rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k |
|---|---|---|
public static StringBuffer formatLocationBlock(Location loc, int strand, String leader, int wrapWidth) | public static StringBuffer formatLocationBlock(final Location loc, final int strand, final String leader, final int wrapWidth) | public static StringBuffer formatLocationBlock(Location loc, int strand, String leader, int wrapWidth) { // Indicates how many characters have been added to the // current line int position = leader.length(); boolean join = false; boolean complement = false; List l... |
Location [] la = (Location[]) locs.toArray(new Location [0]); | Collections.sort(locs, Location.naturalOrder); | public static StringBuffer formatLocationBlock(Location loc, int strand, String leader, int wrapWidth) { // Indicates how many characters have been added to the // current line int position = leader.length(); boolean join = false; boolean complement = false; List l... |
sb.append("complement("); position += 11; | public static StringBuffer formatLocationBlock(Location loc, int strand, String leader, int wrapWidth) { // Indicates how many characters have been added to the // current line int position = leader.length(); boolean join = false; boolean complement = false; List l... | |
for (int i = 0; i < la.length; i++) | for (Iterator li = locs.iterator(); li.hasNext();) | public static StringBuffer formatLocationBlock(Location loc, int strand, String leader, int wrapWidth) { // Indicates how many characters have been added to the // current line int position = leader.length(); boolean join = false; boolean complement = false; List l... |
boolean point = (PointLocation.class.isInstance(la[i])) ? true : false; boolean fuzzy = (FuzzyLocation.class.isInstance(la[i])) ? true : false; boolean fuzzyPoint = (FuzzyPointLocation.class.isInstance(la[i])) ? true : false; | if (PointLocation.class.isInstance(thisLoc)) locType = POINT; else if (FuzzyLocation.class.isInstance(thisLoc)) locType = FUZZY_RANGE; else if (FuzzyPointLocation.class.isInstance(thisLoc)) locType = FUZZY_POINT; else locType = RANGE; | public static StringBuffer formatLocationBlock(Location loc, int strand, String leader, int wrapWidth) { // Indicates how many characters have been added to the // current line int position = leader.length(); boolean join = false; boolean complement = false; List l... |
if (point) { sb.append(la[i].getMin()); } else if (fuzzy) | switch (locType) | public static StringBuffer formatLocationBlock(Location loc, int strand, String leader, int wrapWidth) { // Indicates how many characters have been added to the // current line int position = leader.length(); boolean join = false; boolean complement = false; List l... |
FuzzyLocation fl = (FuzzyLocation) la[i]; | case POINT: PointLocation pl = (PointLocation) thisLoc; | public static StringBuffer formatLocationBlock(Location loc, int strand, String leader, int wrapWidth) { // Indicates how many characters have been added to the // current line int position = leader.length(); boolean join = false; boolean complement = false; List l... |
if (! fl.hasBoundedMin()) { sb.append("<"); sb.append(fl.getMin()); } else if (fl.getOuterMin() != fl.getInnerMin()) { sb.append("(" + fl.getOuterMin()); sb.append("."); sb.append(fl.getInnerMin() + ")"); } else sb.append(fl.getMin()); | sb.append(complement ? toComplement(formatPoint(pl)) : formatPoint(pl)); break; | public static StringBuffer formatLocationBlock(Location loc, int strand, String leader, int wrapWidth) { // Indicates how many characters have been added to the // current line int position = leader.length(); boolean join = false; boolean complement = false; List l... |
sb.append(".."); | case FUZZY_RANGE: FuzzyLocation fl = (FuzzyLocation) thisLoc; | public static StringBuffer formatLocationBlock(Location loc, int strand, String leader, int wrapWidth) { // Indicates how many characters have been added to the // current line int position = leader.length(); boolean join = false; boolean complement = false; List l... |
if (! fl.hasBoundedMax()) { sb.append(">"); sb.append(la[i].getMax()); } else if (fl.getInnerMax() != fl.getOuterMax()) { sb.append("(" + fl.getInnerMax()); sb.append("."); sb.append(fl.getOuterMax() + ")"); } else sb.append(fl.getMax()); } else if (fuzzyPoint) { FuzzyPointLocation fpl = (FuzzyPointLocation) la[i]; | sb.append(complement ? toComplement(formatFuzzyRange(fl)) : formatFuzzyRange(fl)); break; | public static StringBuffer formatLocationBlock(Location loc, int strand, String leader, int wrapWidth) { // Indicates how many characters have been added to the // current line int position = leader.length(); boolean join = false; boolean complement = false; List l... |
