rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k |
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stream.println(sq); } | String count = Integer.toString((i * 60) + len); sq.replace((80 - count.length()), 80, count); | public void addSymbols(final Alphabet alpha, final Symbol [] syms, final int start, final int length) throws IllegalAlphabetException { try { int aCount = 0; int cCount = 0; int gCount = 0; int tCoun... |
stream.println(" } catch (IllegalSymbolException ex) { throw new IllegalAlphabetException(ex, "DNA not tokenizing"); } | stream.println(sq); } stream.println(" } catch (IllegalSymbolException ex) { throw new IllegalAlphabetException(ex, "DNA not tokenizing"); } | public void addSymbols(final Alphabet alpha, final Symbol [] syms, final int start, final int length) throws IllegalAlphabetException { try { int aCount = 0; int cCount = 0; int gCount = 0; int tCoun... |
return temp.toString(); | return temp.substring(0); | private String sequenceBufferCreator(Object key, Object value) { StringBuffer temp = new StringBuffer(); if (value == null) { temp.append((String) key); } else if (value instanceof ArrayList) { Iterator iter = ((ArrayList) value).iterator(); while (iter.h... |
public void setName(final String id) throws ParseException { | public void setName(String id) throws ParseException { | public void setName(final String id) throws ParseException { idb = new StringBuffer("ID " + id); } |
public void setPrintStream(final PrintStream stream) | public void setPrintStream(PrintStream stream) | public void setPrintStream(final PrintStream stream) { this.stream = stream; } |
public void setURI(final String uri) throws ParseException { } | public void setURI(String uri) throws ParseException { } | public void setURI(final String uri) throws ParseException { } |
public void startFeature(final Feature.Template templ) | public void startFeature(Feature.Template templ) | public void startFeature(final Feature.Template templ) throws ParseException { // There are 19 spaces in the leader String leader = "FT "; int strand = 0; if (templ instanceof StrandedFeature.Template) strand = ((StrandedFeature.Template) templ).... |
IllegalTransitionException | IllegalTransitionException, BioException | public PairwiseDP(MarkovModel mm) throws IllegalResidueException, IllegalTransitionException { super(mm); magicalState = mm.magicalState(); magicalResidue = MagicalState.MAGICAL_RESIDUE; } |
throws IllegalAlphabetException | throws IllegalResidueException | private static Residue getResWrapper(CrossProductAlphabet a, List l) throws IllegalAlphabetException {// System.out.println(a.getName() + " getting:");// for (Iterator i = l.iterator(); i.hasNext(); ) {// Residue blah = (Residue) i.next();// System.out.println(blah.getName());... |
UnigeneDB unigene = UnigeneTools.FLAT_FILE_FACTORY.createUnigene(url); | UnigeneDB unigene = UnigeneTools.createUnigene(url); | public static void main(String[] args) throws Exception { URL url = new URL(new URL("file:"), args[0]); UnigeneDB unigene = UnigeneTools.FLAT_FILE_FACTORY.createUnigene(url); } |
templ.type = rs.getString(2); templ.source = rs.getString(3); | templ.type = rs.getString(2).trim(); templ.source = rs.getString(3).trim(); | protected synchronized SimpleFeatureHolder getFeatures() { if (features == null) { try { Connection conn = seqDB.getPool().takeConnection(); Map fmap = new HashMap(); Map qmap = new HashMap(); Map lmap = new HashMap(); PreparedStatement get_features = conn.prepareStatement( "select s... |
lqm.qualifier_name = rs.getString(2); lqm.qualifier_value = rs.getString(3); | lqm.qualifier_name = rs.getString(2).trim(); lqm.qualifier_value = rs.getString(3).trim(); | protected synchronized SimpleFeatureHolder getFeatures() { if (features == null) { try { Connection conn = seqDB.getPool().takeConnection(); Map fmap = new HashMap(); Map qmap = new HashMap(); Map lmap = new HashMap(); PreparedStatement get_features = conn.prepareStatement( "select s... |
