = 0.0 ; | fudgeAcross = - maxBounds.getCenterX(); | public void paint( Graphics2D g, SequenceRenderContext src ) { SymbolList seq = src.getSymbols(); int direction = src.getDirection(); g.setFont(src.getFont()); Rectangle2D oldClip = g.getClipBounds(); // AffineTransform oldTrans = g.getTransform(); g.setColor(C... |
String cachePolicy = l2Properties.getProperty("object.cachePolicy").toUpperCase(); | String cachePolicy = l2Properties.getProperty("objectmanager.cachePolicy").toUpperCase(); | public synchronized void start() throws IOException, DatabaseException, LocationNotCreatedException, FileNotCreatedException { try { startJMXServer(); } catch (Throwable t) { logger.error("Error starting jmx server", t); } NIOWorkarounds.solaris10Workaround(); this.configSetupManager.com... |
public WagonTestCase( String name ) | public WagonTestCase() | public WagonTestCase( String name ) { super( name ); } |
super( name ); | public WagonTestCase( String name ) { super( name ); } | |
prefix.accept(s); | if(prefix != null) prefix.accept(s); | public void recurse(IVisitor s) { prefix.accept(s); } |
String s = this.request.getParameter("start"); | private int preparePagination(int totalUsers) { String s = this.request.getParameter("start"); int start = ViewCommon.getStartPage(); int usersPerPage = SystemGlobals.getIntValue(ConfigKeys.USERS_PER_PAGE); this.context.put("totalPages", new Double(Math.ceil( (double)totalUsers / usersPerPage ))); this.context.... | |
public static List saveUser(int userId) throws Exception | public static List saveUser(int userId) | public static List saveUser(int userId) throws Exception { List errors = new ArrayList(); UserDAO um = DataAccessDriver.getInstance().newUserDAO(); User u = um.selectById(userId); ActionServletRequest request = JForumExecutionContext.getRequest(); boolean isAdmin = SessionFacade.getUserSession().isAdmin(); i... |
public static void reprocessRequest() throws Exception | public static void reprocessRequest() | public static void reprocessRequest() throws Exception { Map data = (Map)SessionFacade.getAttribute(ConfigKeys.REQUEST_DUMP); if (data == null) { throw new RequestEmptyException("A call to ViewCommon#reprocessRequest() was made, but no data found"); } String module = (String)data.get("module"); String action ... |
((Command)Class.forName(moduleClass).newInstance()).process(JForumExecutionContext.getRequest(), | Command command; try { command = ((Command) Class.forName(moduleClass).newInstance()); } catch (Exception e) { String es = "Erorr reprocessRequest()"; log.error(es, e); throw new RuntimeException(es, e); } command.process(JForumExecutionContext.getRequest(), | public static void reprocessRequest() throws Exception { Map data = (Map)SessionFacade.getAttribute(ConfigKeys.REQUEST_DUMP); if (data == null) { throw new RequestEmptyException("A call to ViewCommon#reprocessRequest() was made, but no data found"); } String module = (String)data.get("module"); String action ... |
TypeFactory factory = context.getTypeFactory(); JExpression expr; if(prefix != null) { prefix = prefix.analyse(context); } expr = new JMethodCallExpression(getTokenReference(), prefix, ident, args); | TypeFactory factory = context.getTypeFactory(); | public JExpression analyse(CExpressionContext context) throws PositionedError { TypeFactory factory = context.getTypeFactory(); JExpression expr; /* if(prefix != null) { prefix = prefix.analyse(context); CType prefixType = p... |
expr = expr.analyse(context); | expr = (JMethodCallExpression)expr.analyse(context); | public JExpression analyse(CExpressionContext context) throws PositionedError { TypeFactory factory = context.getTypeFactory(); JExpression expr; /* if(prefix != null) { prefix = prefix.analyse(context); CType prefixType = p... |
if(prefix instanceof JSuperExpression) { contextClassName = context.getClassContext().getCClass().convertToIfcQn(); | CClass prefixClass = expr.getPrefixType().getCClass(); if(prefixClass.isMixin()) { contextClassName = context.getClassContext().getCClass().convertToIfcQn(); | public JExpression analyse(CExpressionContext context) throws PositionedError { TypeFactory factory = context.getTypeFactory(); JExpression expr; /* if(prefix != null) { prefix = prefix.analyse(context); CType prefixType = p... |