if (! fpl.hasBoundedMin()) { sb.append("<"); sb.append(fpl.getMax()); } else if (! fpl.hasBoundedMax()) { sb.append(">"); sb.append(fpl.getMin()); } else { sb.append("(" + fpl.getMin()); sb.append("."); sb.append(fpl.getMax() + ")"); } } else { sb.append(la[i].getMin()); sb.append(".."); sb.append(la[i].getMax()); | case FUZZY_POINT: FuzzyPointLocation fpl = (FuzzyPointLocation) thisLoc; sb.append(complement ? toComplement(formatFuzzyPoint(fpl)) : formatFuzzyPoint(fpl)); break; case RANGE: RangeLocation rl = (RangeLocation) thisLoc; sb.append(complement ? toComplement(formatRange(rl))... | public static StringBuffer formatLocationBlock(Location loc, int strand, String leader, int wrapWidth) { // Indicates how many characters have been added to the // current line int position = leader.length(); boolean join = false; boolean complement = false; List l... |
if (i + 1 < la.length) | if ((locs.indexOf(thisLoc) + 1) < locs.size()) | public static StringBuffer formatLocationBlock(Location loc, int strand, String leader, int wrapWidth) { // Indicates how many characters have been added to the // current line int position = leader.length(); boolean join = false; boolean complement = false; List l... |
if (complement) { sb.append(")"); if ((position + 1) > wrapWidth) { sb.insert((sb.length() - diff), "\n" + leader); } } | public static StringBuffer formatLocationBlock(Location loc, int strand, String leader, int wrapWidth) { // Indicates how many characters have been added to the // current line int position = leader.length(); boolean join = false; boolean complement = false; List l... | |
public static StringBuffer formatQualifierBlock(String text, String leader, int wrapWidth) | public static StringBuffer formatQualifierBlock(final String text, final String leader, final int wrapWidth) | public static StringBuffer formatQualifierBlock(String text, String leader, int wrapWidth) { int tokenType = FIRST; int position = leader.length(); StringBuffer output = new StringBuffer(text.length()); output.append(leader); StringTokenizer t = new StringTokenizer(text); TOKEN: while (t... |
public static StringBuffer formatTokenBlock(Symbol [] syms, int blockSize) | public static StringBuffer formatTokenBlock(final Symbol [] syms, final int blockSize) | public static StringBuffer formatTokenBlock(Symbol [] syms, int blockSize) { StringBuffer sb = new StringBuffer(syms.length); for (int i = 0; i < syms.length; i++) { sb.append(syms[i].getToken()); if ((i > 0) && ((i + 1) % blockSize == 0)) sb.append(' '); } return sb; } |
public static void loadFeatureData(String featureDataFile, Map featureData, Map qualifierData) | public static void loadFeatureData(final String featureDataFile, final Map featureData, final Map qualifierData) | public static void loadFeatureData(String featureDataFile, Map featureData, Map qualifierData) { try { InputStream featureDataStream = EmblFileFormer.class.getClassLoader().getResourceAsStream(featureDataFile); if (featureDataStream == null) throw new BioError("Unable to find... |
public FastaSearchBuilder(SequenceDBInstallation subjectDBs, SequenceDB querySeqHolder) | public FastaSearchBuilder(final SequenceDBInstallation subjectDBs, final SequenceDB querySeqHolder) | public FastaSearchBuilder(SequenceDBInstallation subjectDBs, SequenceDB querySeqHolder) { this.subjectDBs = subjectDBs; this.querySeqHolder = querySeqHolder; } |
private Alignment createAlignment(String subjectSeqID, Map dataMap) | private Alignment createAlignment(final String subjectSeqID, final Map dataMap) | private Alignment createAlignment(String subjectSeqID, Map dataMap) throws IllegalSymbolException { String seqType = (String) dataMap.get("query"); FiniteAlphabet alpha; // What happens if Fasta is given an RNA sequence? if (seqType.equals("dna")) alpha = DNATools.getDNA(); else alpha = ProteinT... |
private Annotation createAnnotation(Map preAnnotation) | private Annotation createAnnotation(final Map preAnnotation) | private Annotation createAnnotation(Map preAnnotation) { Annotation annotation = new SimpleAnnotation(); Set annotationKeySet = preAnnotation.keySet(); for (Iterator ksi = annotationKeySet.iterator(); ksi.hasNext();) { Object annotationKey = ksi.next(); Object annotationValue = preAnnotation.get(annot... |