tokenSeed++, ""+tokenSeed, Annotation.EMPTY_ANNOTATION, l, this | tokenSeed++, Annotation.EMPTY_ANNOTATION, l, this | protected AtomicSymbol getSymbolImpl(List sList) throws IllegalSymbolException { AtomicSymbol s; synchronized(gopher) { gopher.setList(sList); s = (AtomicSymbol) knownSymbols.get(gopher); } if(s == null) { List l = new ArrayList(sList); s = (AtomicSymbol) AlphabetManager.createSymbol(... |
this.translation = temp.location.getMax() - temp.componentLocation.getMin(); | this.translation = temp.location.getMax() + temp.componentLocation.getMin(); | public SimpleComponentFeature(FeatureHolder parent, ComponentFeature.Template temp) throws BioException { if (locationContent(temp.location) != locationContent(temp.componentLocation)) { throw new BioException("Component and container locations must contain an equal number of symbols."); } i... |
public SimpleNCBITaxonName(String nameClass, String name) { if (nameClass==null) throw new IllegalArgumentException("Name class cannot be null"); if (name==null) throw new IllegalArgumentException("Name cannot be null"); this.nameClass = nameClass; this.name = name; } | protected SimpleNCBITaxonName() {} | public SimpleNCBITaxonName(String nameClass, String name) { if (nameClass==null) throw new IllegalArgumentException("Name class cannot be null"); if (name==null) throw new IllegalArgumentException("Name cannot be null"); this.nameClass = nameClass; this.name = name; } |
featureTemplate = locParser.parseLocation(featureBuf.toString(), featureTemplate); listener.startFeature(featureTemplate); featureStatus = WITHIN; } break; case WITHIN: if (line.charAt(0) == '/') { if (countChar(line, '"') % 2 == 0) processAttribute(line); else { featureBuf.setLength(0); featureBuf.append(line); featu... | featureTemplate = locParser.parseLocation(featureBuf.toString(), featureTemplate); listener.startFeature(featureTemplate); featureStatus = WITHIN; } break; case WITHIN: if (line.charAt(0) == '/') { if (countChar(line, '"') % 2 == 0) processAttribute(line); else { featureBuf.setLength(0); featureBuf.append(line); feat... | public void featureData(String line) throws BioException { switch (featureStatus) { case LOCATION: featureBuf.append(line); if (countChar(featureBuf, '(') == countChar(featureBuf, ')')) { // Save the original location in the feature's // annotation bundle try { Map dat = new HashMap(); dat... |
public void testSubList() | public void testSubList() throws Exception | public void testSubList() { assertTrue(symsEq(circ.subList(-2,2), circ.subList(8,12))); } |
SymbolList s = DNATools.createDNA("agaatc"); assertTrue(s.equals(circ.subList(-2,3))); | public void testSubList() { assertTrue(symsEq(circ.subList(-2,2), circ.subList(8,12))); } | |
public CircularView(Sequence seq){ super(seq); | public CircularView(Sequence seq, FeatureRealizer fr){ super(seq, fr); | public CircularView(Sequence seq){ super(seq); } |
SymbolList toEnd = super.subList(start,super.length()); SymbolList fromStart = super.subList(1,end); SimpleSymbolList sl = new SimpleSymbolList(toEnd); Edit edit = new Edit(sl.length() +1, 0, fromStart); | SimpleSymbolList fromStart = new SimpleSymbolList(super.subList(1,end)); SimpleSymbolList toEnd = new SimpleSymbolList(super.subList(start,length())); Edit edit = new Edit(toEnd.length() +1, 0, fromStart); | public SymbolList subList(int start, int end){ start = realValue(start); end = realValue(end); if(start <= end){ return super.subList(start, end); } else{ SymbolList toEnd = super.subList(start,super.length()); SymbolList fromStart = super.subList(1,end); SimpleSymbolList sl = new S... |
sl.edit(edit); | toEnd.edit(edit); | public SymbolList subList(int start, int end){ start = realValue(start); end = realValue(end); if(start <= end){ return super.subList(start, end); } else{ SymbolList toEnd = super.subList(start,super.length()); SymbolList fromStart = super.subList(1,end); SimpleSymbolList sl = new S... |