else if(prefix != null) { contextClassName = prefix.getType(factory).getCClass().convertToIfcQn(); } else if(context.getClassContext().getCClass().isMixin()) { contextClassName = context.getClassContext().getCClass().convertToIfcQn(); | else { contextClassName = prefixClass.getQualifiedName(); | public JExpression analyse(CExpressionContext context) throws PositionedError { TypeFactory factory = context.getTypeFactory(); JExpression expr; /* if(prefix != null) { prefix = prefix.analyse(context); CType prefixType = p... |
expr = new JCastExpression( | JExpression res = new JCastExpression( | public JExpression analyse(CExpressionContext context) throws PositionedError { TypeFactory factory = context.getTypeFactory(); JExpression expr; /* if(prefix != null) { prefix = prefix.analyse(context); CType prefixType = p... |
return res.analyse(context); | public JExpression analyse(CExpressionContext context) throws PositionedError { TypeFactory factory = context.getTypeFactory(); JExpression expr; /* if(prefix != null) { prefix = prefix.analyse(context); CType prefixType = p... | |
if(prefix != null) prefix.accept(p); for (int i = 0; i < args.length; i++) { args[i].accept(p); } | expr.accept(p); | public void recurse(IVisitor p) { if(prefix != null) prefix.accept(p); for (int i = 0; i < args.length; i++) { args[i].accept(p); } } |
throw new AuthorizationException( "Access denided to: " + dest ); | throw new AuthorizationException( "Access denied to: " + dest ); | public void put( File source, String resourceName ) throws TransferFailedException, ResourceDoesNotExistException, AuthorizationException { Repository repository = getRepository(); String basedir = repository.getBasedir(); resourceName = StringUtils.replace( resourceName, "\\", "/" );... |
Header contentEncoding = method.getResponseHeader( "Content-Encoding" ); boolean isGZipped = contentEncoding == null ? false : "gzip".equalsIgnoreCase(contentEncoding.getValue()); if (isGZipped) { return new GZIPInputStream(method.getResponseBodyAsStream()); } | public InputStream getMethodData( String path ) throws IOException { setClient(); GetMethod method = new GetMethod( URIUtil.encodePathQuery( path ) ); generateTransactionHeader( method ); generateAdditionalHeaders( method ); client.executeMethod( method ); int sta... | |
String indexFilename = "indexDEscription"; | String indexFilename = "indexDescription"; | public void generateDescriptionPage() throws IOException { if (publishManager.getAlbumDescription().length() > 0) { SimpleDateFormat sdf = new SimpleDateFormat( resOutput.getString("DATE_FORMAT") ); String todaysDate = sdf.format( new Date() ); String indexFilename = "i... |
out.print( " - Page " + (index + 1) + " of " + numPages ); | out.print( " - " + resOutput.getString("PAGE") + " " + (index + 1) + " " + resOutput.getString("OF") + " " + numPages ); | public void generateThumbnailPage( int index, int perPage, int numPages ) throws IOException { ArrayList photos = publishManager.getPhotoSource().getSelectedPhotos(); int numPhotos = photos.size(); int beginIndex = index * perPage; int endIndex = (index + 1) * perPage -... |
UserModel um = DataAccessDriver.getInstance().newUserModel(); | public void validateLogin() throws Exception { UserModel um = DataAccessDriver.getInstance().newUserModel(); boolean validInfo = false; if (JForum.getRequest().getParameter("password").length() > 0) { User user = um.validateLogin(JForum.getRequest().getParameter("username"), JForum.getRequest().getParameter("p... | |