private SeqSimilaritySearchHit createHit(Map dataMap, Annotation hitAnnotation) | private SeqSimilaritySearchHit createHit(final Map dataMap, final Annotation hitAnnotation) | private SeqSimilaritySearchHit createHit(Map dataMap, Annotation hitAnnotation) throws BioException { String subjectSeqID = (String) dataMap.get("id"); Double score = (Double) dataMap.get("fa_z-score"); Double eValue = (Double) dataMap.get("fa_expect"); Double pValue = (Dou... |
private String prepSeqTokens(String name, Map dataMap) | private String prepSeqTokens(final String name, final Map dataMap) | private String prepSeqTokens(String name, Map dataMap) { // System.out.println("dataMap: " + dataMap); Integer alDispStart = (Integer) dataMap.get(name + "AlDispStart"); Integer alStart = (Integer) dataMap.get(name + "AlStart"); Integer alStop = (Integer) dataMap.get(name + "AlStop"); StringBuffer s... |
void setHitAnnotationData(Map hitPreAnnotation) | void setHitAnnotationData(final Map hitPreAnnotation) | void setHitAnnotationData(Map hitPreAnnotation) { this.hitPreAnnotation = hitPreAnnotation; } |
void setHitData(Map hitData) | void setHitData(final Map hitData) | void setHitData(Map hitData) { this.hitData = hitData; } |
void setQuerySeq(String querySeqID) | void setQuerySeq(final String querySeqID) | void setQuerySeq(String querySeqID) throws BioException { try { // System.out.println("Setting Query sequence with ID: " + querySeqID); querySeq = (SymbolList) querySeqHolder.getSequence(querySeqID); } catch (BioException bex) { throw new BioException(bex, "Failed to retrieve query sequence from hold... |
void setSearchAnnotationData(Map resultPreAnnotation) | void setSearchAnnotationData(final Map resultPreAnnotation) | void setSearchAnnotationData(Map resultPreAnnotation) { this.resultPreAnnotation = resultPreAnnotation; } |
void setSearchResultData(Map resultData) | void setSearchResultData(final Map resultData) | void setSearchResultData(Map resultData) { searchParameters = resultData; } |
void setSubjectDB(String subjectDBFileName) | void setSubjectDB(final String subjectDBFileName) | void setSubjectDB(String subjectDBFileName) throws BioException { // System.out.println("Setting subject DB with filename/ID: " + subjectDBFileName); subjectDB = subjectDBs.getSequenceDB(subjectDBFileName); if (subjectDB == null) throw new BioException("Failed to retrieve database from installation using ID:... |
assertEquals("g", charSeq.subSequence(0, 1)); assertEquals("t", charSeq.subSequence(3, 4)); assertEquals("gc", charSeq.subSequence(0, 2)); assertEquals("ca", charSeq.subSequence(1, 3)); assertEquals("at", charSeq.subSequence(2, 4)); | assertEquals("g", charSeq.subSequence(0, 1).toString()); assertEquals("t", charSeq.subSequence(3, 4).toString()); assertEquals("gc", charSeq.subSequence(0, 2).toString()); assertEquals("ca", charSeq.subSequence(1, 3).toString()); assertEquals("at", charSeq.subSequence(2, 4).toString()); | public void testSubSequence() throws Exception { CharSequence charSeq = new SymbolListCharSequence(DNATools.createDNA("GCAT")); assertEquals("g", charSeq.subSequence(0, 1)); assertEquals("t", charSeq.subSequence(3, 4)); assertEquals("gc", charSeq.subSequence(0, 2)); ... |
return new OPH(getIdentifier()); | return new WellKnownAtomicSymbol.OPH(getIdentifier()); | private Object writeReplace() { return new OPH(getIdentifier()); } |
throws NoSuchMethodException { this.templateClass = templateClass; this.featureClass = featureClass; this.con = featureClass.getConstructor(conTypes); } | throws NoSuchMethodException { Class[] conTypes = new Class[2]; conTypes[0] = Sequence.class; conTypes[1] = templateClass; this.templateClass = templateClass; this.featureClass = featureClass; this.con = featureClass.getConstructor(conTypes); } | public TemplateFeature(Class templateClass, Class featureClass) throws NoSuchMethodException { this.templateClass = templateClass; this.featureClass = featureClass; this.con = featureClass.getConstructor(conTypes); } |
if(template.getClass().isInstance(tf.templateClass)) { | if(tf.templateClass.isInstance(template)) { | protected static Feature createFeatureFromTemplate(Sequence parent, Feature.Template template) throws SeqException { for(Iterator i = templateClassToFeatureClass.iterator(); i.hasNext(); ) { TemplateFeature tf = (TemplateFeature) i.next(); if(template.getClass().isInstance(tf.templateClass)) { tr... |
syncDelegate(); delegateUpdate = new ChangeListener() { public void preChange(ChangeEvent ce) {} public void postChange(ChangeEvent ce) { ChangeType ct = ce.getType(); Object change = ce.getChange(); if(ct == Distribution.WEIGHTS) { boolean synced = false; if((change != null) && (change instanceof Object[]) ) { Object... | public TranslatedDistribution( ReversibleTranslationTable table, Distribution other, DistributionFactory distFact ) throws IllegalAlphabetException { if(!table.getTargetAlphabet().equals(other.getAlphabet())) { throw new IllegalAlphabetException( "Table target alphabet and distribution alphab... | |