synchronized (target) { target.createFeature(t); } | target.createFeature(t); | public void run() { SymbolListCharSequence charSeq = new SymbolListCharSequence(target); try { Pattern [] patterns = RestrictionEnzymeManager.getPatterns(enzyme); int siteLen = enzyme.getRecognitionSite().length(); int seqLen = target.length(); in... |
public SequenceDBSearchSubHit(double score, double eValue, double pValue, Alignment alignment) | public SequenceDBSearchSubHit(final double score, final double eValue, final double pValue, final Alignment alignment) | public SequenceDBSearchSubHit(double score, double eValue, double pValue, Alignment alignment) { this.score = score; this.pValue = eValue; this.eValue = pValue; this.alignment = alignment; // Lock alignment by vetoing all changes this.alignment.addChangeListener(ChangeListener.A... |
public boolean equals(Object other) | public boolean equals(final Object other) | public boolean equals(Object other) { if (other == this) return true; if (other == null) return false; // Eliminate other if its class is not the same if (! other.getClass().equals(this.getClass())) return false; // Downcast and compare fields SequenceDBSearchSubHit that = (SequenceDBSearchSubHit) other; if ... |
alphaResolver = new AlphabetResolver(); | public SimilarityPairBuilder() { resultData = new HashMap(); hitData = new HashMap(); subHitData = new HashMap(); queryViewCache = new HashMap(); subjectViewCache = new HashMap(); alphaResolver = new AlphabetResolver(); tokenBuffer =... | |
String subjectID = (String) hitData.get("subjectId"); | private void makeSimilarity() throws BioException { subHitData.putAll(resultData); subHitData.putAll(hitData); // Try to get a valid TokenParser if (tokenParser == null) { String identifier; // Try explicit sequence type first if (subHitData.con... | |
Sequence subjectView = makeSubjectViewSequence(subjectID); | private void makeSimilarity() throws BioException { subHitData.putAll(resultData); subHitData.putAll(hitData); // Try to get a valid TokenParser if (tokenParser == null) { String identifier; // Try explicit sequence type first if (subHitData.con... | |
if (identifier.endsWith("blastn")) return DNATools.getDNA(); else if (identifier.endsWith("blastp") || identifier.endsWith("blastx")) return ProteinTools.getTAlphabet(); else if (identifier.equalsIgnoreCase("dna")) return DNATools.getDNA(); else if (identifier.equalsIgnoreCase("protein")) return ProteinTools.getTAl... | int type = 0; identifier = identifier.toUpperCase(); if (identifier.indexOf("TBLASTN") != -1) type = PROTEIN; else if (identifier.indexOf("TBLASTX") != -1) type = PROTEIN; else if (identifier.indexOf("BLASTN") != -1) type = DNA; else if (identifier.indexOf("BLASTP") != -1) type = PROTEIN; else if (identifier.indexOf(... | FiniteAlphabet resolveAlphabet(String identifier) throws BioException { // For (T)BLASTN/P/X if (identifier.endsWith("blastn")) return DNATools.getDNA(); else if (identifier.endsWith("blastp") || identifier.endsWith("blastx")) // Use T(ermination)... |
switch (type) { case DNA: return DNATools.getDNA(); case PROTEIN: return ProteinTools.getTAlphabet(); default: throw new BioError("Internal error in AlphabetResolver: failed to resolve to either DNA or protein alphabets"); } | FiniteAlphabet resolveAlphabet(String identifier) throws BioException { // For (T)BLASTN/P/X if (identifier.endsWith("blastn")) return DNATools.getDNA(); else if (identifier.endsWith("blastp") || identifier.endsWith("blastx")) // Use T(ermination)... | |
FeatureFilter dbFilter = FilterUtils.or(tsSchema, FilterUtils.or(exSchema, reSchema)); | FeatureFilter dbFilter = FilterUtils.or( new FeatureFilter[] { tsSchema, exSchema, reSchema } ); | public void testUseCases() { // schemas for our database features FeatureFilter transcript = FilterUtils.byType("transcript"); FeatureFilter exon = FilterUtils.byType("exon"); FeatureFilter repeat = FilterUtils.byType("repeat"); AnnotationType.Impl tsType = new AnnotationType.Impl(); ... |