if (JForum.getRequest().getParameter("password").length() > 0) { User user = um.validateLogin(JForum.getRequest().getParameter("username"), JForum.getRequest().getParameter("password")); | String password = JForum.getRequest().getParameter("password"); if (password.length() > 0) { User user = validateLogin(JForum.getRequest().getParameter("username"), password); | public void validateLogin() throws Exception { UserModel um = DataAccessDriver.getInstance().newUserModel(); boolean validInfo = false; if (JForum.getRequest().getParameter("password").length() > 0) { User user = um.validateLogin(JForum.getRequest().getParameter("username"), JForum.getRequest().getParameter("p... |
return ImageDescriptor.createFromURL(SchemeScriptPlugin.getDefault().find(new Path(relativePath))); | return ImageDescriptor.createFromURL(SchemeScriptPlugin.findFile(new Path(relativePath))); | public static ImageDescriptor getImageDescriptor(String relativePath) { return ImageDescriptor.createFromURL(SchemeScriptPlugin.getDefault().find(new Path(relativePath))); } |
void addExpected(long expected); | void addExpected( Object expected ); | void addExpected(long expected); |
void addActual(long actual); | void addActual( Object actual ); | void addActual(long actual); |
int k = 0; CCjSourceAccessorMethod accessorMethod = (CCjSourceAccessorMethod)method; JAccessorMethod accessorMethodDecl = accessorMethod.getDecl(); CClass clazz = accessorMethod.getOwner(); CContext ctx = context.getBlockContext(); while (!(ctx instanceof CClassContext)){ ctx = ctx.getParentContext(); k++; } whi... | try { int k = 0; CCjSourceAccessorMethod accessorMethod = (CCjSourceAccessorMethod)method; JAccessorMethod accessorMethodDecl = accessorMethod.getDecl(); CClass clazz = accessorMethod.getOwner(); CContext ctx = context.getBlockContext(); while (!(ctx instanceof CClassContext)){ | public JExpression analyse(CExpressionContext context) throws PositionedError { TypeFactory factory = context.getTypeFactory(); if (analysed) { return this; } //Walter: this method is called now //rather than analise the args directly CType[] argTypes = getArgumentTypes(context, args, factory); CClass local ... |
} CMember accessedMember = accessorMethodDecl.getMember(); if(accessedMember instanceof CField) { CField accessedField = (CField)accessedMember; if(accessedField.getIdent().equals(JAV_OUTER_THIS)) { family = new ContextExpression(null, k+2, null); thisAsFamily = new ContextExpression(null, k+1, null); | while ( ((CClassContext)ctx).getCClass() != clazz) { ctx = ctx.getParentContext(); k++; check( context, !(ctx == null || ctx.getClassContext() == null ), CaesarMessages.ILLEGAL_PATH_ELEMENT, "accessor method not returning a outer reference" ); while(!(ctx instanceof CClassContext)) { ctx = ctx.getParentContext(); k... | public JExpression analyse(CExpressionContext context) throws PositionedError { TypeFactory factory = context.getTypeFactory(); if (analysed) { return this; } //Walter: this method is called now //rather than analise the args directly CType[] argTypes = getArgumentTypes(context, args, factory); CClass local ... |
else { family = new ContextExpression(null, k, null); thisAsFamily = new FieldAccess( accessedField.isFinal(), new ContextExpression(null, k, null), accessedField.getIdent(), (CReferenceType)accessedField.getType() ); } | } catch (UnpositionedError e) { throw e.addPosition(getTokenReference()); | public JExpression analyse(CExpressionContext context) throws PositionedError { TypeFactory factory = context.getTypeFactory(); if (analysed) { return this; } //Walter: this method is called now //rather than analise the args directly CType[] argTypes = getArgumentTypes(context, args, factory); CClass local ... |
if(isArrayType()){ return false; } | public boolean isCaesarReference() { return isReference() && (getCClass().isMixinInterface() || getCClass().isMixin()); } | |
context, | adviceContext, | public void checkBody1(CClassContext context) throws PositionedError { super.checkBody1(context); //create a method attribute for the advice // this has to be done after the pointcut declarations are resolved getCaesarAdvice().createAttribute( context, context.getC... |