delegate.addChangeListener(forwarder, Distribution.WEIGHTS); | other.addChangeListener(forwarder, Distribution.WEIGHTS); | protected ChangeSupport getChangeSupport(ChangeType ct) { ChangeSupport cs = super.getChangeSupport(ct); if(forwarder == null && (Distribution.WEIGHTS.isMatchingType(ct) || ct.isMatchingType(Distribution.WEIGHTS))) { forwarder = new Forwarder(this, cs); delegate.addChangeListener(forwarder, D... |
throws ChangeVetoException { DistributionTrainerContext subCtxt = new SimpleDistributionTrainerContext(); subCtxt.setNullModelWeight(weight); subCtxt.registerDistribution(delegate); for( Iterator i = ((FiniteAlphabet) other.getAlphabet()).iterator(); i.hasNext(); ) { AtomicSymbol sym = (AtomicSymbol) i.next(); try { s... | throws ChangeVetoException { | public void registerWithTrainer(DistributionTrainerContext dtc) { dtc.registerDistribution(other); dtc.registerTrainer(this, new DistributionTrainer() { public void addCount( DistributionTrainerContext dtc, AtomicSymbol s, double count ) throws IllegalSymbolException { dtc.... |
throws IllegalSymbolException, ChangeVetoException { delegate.setWeight(sym, weight); | throws IllegalSymbolException, ChangeVetoException { throw new ChangeVetoException("Can't directly edit a TranslatedDistribution"); | public void setWeight(Symbol sym, double weight) throws IllegalSymbolException, ChangeVetoException { delegate.setWeight(sym, weight); } |
+ ((sym == null)?999:alfaIdx.indexForSymbol(sym)); | + alphaIndex(sym); | public int hashCode() { try { return (source.getID() << 20) + (dest.getID() << 10) + ((sym == null)?999:alfaIdx.indexForSymbol(sym)); } catch (IllegalSymbolException ise) { throw new BioError("Fatal error: Unexpected Il... |
for (Iterator j = ((Set)this.namesMap.get(nameClass)).iterator(); j.hasNext(); ) { | if (items!=null) for (Iterator j = items.iterator(); j.hasNext(); ) { | public Set getNames(String nameClass) throws IllegalArgumentException { if (nameClass==null) throw new IllegalArgumentException("Name class cannot be null"); Set n = new TreeSet(); for (Iterator j = ((Set)this.namesMap.get(nameClass)).iterator(); j.hasNext(); ) { SimpleNCBITaxonName ... |
public static Distribution[] distOverAlignment(Alignment a, boolean countGaps){ | public static Distribution[] distOverAlignment(Alignment a, boolean countGaps, double nullWeight){ | public static Distribution[] distOverAlignment(Alignment a, boolean countGaps){ List seqs = a.getLabels(); Distribution[] pos = new Distribution[a.length()]; FiniteAlphabet dna = DNATools.getDNA(); try{ for(int i = 0; i < a.length(); i++){// For each position pos[i] = DistributionFactory.DEFAU... |
FiniteAlphabet dna = DNATools.getDNA(); | public static Distribution[] distOverAlignment(Alignment a, boolean countGaps){ List seqs = a.getLabels(); Distribution[] pos = new Distribution[a.length()]; FiniteAlphabet dna = DNATools.getDNA(); try{ for(int i = 0; i < a.length(); i++){// For each position pos[i] = DistributionFactory.DEFAU... | |
pos[i] = DistributionFactory.DEFAULT.createDistribution(dna); | pos[i] = DistributionFactory.DEFAULT.createDistribution(alpha); | public static Distribution[] distOverAlignment(Alignment a, boolean countGaps){ List seqs = a.getLabels(); Distribution[] pos = new Distribution[a.length()]; FiniteAlphabet dna = DNATools.getDNA(); try{ for(int i = 0; i < a.length(); i++){// For each position pos[i] = DistributionFactory.DEFAU... |
dtc.setNullModelWeight(nullWeight); | public static Distribution[] distOverAlignment(Alignment a, boolean countGaps){ List seqs = a.getLabels(); Distribution[] pos = new Distribution[a.length()]; FiniteAlphabet dna = DNATools.getDNA(); try{ for(int i = 0; i < a.length(); i++){// For each position pos[i] = DistributionFactory.DEFAU... | |
pc.setKernel(pc.polyKernel); | pc.setKernel(PointClassifier.polyKernel); | public static void main(String args[]) { JFrame f = new JFrame(); f.addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent we) { System.exit(0); } }); f.getContentPane().setLayout(new BorderLayout()); final PointClassifier pc = new PointClassifier(); f.getCont... |
pc.setKernel(pc.rbfKernel); | pc.setKernel(PointClassifier.rbfKernel); | public static void main(String args[]) { JFrame f = new JFrame(); f.addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent we) { System.exit(0); } }); f.getContentPane().setLayout(new BorderLayout()); final PointClassifier pc = new PointClassifier(); f.getCont... |