System.err.println(depth + ":" + "Optimizing " + filter); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "is AND"); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "as list: " + filters); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
filters.set(i, (FeatureFilter) filters.get(i)); | filters.set(i, optimize((FeatureFilter) filters.get(i))); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... |
System.err.println(depth + ":" + "i: " + i); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "j: " + j); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "Comparing " + a + ", " + b + " of " + filters); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "Disjoint. Returning none()"); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "a < b. Removing b"); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "a > b. Removing a"); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "Attempting to calculate intersection"); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "got intersection: " + intersect); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "no luck - moving on"); } } } } System.err.println(depth + ":" + "Reduced to: " + filters); | } } } } | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... |
System.err.println(depth + ":" + "empty filter set. Returning none()"); return none(); | if(ors.isEmpty()) { return none(); } else { FeatureFilter andedOrs = FilterUtils.and((FeatureFilter[]) filters.toArray(new FeatureFilter[] {})); return andedOrs; } | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... |
System.err.println(depth + ":" + "No ors, just returning anded values: " + ands); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "Mixing in ors: " + ors); System.err.println(depth + ":" + "to: " + ands); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "Returning optimized or: " + res); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "is OR"); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "filters: " + filters); System.err.println(depth + ":" + "ands: " + ands); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "Found an all. Returning all()"); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "a < b. Removing a"); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "a > b. Removing b"); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "Trying to calculate union"); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "Got union: " + union); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
return optimize(and((FeatureFilter[]) ands.toArray(new FeatureFilter[] {}))); | FeatureFilter oredAnds = or((FeatureFilter[]) ands.toArray(new FeatureFilter[] {})); return oredAnds; | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... |
System.err.println(depth + ":" + "no ands, returning ors: " + ors); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "Mixing in ands: " + ands); System.err.println(depth + ":" + "to: " + ors); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
System.err.println(depth + ":" + "returning anded values: " + val); | public final static FeatureFilter optimize(FeatureFilter filter) { System.err.println(depth + ":" + "Optimizing " + filter); depth++; try { if(filter instanceof FeatureFilter.And) { System.err.println(depth + ":" + "is AND"); List filters = new ArrayList(); expandAnd(filter, filters);... | |
Position endPos = null; | private static Position parsePosition(String position) throws ParseException { // First attempt to find the group enclosing everything we've been passed Matcher sm = sp.matcher(position); if (!sm.matches()) throw new ParseException("Could not understand position: "+position); String star... | |
String desc = m.group(3); | public boolean readSequence( BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol ) throws IllegalSymbolException, IOException, ParseException { String line = reader.readLine(); if (line == null) { ... | |