CBinaryTypeContext typeContext = new CBinaryTypeContext( context.getClassReader(), context.getTypeFactory(), context, (modifiers & ACC_STATIC) == 0); | CBinaryTypeContext typeContext = null; CClassContext c = null; if (this.originalClass != null && this.originalClass.self != null) { c = originalClass.constructContext( originalClass.self.getCompilationUnitContext()); typeContext = new CBinaryTypeContext( c.getClassReader(), c.getTypeFactory(), c, (modifiers & ACC_STAT... | public CSourceMethod checkInterface(CClassContext context) throws PositionedError { try { if (returnType.isReference()) { returnType = returnType.checkType(context); } } catch (UnpositionedError e) { // FJTODO what to do with exception ... |
out.print("\r\n"); | if (!session.isDataMode()) out.print("\r\n"); | public void run() { // TODO(imf): Refactor try { out.print("220 " + serverContext.getHostname() + " ESMTP SubethaMail" + "\r\n");// Postfix doesn't output this, so why are we?// try// {// out.print("220 You are "// + serverContext// .resolveHost(session.getRemoteHostname())// + "\r\n")... |
if ((major > 4) || ((major == 4) && (minor >= 2))) { | if ((major > 4) || ((major == 4) && (minor >= 0))) { | public MySQLDBHelper(Connection connection) { DeleteStyle deleteStyle = DELETE_GENERIC; try { DatabaseMetaData metadata = connection.getMetaData(); int major = metadata.getDatabaseMajorVersion(); int minor = metadata.getDatabaseMinorVersion(); if ((major > 4... |
public void addRole(int id, Role role) throws Exception; | public void addRole(int id, Role role) ; | public void addRole(int id, Role role) throws Exception; |
public void addRoleValue(int id, Role role, RoleValueCollection rvc) throws Exception; | public void addRoleValue(int id, Role role, RoleValueCollection rvc) ; | public void addRoleValue(int id, Role role, RoleValueCollection rvc) throws Exception; |
public void deleteAllRoles(int id) throws Exception; | public void deleteAllRoles(int id) ; | public void deleteAllRoles(int id) throws Exception; |
public void deleteRole(int id, String roleName) throws Exception; | public void deleteRole(int id, String roleName) ; | public void deleteRole(int id, String roleName) throws Exception; |
public RoleCollection loadRoles(int id) throws Exception; | public RoleCollection loadRoles(int id) ; | public RoleCollection loadRoles(int id) throws Exception; |
public ImageIOWriter(String format, String[] suffixes, String kind) { super(format, suffixes); | public ImageIOWriter(String format, String suffix, String kind) { super(format, suffix); | public ImageIOWriter(String format, String[] suffixes, String kind) { super(format, suffixes); this.kind = kind; } |
collabDecl.setOriginalCompUnit(cu); | nestedDecl.setOriginalCompUnit(cu); | protected void moveInners(JCompilationUnit cu, CjVirtualClassDeclaration collabDecl) { JTypeDeclaration inners[] = cu.getInners(); for (int i1 = 0; i1 < inners.length; i1++) { if (inners[i1] instanceof CjVirtualClassDeclaration) { CjVirtualClassDeclaration nestedDecl = (CjVirtu... |
String recordKey = getRecordKey(record); | String recordKey = getRecordKey(record).trim();; | public Object [] findRecord(String identifier) throws IOException { long startRecord = 0; long endRecord = recordCount - 1; while (startRecord <= endRecord) { long midPoint = (startRecord + endRecord) / 2; raIndexFile.seek(headerLength + (midPoint * reco... |
decl.join(context.getClassContext()); decl.checkInterface(context.getClassContext()); | decl.join(context); decl.checkInterface(context); | public JExpression analyse(CExpressionContext context) throws PositionedError { TypeFactory factory = context.getTypeFactory(); CType[] argsType; CClass owner = context.getClassContext().getCClass(); CReferenceType superClass; try { type = (CReferenceType)type.ch... |
public SimpleSeqSimilaritySearchSubHit(SeqSimilaritySearchHit hit, double score, double pValue, double eValue, Alignment alignment) { Contract.pre(hit != null, "hit not null"); Contract.pre(!Double.isNaN(score), "score not NaN"); | public SimpleSeqSimilaritySearchSubHit(SeqSimilaritySearchHit hit, double score, double pValue, double eValue, Alignment alignment) { Contract.pre(hit != null, "hit was null"); Contract.pre(!Double.isNaN(score), "score was NaN"); | public SimpleSeqSimilaritySearchSubHit(SeqSimilaritySearchHit hit, double score, double pValue, double eValue, Alignment alignment) { Contract.pre(hit != null, "hit not null"); Contract.pre(!Double.isNaN(score), "score not NaN"); // pValue may be NaN // eValue may be NaN // alignment may be null ... |