pc.setKernel(pc.polyKernel); | pc.setKernel(PointClassifier.polyKernel); | public void itemStateChanged(ItemEvent e) { if(e.getStateChange() == ItemEvent.SELECTED) { Object o = e.getItem(); if(o.equals("polynomeal")) { pc.setKernel(pc.polyKernel); } else if(o.equals("rbf")) { pc.setKernel(pc.rbfKernel); } } } |
pc.setKernel(pc.rbfKernel); | pc.setKernel(PointClassifier.rbfKernel); | public void itemStateChanged(ItemEvent e) { if(e.getStateChange() == ItemEvent.SELECTED) { Object o = e.getItem(); if(o.equals("polynomeal")) { pc.setKernel(pc.polyKernel); } else if(o.equals("rbf")) { pc.setKernel(pc.rbfKernel); } } } |
stackTop.getAnnotation().setProperty(key, value); | Annotation ann = stackTop.getAnnotation(); if (ann.containsProperty(key)) { Object o = ann.getProperty(key); Collection col; if (o instanceof Collection) { col = (Collection) o; } else { col = new ArrayList(); col.add(o); ann.setProperty(key, col); } col.add(value); } else { stackTop.getAnnotation().setProperty(key, v... | public void addFeatureProperty(Object key, Object value) throws ParseException { if (stackTop == null) { // Feature we're skipping return; } try { if (key.equals(XFFFeatureSetHandler.PROPERTY_XFF_ID)) { stackTop.getAnnotation().setProperty(DASSequence.PROPERTY_FEATUREID, value); } else { ... |
private void setObject(ComparableTerm object) { this.object = object; } | void setObject(ComparableTerm object) { this.object = object; } | private void setObject(ComparableTerm object) { this.object = object; } |
private void setOntology(ComparableOntology ontology) { this.ontology = ontology; } | void setOntology(ComparableOntology ontology) { this.ontology = ontology; } | private void setOntology(ComparableOntology ontology) { this.ontology = ontology; } |
private void setPredicate(ComparableTerm predicate) { this.predicate = predicate; } | void setPredicate(ComparableTerm predicate) { this.predicate = predicate; } | private void setPredicate(ComparableTerm predicate) { this.predicate = predicate; } |
private void setSubject(ComparableTerm subject) { this.subject = subject; } | void setSubject(ComparableTerm subject) { this.subject = subject; } | private void setSubject(ComparableTerm subject) { this.subject = subject; } |
public Collection getPaymentItems(String communeNumber, String personalId) throws java.rmi.RemoteException; | public Collection getPaymentItems(String communeNumber, String personalId, String endpoint) throws java.rmi.RemoteException; | public Collection getPaymentItems(String communeNumber, String personalId) throws java.rmi.RemoteException; |
IWTimestamp toStamp) throws java.rmi.RemoteException; | IWTimestamp toStamp, String endpoint) throws java.rmi.RemoteException; | public Collection getStatementItems(String communeNumber, String personalId, PaymentItem pType, IWTimestamp fromStamp, IWTimestamp toStamp) throws java.rmi.RemoteException; |
String modelFile = args[1]; | public static void main(String[] args) throws Throwable { if (args.length < 2) { throw new Exception("usage: stats.svm.tools.TrainRegression <train_examples> <model_file>"); } String trainFile = args[0]; String modelFile = args[1]; List examples = new ArrayList(); BufferedReader r = new Buffered... | |
dbAttrs.addAttribute(biojavaUri, "id", "id", CDATA, queryId); | dbAttrs.addAttribute(biojavaUri, "id", "id", CDATA, databaseId); | private void initDelegation() { // delegate handling of <BlastOutput_param>// super.addHandler(new ElementRecognizer.ByLocalName("BlastOutput_param"),// BlastOutputParamHandler.BLAST_OUTPUT_PARAM_HANDLER_FACTORY); // delegate handling of <BlastOutput_program> super.addHandl... |
dbAttrs.addAttribute(biojavaUri, "id", "id", CDATA, queryId); | dbAttrs.addAttribute(biojavaUri, "id", "id", CDATA, databaseId); | public StAXContentHandler getHandler(StAXFeatureHandler staxenv) { return new BlastOutputIterationsHandler(staxenv) { public void startElementHandler( String nsURI, String localName, ... |
dbAttrs.addAttribute(biojavaUri, "id", "id", CDATA, queryId); | dbAttrs.addAttribute(biojavaUri, "id", "id", CDATA, databaseId); | public void startElementHandler( String nsURI, String localName, String qName, Attributes attrs) throws SAXException { ... |
if (context.getDirection() == context.HORIZONTAL) | if (context.getDirection() == SequenceRenderContext.HORIZONTAL) | public void renderBead(Graphics2D g2, Feature f, SequenceRenderContext context) { Location loc = f.getLocation(); int min = loc.getMin(); int max = loc.getMax(); int dif = max - min; if (context.getDir... |