System.err.println("Got hierarchy entry: " + parent + " : " + child); | protected synchronized SimpleFeatureHolder getFeatures() { if (features == null) { try { Connection conn = seqDB.getPool().takeConnection(); Map fmap = new HashMap(); Map lmap = new HashMap(); PreparedStatement get_features = conn.prepareStatement( "select seqfeature.seqfeature_id, " ... | |
System.err.println("ReRealizeFeature " + fid); | private Feature reRealizeFeature(Integer fid, Map fmap, Map featureHierarchy, FeatureHolder parent) throws BioException, ChangeVetoException { System.err.println("ReRealizeFeature " + fid); Feature.Template templ = (Feature.Template) fmap.get(fid); Feature f = realizeFeature(parent, templ); if (f instance... | |
System.err.println("Doing magical bits"); | private Feature reRealizeFeature(Integer fid, Map fmap, Map featureHierarchy, FeatureHolder parent) throws BioException, ChangeVetoException { System.err.println("ReRealizeFeature " + fid); Feature.Template templ = (Feature.Template) fmap.get(fid); Feature f = realizeFeature(parent, templ); if (f instance... | |
Graphics2D g2 = lCtxt.getGraphics(); | public void paintLogo(LogoContext lCtxt) { Graphics2D g2 = lCtxt.getGraphics(); Distribution dis = lCtxt.getDistribution(); SymbolStyle style = lCtxt.getStyle(); BlockPainter blockPainter = lCtxt.getBlockPainter(); Rectangle bounds = lCtxt.getBounds(); double width = bounds.getWidth(); double ste... | |
SymbolStyle style = lCtxt.getStyle(); | public void paintLogo(LogoContext lCtxt) { Graphics2D g2 = lCtxt.getGraphics(); Distribution dis = lCtxt.getDistribution(); SymbolStyle style = lCtxt.getStyle(); BlockPainter blockPainter = lCtxt.getBlockPainter(); Rectangle bounds = lCtxt.getBounds(); double width = bounds.getWidth(); double ste... | |
this.endNode = endNode; | public FilterByQuery( Query query, Node startNode, Filter.CompareInteger.Comparison comparison, int value ) { this.query = query; this.startNode = startNode; this.comparison = comparison; this.value = value; } | |
endNode, | public boolean accept(Object object) throws OperationException { Queryable res = QueryTools.select( query, startNode, QueryTools.createQueryable(Collections.singleton(object), Object.class) ); return comparison.compare(res.size(), value); } | |
return Object.class; | return startNode.getInputClass(); | public Class getInputClass() { return Object.class; } |
return Object.class; | return startNode.getInputClass(); | public Class getOutputClass() { return Object.class; } |
public static Queryable select(Query query, Node currentNode, Queryable items) throws OperationException { | public static Queryable select( Query query, Node startNode, Node endNode, Queryable items ) throws OperationException { final boolean debug = false; if(debug) System.out.println("Executing at " + startNode + " with " + items); if(items.size() == 0) { if(debug) System.out.println("No items to process. Returning empty... | public static Queryable select(Query query, Node currentNode, Queryable items) throws OperationException { Queryable selected; if(currentNode instanceof ResultNode) { selected = items; } else { selected = new Queryable.Empty(items.getQueryClass()); } Iterator ai = query.getArcsFrom(curre... |
if(currentNode instanceof ResultNode) { | if(startNode == endNode) { if(debug) System.out.println("reached end node - selecting current items"); | public static Queryable select(Query query, Node currentNode, Queryable items) throws OperationException { Queryable selected; if(currentNode instanceof ResultNode) { selected = items; } else { selected = new Queryable.Empty(items.getQueryClass()); } Iterator ai = query.getArcsFrom(curre... |
Iterator ai = query.getArcsFrom(currentNode).iterator(); | if(debug) System.out.println("Following " + query.getArcsFrom(startNode).size() + " paths."); Iterator ai = query.getArcsFrom(startNode).iterator(); | public static Queryable select(Query query, Node currentNode, Queryable items) throws OperationException { Queryable selected; if(currentNode instanceof ResultNode) { selected = items; } else { selected = new Queryable.Empty(items.getQueryClass()); } Iterator ai = query.getArcsFrom(curre... |