public String toString() { return "SimpleSeqSimilaritySearchSubHit of " + getHit(); } | public String toString() { return "SimpleSeqSimilaritySearchSubHit with score " + getScore(); } | public String toString() { return "SimpleSeqSimilaritySearchSubHit of " + getHit(); } |
final int wrapWidth, final String joinType) | final int wrapWidth) | StringBuffer formatLocationBlock(final StringBuffer sb, final Location loc, final int strand, final String leader, final int wrapWidth, final String joinType) { // Get separator for system String nl = System.getProperty("line.separator"); // In... |
String nl = System.getProperty("line.separator"); int position = leader.length(); boolean join = false; boolean complement = false; List locs = new ArrayList(); for (Iterator li = loc.blockIterator(); li.hasNext();) { locs.add(li.next()); | return this.formatLocationBlock(sb, loc, strand, leader, wrapWidth, "join"); | StringBuffer formatLocationBlock(final StringBuffer sb, final Location loc, final int strand, final String leader, final int wrapWidth, final String joinType) { // Get separator for system String nl = System.getProperty("line.separator"); // In... |
Collections.sort(locs, Location.naturalOrder); if (loc instanceof CompoundLocation) { join = true; sb.append(joinType); sb.append("("); position += 5; } if (strand == -1) { Collections.reverse(locs); complement = true; } int locType = 0; int pre, post; int diff = 0; for (Iterator li = locs.iterator(); li.hasNext... | StringBuffer formatLocationBlock(final StringBuffer sb, final Location loc, final int strand, final String leader, final int wrapWidth, final String joinType) { // Get separator for system String nl = System.getProperty("line.separator"); // In... | |
private void generateSupportMembers(KjcEnvironment environment) { | protected void generateSupportMembers(KjcEnvironment environment) { | private void generateSupportMembers(KjcEnvironment environment) { try { CClassPreparation.instance().generateSupportMethods( this, environment ); } catch (UnpositionedError e) { reportTrouble(e); } } |
StructureModelManager.INSTANCE.getStructureModel().setRoot( new ProgramElementNode( "<root>", ProgramElementNode.Kind.FILE_JAVA, new LinkedList()) ); | protected void initialize(KjcEnvironment environment) { super.initialize(environment); messageHandler = new CaesarMessageHandler(this); // create static instance of bcel world CaesarBcelWorld.createInstance(options.classpath); CaesarBcelWorld world = CaesarBcelWorl... | |
checkVirtualClassMethodSignatures(tree); if(errorFound) return false; completeCClassInterfaces(tree); if(errorFound) return false; completeMixinCloneTypeInfo(environment, tree[0]); | public boolean run(String[] args) { errorFound = false; if (!parseArguments(args)) { return false; } KjcEnvironment environment = createEnvironment(options); setSourceVersion(environment.getSourceVersion()); initialize(environment); if (inf... | |
protected void writeConnectionFactories(PrintWriter aWriter, String prefixEndingInSlash) { | protected void writeConnectionFactories(PrintWriter aWriter) { | protected void writeConnectionFactories(PrintWriter aWriter, String prefixEndingInSlash) { Map connectionFactories = getTheProvider().getConnectionFactories(); for (Iterator i = connectionFactories.keySet().iterator(); i.hasNext();) { String factor... |
String factoryName = (String) i.next(); aWriter.print(prefixEndingInSlash + factoryName); aWriter.println(); | aWriter.println((String) i.next()); | protected void writeConnectionFactories(PrintWriter aWriter, String prefixEndingInSlash) { Map connectionFactories = getTheProvider().getConnectionFactories(); for (Iterator i = connectionFactories.keySet().iterator(); i.hasNext();) { String factor... |