Node cnode2 = (Node) children.item(j); | Node cnode2 = (Node) proteaseNodes.item(j); | public static Protease getProteaseByName(String proteaseName){ Protease protease = null; NodeList children = doc.getDocumentElement().getChildNodes(); for(int i = 0; i < children.getLength(); i++) { Node cnode = (Node) children.item(i); if(! (cnode instanc... |
if (sequences == null) { | if (!gotAllIDs) { | public Set ids() { if (sequences == null) { try { URL epURL = new URL(dataSourceURL, "entry_points"); HttpURLConnection huc = (HttpURLConnection) epURL.openConnection(); try { huc.connect(); } catch (Exception e) { throw new BioException(e, "Can't connect to " + epURL); } int status = huc.getHea... |
sequences.put(el.getAttribute("id"), null); | String id = el.getAttribute("id"); if (! sequences.containsKey(id)) sequences.put(id, null); | public Set ids() { if (sequences == null) { try { URL epURL = new URL(dataSourceURL, "entry_points"); HttpURLConnection huc = (HttpURLConnection) epURL.openConnection(); try { huc.connect(); } catch (Exception e) { throw new BioException(e, "Can't connect to " + epURL); } int status = huc.getHea... |
xw.openTag("biojava:prop"); | xw.openTag(XFFTools.XFF_BIOJAVA_NS, "prop"); | public void writeDetails(XMLWriter xw, Feature f) throws IOException { Annotation a = f.getAnnotation(); for (Iterator ai = a.keys().iterator(); ai.hasNext(); ) { Object key = ai.next(); if (! (key instanceof String)) continue; Object value = a.getPr... |
xw.closeTag("biojava:prop"); | xw.closeTag(XFFTools.XFF_BIOJAVA_NS, "prop"); | public void writeDetails(XMLWriter xw, Feature f) throws IOException { Annotation a = f.getAnnotation(); for (Iterator ai = a.keys().iterator(); ai.hasNext(); ) { Object key = ai.next(); if (! (key instanceof String)) continue; Object value = a.getPr... |
AlphabetManager.getGapSymbol(Collections.singletonList(DNATools.getDNA()))); | DNATools.getDNA().getGapSymbol()); | public void testNormalGap() throws Exception{ doSymbolTest( AlphabetManager.getGapSymbol(Collections.singletonList(DNATools.getDNA()))); } |
if(forwarder == null && ct.isMatchingType(Distribution.WEIGHTS)) { | if(forwarder == null && (Distribution.WEIGHTS.isMatchingType(ct) || ct.isMatchingType(Distribution.WEIGHTS))) { | protected ChangeSupport getChangeSupport(ChangeType ct) { ChangeSupport cs = super.getChangeSupport(ct); if(forwarder == null && ct.isMatchingType(Distribution.WEIGHTS)) { forwarder = new Forwarder(this, cs); delegate.addChangeListener(forwarder, Distribution.WEIGHTS); } return cs; } |
throw new BioRuntimeException("Error adding BioSQL tables" + (rolledback ? " (rolled back successfully)" : ""), ex); | throw new BioRuntimeException( "Error adding sequence: " + seq.getName() + (rolledback ? " (rolled back successfully)" : ""), ex); | private void _addSequence(Sequence seq) throws ChangeVetoException, BioException { String seqName = idmaker.calcID(seq); int version = 1; Alphabet seqAlpha = seq.getAlphabet(); SymbolTokenization seqToke; try { seqToke = seqAlpha.getTokenization("token"); } catch (Exception ex) { throw new BioExce... |
public double getMinimumLeader(SequenceRenderContext src) { return 0.0; } | public double getMinimumLeader(SequenceRenderContext context) { return 0.0; } | public double getMinimumLeader(SequenceRenderContext src) { return 0.0; } |
public double getMinimumTrailer(SequenceRenderContext src) { String lengthString = String.valueOf(src.getSymbols().length()); Font f = src.getFont(); FontRenderContext frc = new FontRenderContext(null, true, true); GlyphVector gv = f.createGlyphVector(frc, lengthString); return gv.getVisualBounds().getWidth(); } | public double getMinimumTrailer(SequenceRenderContext context) { return 0.0; } | public double getMinimumTrailer(SequenceRenderContext src) { String lengthString = String.valueOf(src.getSymbols().length()); Font f = src.getFont(); FontRenderContext frc = new FontRenderContext(null, true, true); GlyphVector gv = f.createGlyphVector(frc, lengthString); return gv.getVisualBounds().get... |
public void paint( Graphics2D g, SequenceRenderContext src ) { g.setPaint(Color.black); int min = src.getRange().getMin(); int max = src.getRange().getMax(); double minX = src.sequenceToGraphics(min); double maxX = src.sequenceToGraphics(max); double scale = src.getScale(); double halfScale = scale * 0.5; Line2D line;... | public void paint(final Graphics2D g2, final SequenceRenderContext context) { AffineTransform prevTransform = g2.getTransform(); | public void paint( Graphics2D g, SequenceRenderContext src ) { g.setPaint(Color.black); int min = src.getRange().getMin(); int max = src.getRange().getMax(); double minX = src.sequenceToGraphics(min); double maxX = src.sequenceToGraphics(max); double scale = src.getScale(); double halfSca... |