selected = QueryTools.union(selected, select(query, arc.to, res)); | if(res.size() != 0) { selected = QueryTools.union(selected, select( query, arc.to, endNode, res )); } | public static Queryable select(Query query, Node currentNode, Queryable items) throws OperationException { Queryable selected; if(currentNode instanceof ResultNode) { selected = items; } else { selected = new Queryable.Empty(items.getQueryClass()); } Iterator ai = query.getArcsFrom(curre... |
if(debug) System.out.println("Selected " + startNode + " " + selected); | public static Queryable select(Query query, Node currentNode, Queryable items) throws OperationException { Queryable selected; if(currentNode instanceof ResultNode) { selected = items; } else { selected = new Queryable.Empty(items.getQueryClass()); } Iterator ai = query.getArcsFrom(curre... | |
throw new RegistryException("BioSQL databases require a `location' option"); | throw new RegistryException("BioSQL provider requires" + " a 'location' parameter"); | public SequenceDBLite getSequenceDB(Map config) throws RegistryException, BioException { String location = (String) config.get("location"); if (location == null) { throw new RegistryException("BioSQL databases require a `location' option"); } String userName = (String) config.get("userName"); if (user... |
String userName = (String) config.get("userName"); if (userName == null) { throw new RegistryException("BioSQL databases require a `userName' option"); | String dbName = (String) config.get("dbname"); if (dbName == null) { throw new RegistryException("BioSQL provider requires" + " a 'dbname' parameter"); | public SequenceDBLite getSequenceDB(Map config) throws RegistryException, BioException { String location = (String) config.get("location"); if (location == null) { throw new RegistryException("BioSQL databases require a `location' option"); } String userName = (String) config.get("userName"); if (user... |
String password = (String) config.get("password"); if (password == null) { password = ""; | String biodatabase = (String) config.get("biodbname"); if (biodatabase == null) { throw new RegistryException("BioSQL provider requires" + " a 'biodbname' parameter"); | public SequenceDBLite getSequenceDB(Map config) throws RegistryException, BioException { String location = (String) config.get("location"); if (location == null) { throw new RegistryException("BioSQL databases require a `location' option"); } String userName = (String) config.get("userName"); if (user... |
String biodatabase = (String) config.get("biodatabase"); if (biodatabase == null) { throw new RegistryException("BioSQL database require a `biodatabase' option"); | String userName = (String) config.get("user"); if (userName == null) { throw new RegistryException("BioSQL provider requires" + " a 'user' parameter"); } String password = (String) config.get("passwd"); if (password == null) { throw new RegistryException("BioSQL provider requires" + " a 'passwd' parameter"); } String... | public SequenceDBLite getSequenceDB(Map config) throws RegistryException, BioException { String location = (String) config.get("location"); if (location == null) { throw new RegistryException("BioSQL databases require a `location' option"); } String userName = (String) config.get("userName"); if (user... |
super(symbol, name, annotation); | super(name, symbol, annotation); | public SimpleDotState(char symbol, String name, Annotation annotation) { super(symbol, name, annotation); } |
(float) (getDepth(src) + 2.0) | (float) (getDepth(src) - 2.0) | public void renderFeature( Graphics2D g, Feature feat, SequenceRenderContext src ) { Location loc = feat.getLocation(); String label = labelMaker.makeLabel(feat); g.setPaint(Color.black); int min = Math.max(loc.getMin(), src.getRange().getMin()); int max = Math.min(loc.getMax(), src.getRange(... |