aWriter.println(prefixEndingInSlash + factoryName); | protected void writeConnectionFactoryListings(PrintWriter aWriter, String prefixEndingInSlash) { Map connectionFactories = getTheProvider().getConnectionFactories(); for (Iterator i = connectionFactories.keySet().iterator(); i.hasNext();) { S... | |
String destinationName = (String) i.next(); aWriter.println(prefixEndingInSlash + destinationName); | aWriter.println(PathNaming.DESTINATION + '/' + ((String) i.next())); | protected void writeDestinations(PrintWriter aWriter, String prefixEndingInSlash) { Map destinations = getTheProvider().getDestinations(); for (Iterator i = destinations.keySet().iterator(); i.hasNext();) { String destinationName = (String) i.next(); ... |
writeConnectionFactories(pw, prefixEndingInSlash); | writeConnectionFactories(pw); | public void writeListing(Writer aWriter, String prefix, boolean recurse) { PrintWriter pw = new PrintWriter(aWriter); String prefixEndingInSlash = prefix.endsWith("/") ? prefix : prefix + "/"; writeDestinations(pw, prefixEndingInSlash); writeConnectionFactories(pw, prefixE... |
pnlCurrent.setBorder(new javax.swing.border.EmptyBorder(new java.awt.Insets(5, 5, 5, 5))); | pnlCurrent.setBorder(javax.swing.BorderFactory.createEmptyBorder(5, 5, 5, 5)); | private void initComponents() { java.awt.GridBagConstraints gridBagConstraints; pnlCurrent = new javax.swing.JPanel(); pnlButtons = new javax.swing.JPanel(); btnRestart = new javax.swing.JButton(); btnBack = new javax.swing.JButton(); btnNext = new javax.swing.JButton(); ... |
ResultSet rs = null;; | ResultSet rs = null; | public PrivateMessage selectById(PrivateMessage pm) throws Exception { PreparedStatement p = null; p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("PrivateMessageModel.selectById"), ResultSet.TYPE_SCROLL_INSENSITIVE, ResultSet.CONCUR_UPDATABLE); p.setInt(1, pm.getId()); ResultSet rs = nu... |
RangeLocation visible = GUITools.getVisibleRange(context, g2); | Location visible = GUITools.getVisibleRange(context, g2); | public void paint(Graphics2D g2, SequenceRenderContext context) { Rectangle2D prevClip = g2.getClipBounds(); AffineTransform prevTransform = g2.getTransform(); g2.setPaint(outline); Font font = context.getFont(); Rectangle2D maxCharBounds = font.getMaxCharBounds(g2.getFontRenderContext()); ... |
new CType[0], new CReferenceType[0],false, false, | new JFormalParameter[0], new CType[0], new CReferenceType[0],false, false, | public CClassBodyContext( CClassContext cctx, KjcEnvironment env ){ super(cctx, env, null); method = new CSourceMethod( getClassContext().getCClass(),ACC_PRIVATE,METHOD_NAME,new CVoidType(), new CType[0], new CReferenceType[0],false, false, ... |
"CaesarTestCase_3.java", | protected void setUp() throws Exception { System.out.println("AutomaticCaesartests Setup starts"); super.setUp(); if (doSetUp) { try { removeClassFiles(); allUnits = new Vector(); // these files should not raise errors String[] args = new String[] { "CaesarTestCase_0.java", "CaesarTestCa... | |
"CaesarTestCase_11.java", | protected void setUp() throws Exception { System.out.println("AutomaticCaesartests Setup starts"); super.setUp(); if (doSetUp) { try { removeClassFiles(); allUnits = new Vector(); // these files should not raise errors String[] args = new String[] { "CaesarTestCase_0.java", "CaesarTestCa... | |
setText("Format the selection"); | setText("Format"); | public FormatAction(SchemeEditor editor) { Assert.isNotNull(editor); setText("Format the selection"); setToolTipText("Formats the current selection"); mEditor = editor; } |
parameterMap.put(HJBConstants.LISTING_RECURSE, new Boolean(false)); | parameterMap.put(HJBConstants.LISTING_RECURSE, new String[] {"anythingGoes"}); | protected Map generateMockParameterMap() { Map parameterMap = new HashMap(); parameterMap.put(HJBConstants.LISTING_RECURSE, new Boolean(false)); return Collections.unmodifiableMap(parameterMap); } |
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