if(src.getDirection() == src.HORIZONTAL) { line = new Line2D.Double(minX - halfScale, 0.0, maxX + halfScale, 0.0); } else { line = new Line2D.Double(0.0, minX - halfScale, 0.0, maxX + halfScale); | g2.setPaint(Color.black); int min = context.getRange().getMin(); int max = context.getRange().getMax(); double minX = context.sequenceToGraphics(min); double maxX = context.sequenceToGraphics(max); double scale = context.getScale(); double halfScale = scale * 0.5; if (context.getDirection() == SequenceRenderContext.... | public void paint( Graphics2D g, SequenceRenderContext src ) { g.setPaint(Color.black); int min = src.getRange().getMin(); int max = src.getRange().getMax(); double minX = src.sequenceToGraphics(min); double maxX = src.sequenceToGraphics(max); double scale = src.getScale(); double halfSca... |
g.draw(line); double ten = Math.log(10); FontMetrics myFontMetrics = g.getFontMetrics(); int coordWidth = myFontMetrics.stringWidth(Integer.toString(max)); double minGap = (double) Math.max(coordWidth, 40); int realSymsPerGap = (int) Math.ceil(((minGap + 5.0) / src.getScale())); double exponent = Math.floor(M... | public void paint( Graphics2D g, SequenceRenderContext src ) { g.setPaint(Color.black); int min = src.getRange().getMin(); int max = src.getRange().getMax(); double minX = src.sequenceToGraphics(min); double maxX = src.sequenceToGraphics(max); double scale = src.getScale(); double halfSca... | |
public SequenceViewerEvent processMouseEvent( SequenceRenderContext src, MouseEvent me, List path ) { path.add(this); int sPos = src.graphicsToSequence(me.getPoint()); return new SequenceViewerEvent(this, null, sPos, me, path); } | public SequenceViewerEvent processMouseEvent(final SequenceRenderContext context, final MouseEvent me, final List path) { path.add(this); int sPos = context.graphicsToSequence(me.getPoint()); return new SequenceViewerEvent(this, null, sPos, me, path); } | public SequenceViewerEvent processMouseEvent( SequenceRenderContext src, MouseEvent me, List path ) { path.add(this); int sPos = src.graphicsToSequence(me.getPoint()); return new SequenceViewerEvent(this, null, sPos, me, path); } |
public boolean equals(final Object other) | public boolean equals(Object other) | public boolean equals(final 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 SequenceDBSearchH... |
private void fireHits( | public void fireHits( | private void fireHits( int word, int offset, SearchListener listener ) { int hitOffset = hashTable.get(word); if(hitOffset >= 0) { try { hitTable.position(hitOffset); } catch (IllegalArgumentException e) { System.out.println("word:\t" + word); System.out.println("offset:... |
System.err.println("Foo"); | public void search( String seqID, SymbolList symList, SearchListener listener ) { try { int word = PackingFactory.primeWord(symList, wordLength, packing); listener.startSearch(seqID); fireHits(word, 1, listener); System.err.println("Foo"); for(int j = wordLength + 1; j <= symList... | |
dp.setFeature("http: | static SAXParser nonvalidatingSAXParser() { SAXParser dp = new SAXParser(); try { dp.setFeature("http://xml.org/sax/features/validation", false); // dp.setFeature("http://xml.org/sax/features/external-parameter-entities", false); dp.setFeature("http://apache.org/xml/features/nonvalidating/load-dtd-gramm... | |
public WeakTaxa(String scientificName, String commonName) { this.scientificName = scientificName; this.commonName = commonName; | public WeakTaxa() { super(); | public WeakTaxa(String scientificName, String commonName) { this.scientificName = scientificName; this.commonName = commonName; } |
this.advance, | WMAsMM.advance, | public WMAsMM(WeightMatrix wm) throws IllegalSymbolException { try { ChangeSupport changeSupport = getChangeSupport(ChangeType.UNKNOWN); distForwarder = new MarkovModel.DistributionForwarder(this, changeSupport); transFrom = new HashMap(); transTo = new HashMap(); transWeights = new HashMa... |
Character c = (Character) symbolsToCharacters.get(s); if (c == null) { throw new IllegalSymbolException("No mapping for symbol " + s.getName()); } return "" + c.charValue(); | return "" + _tokenizeSymbol(s).charValue(); | public String tokenizeSymbol(Symbol s) throws IllegalSymbolException { Character c = (Character) symbolsToCharacters.get(s); if (c == null) { throw new IllegalSymbolException("No mapping for symbol " + s.getName()); } return "" + c.charValue(); } |