f1 instanceof ByHierachy && f2 instanceof ByHierachy | f1 instanceof ByHierarchy && f2 instanceof ByHierarchy | private static FeatureFilter intersection(FeatureFilter f1, FeatureFilter f2) { if( f1 instanceof FeatureFilter.ContainedByLocation && f2 instanceof FeatureFilter.ContainedByLocation ) { Location loc = LocationTools.intersection( ((FeatureFilter.ContainedByLocation) f1).getLocation(), ... |
ByHierachy f1h = (ByHierachy) f1; ByHierachy f2h = (ByHierachy) f2; | ByHierarchy f1h = (ByHierarchy) f1; ByHierarchy f2h = (ByHierarchy) f2; | private static FeatureFilter intersection(FeatureFilter f1, FeatureFilter f2) { if( f1 instanceof FeatureFilter.ContainedByLocation && f2 instanceof FeatureFilter.ContainedByLocation ) { Location loc = LocationTools.intersection( ((FeatureFilter.ContainedByLocation) f1).getLocation(), ... |
f1 instanceof ByHierachy && f2 instanceof ByHierachy | f1 instanceof ByHierarchy && f2 instanceof ByHierarchy | private static FeatureFilter union(FeatureFilter f1, FeatureFilter f2) { if( f1 instanceof FeatureFilter.ContainedByLocation && f2 instanceof FeatureFilter.ContainedByLocation ) { return containedByLocation(LocationTools.union( ((FeatureFilter.ContainedByLocation) f1).getLocation(), ... |
ByHierachy f1h = (ByHierachy) f1; ByHierachy f2h = (ByHierachy) f2; | ByHierarchy f1h = (ByHierarchy) f1; ByHierarchy f2h = (ByHierarchy) f2; | private static FeatureFilter union(FeatureFilter f1, FeatureFilter f2) { if( f1 instanceof FeatureFilter.ContainedByLocation && f2 instanceof FeatureFilter.ContainedByLocation ) { return containedByLocation(LocationTools.union( ((FeatureFilter.ContainedByLocation) f1).getLocation(), ... |
FeatureHolder overlappingFeatures = seq.filter(new FeatureFilter.OverlapsLocation(new RangeLocation(start, end)), false); features = new ProjectedFeatureHolder(overlappingFeatures, | FeatureFilter overlapping = new FeatureFilter.OverlapsLocation(new RangeLocation(start, end)); features = new ProjectedFeatureHolder(seq, overlapping, | public SubSequence(Sequence seq, int start, int end) { symbols = seq.subList(start, end); FeatureHolder overlappingFeatures = seq.filter(new FeatureFilter.OverlapsLocation(new RangeLocation(start, end)), false); features = new ProjectedFeatureHolder(overlappingFeatures, this, start - 1, ... |
start - 1, | 1 - start, | public SubSequence(Sequence seq, int start, int end) { symbols = seq.subList(start, end); FeatureHolder overlappingFeatures = seq.filter(new FeatureFilter.OverlapsLocation(new RangeLocation(start, end)), false); features = new ProjectedFeatureHolder(overlappingFeatures, this, start - 1, ... |
public void addChangeListener(ChangeListener cl) {} | public void addChangeListener(ChangeListener cl) { if (changeSupport == null) allocChangeSupport(); changeSupport.addChangeListener(cl); } | public void addChangeListener(ChangeListener cl) {} |
public void removeChangeListener(ChangeListener cl) {} | public void removeChangeListener(ChangeListener cl) { if (changeSupport != null) { changeSupport.removeChangeListener(cl); } } | public void removeChangeListener(ChangeListener cl) {} |
this.connPool = connPool; | public SQLUnigeneDB(JDBCConnectionPool connPool) { this.connPool = connPool; this.clusterCache = new WeakValueHashMap(); } | |
for(int j = wordLength + 2; j <= symList.length(); j++) { | for(int j = wordLength + 1; j <= symList.length(); j++) { | public void search( String seqID, SymbolList symList, SearchListener listener ) { try { int word = PackingFactory.primeWord(symList, wordLength, packing); listener.startSearch(seqID); fireHits(word, 1, listener); for(int j = wordLength + 2; j <= symList.length(); j++) { word = ... |
fireHits(word, j - wordLength, listener); | fireHits(word, j - wordLength + 1, listener); | public void search( String seqID, SymbolList symList, SearchListener listener ) { try { int word = PackingFactory.primeWord(symList, wordLength, packing); listener.startSearch(seqID); fireHits(word, 1, listener); for(int j = wordLength + 2; j <= symList.length(); j++) { word = ... |
assertEquals(LocationTools.intersection(r1, r3), | assertEquals(LocationTools.intersection(r1, r2), | public void testIntersection() { assertEquals(LocationTools.intersection(r1, r1), new PointLocation(1)); assertEquals(LocationTools.intersection(r1, r3), Location.empty); } |
( (ct == null) || (ct == MarkovModel.PARAMETER) ) && (distForwarder == null) | MarkovModel.PARAMETER.isMatchingType(ChangeType.UNKNOWN) && distForwarder == null | protected ChangeSupport getChangeSupport(ChangeType ct) { ChangeSupport changeSupport = super.getChangeSupport(ct); if( ( (ct == null) || (ct == MarkovModel.PARAMETER) ) && (distForwarder == null) ) { distForwarder = new MarkovModel.DistributionForwarder( this, changeSupport );... |
if (o == null) return false; if (! o.getClass().equals(this.getClass())) return false; | if (o == null) return false; if (! o.getClass().equals(this.getClass())) return false; SimpleSeqSimilaritySearchResult that = (SimpleSeqSimilaritySearchResult) o; if (! ObjectUtil.equals(this.querySequence, that.querySequence)) return false; if (! ObjectUtil.equals(this.sequenceDB, that.sequenceDB)) return false; if... | public boolean equals(Object o) { if (o == this) return true; // if this class is a direct sub-class of Object: if (o == null) return false; if (! o.getClass().equals(this.getClass())) return false; SimpleSeqSimilaritySearchResult that = (SimpleSeqSimilaritySearchResult) o; // only compare fields of ... |
SimpleSeqSimilaritySearchResult that = (SimpleSeqSimilaritySearchResult) o; if (! ObjectUtil.equals(this.querySequence, that.querySequence)) return false; if (! ObjectUtil.equals(this.sequenceDB, that.sequenceDB)) return false; if (! ObjectUtil.equals(this.searchParameters, that.searchParameters)) return false; if (!... | return true; | public boolean equals(Object o) { if (o == this) return true; // if this class is a direct sub-class of Object: if (o == null) return false; if (! o.getClass().equals(this.getClass())) return false; SimpleSeqSimilaritySearchResult that = (SimpleSeqSimilaritySearchResult) o; // only compare fields of ... |
getProperties().put(key, value); | getProperties().put(key, newValue); | public void setProperty(Object key, Object value) throws ChangeVetoException { if(changeSupport == null) { getProperties().put(key, value); } else { Map properties = getProperties(); ChangeEvent ce = new ChangeEvent( this, Annotation.PROPERTY, new Object[] { key, value }, ... |
new Object[] { key, value }, new Object[] { key, properties.get(value)} | new Object[] { key, newValue }, new Object[] { key, properties.get(key)} | public void setProperty(Object key, Object value) throws ChangeVetoException { if(changeSupport == null) { getProperties().put(key, value); } else { Map properties = getProperties(); ChangeEvent ce = new ChangeEvent( this, Annotation.PROPERTY, new Object[] { key, value }, ... |
properties.put(key, value); | properties.put(key, newValue); | public void setProperty(Object key, Object value) throws ChangeVetoException { if(changeSupport == null) { getProperties().put(key, value); } else { Map properties = getProperties(); ChangeEvent ce = new ChangeEvent( this, Annotation.PROPERTY, new Object[] { key, value }, ... |
new FeatureFilter.Not(new FeatureFilter.IsTopLevel())); | new FeatureFilter.Not(FeatureFilter.top_level)); | public FeatureHolder filter(FeatureFilter ff) { FeatureFilter childFilter = new FeatureFilter.And(new FeatureFilter.ContainedByLocation(getLocation()), new FeatureFilter.Not(new FeatureFilter.IsTopLevel())); ... |
ChunkedSymbolListFactory symsf = new ChunkedSymbolListFactory(new PackedSymbolListFactory()); | public String subStr(RichSequence seq, int start, int end) throws IndexOutOfBoundsException { if (seq instanceof SimpleRichSequence) return super.subStr(seq,start,end); if (seq.length()==0) return ""; // empty seq else if (seq.getCircular()) { StringBuffer result = new StringBuffer()... |
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