Character c = (Character) symbolsToCharacters.get(sym); if (c == null) { throw new IllegalAlphabetException("No mapping for symbol " + sym.getName()); | try { Character c = _tokenizeSymbol(sym); sb.append(c.charValue()); } catch (IllegalSymbolException ex) { throw new IllegalAlphabetException(ex, "Couldn't tokenize"); | public String tokenizeSymbolList(SymbolList sl) throws IllegalAlphabetException { if (sl.getAlphabet() != getAlphabet()) { throw new IllegalAlphabetException("Alphabet " + sl.getAlphabet().getName() + " does not match " + getAlphabet().getName()); } StringBuffer sb = new StringBuffer(); for (Iterator ... |
sb.append(c.charValue()); | public String tokenizeSymbolList(SymbolList sl) throws IllegalAlphabetException { if (sl.getAlphabet() != getAlphabet()) { throw new IllegalAlphabetException("Alphabet " + sl.getAlphabet().getName() + " does not match " + getAlphabet().getName()); } StringBuffer sb = new StringBuffer(); for (Iterator ... | |
List auths = DocRefAuthor.Tools.parseAuthorString(authors); if (consortium!=null) auths.add(new SimpleDocRefAuthor(consortium,true,false)); | List auths = null; if(authors != null) auths = DocRefAuthor.Tools.parseAuthorString(authors); if (consortium!=null){ if(auths == null) auths = new ArrayList(); auths.add(new SimpleDocRefAuthor(consortium,true,false)); } | public boolean readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) throws IllegalSymbolException, IOException, ParseException { String line; boolean hasAnotherSequence = true; //bool... |
desc = m.group(3); | if(m.group(4) != null){ desc = m.group(3)+m.group(4); }else{ desc = m.group(3); } | public boolean readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) throws IllegalSymbolException, IOException, ParseException { String line; boolean hasAnotherSequence = true; //bool... |
val = val.trim().replaceAll("\"",""); | val = val.replaceAll("\"","").trim(); | public boolean readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener) throws IllegalSymbolException, IOException, ParseException { String line; boolean hasAnotherSequence = true; boolean hasInternalWhitespace = fals... |
try { | public static void getSeqIOEvents(Sequence seq, SeqIOListener listener) throws BioException { try { // Inform listener of sequence start listener.startSequence(); // Pass name to listener listener.setName(seq.getName()); // Pass URN to listener listener.setURI(seq.getURN()); // Pass s... | |
for (Iterator fi = subs.iterator(); fi.hasNext();) { Feature.Template t = ((Feature) fi.next()).makeTemplate(); | for (Iterator fi = subs.iterator(); fi.hasNext();) { Feature.Template t = ((Feature) fi.next()).makeTemplate(); try { listener.startFeature(t); } catch (ParseException pe) { pe.printStackTrace(); } | public static void getSeqIOEvents(Sequence seq, SeqIOListener listener) throws BioException { try { // Inform listener of sequence start listener.startSequence(); // Pass name to listener listener.setName(seq.getName()); // Pass URN to listener listener.setURI(seq.getURN()); // Pass s... |
listener.startFeature(t); | try { | public static void getSeqIOEvents(Sequence seq, SeqIOListener listener) throws BioException { try { // Inform listener of sequence start listener.startSequence(); // Pass name to listener listener.setName(seq.getName()); // Pass URN to listener listener.setURI(seq.getURN()); // Pass s... |
listener.endSequence(); } catch (ParseException pe) { throw new BioException("An internal error occurred processing " + seq.toString() + " into SeqIO events"); | public static void getSeqIOEvents(Sequence seq, SeqIOListener listener) throws BioException { try { // Inform listener of sequence start listener.startSequence(); // Pass name to listener listener.setName(seq.getName()); // Pass URN to listener listener.setURI(seq.getURN()); // Pass s... | |
throw new BioException("An internal error occurred processing " | throw new BioException("An internal error occurred processing symbols of " | public static void getSeqIOEvents(Sequence seq, SeqIOListener listener) throws BioException { try { // Inform listener of sequence start listener.startSequence(); // Pass name to listener listener.setName(seq.getName()); // Pass URN to listener listener.setURI(seq.getURN()); // Pass s... |
listener.endSequence(); | public static void getSeqIOEvents(Sequence seq, SeqIOListener listener) throws BioException { try { // Inform listener of sequence start listener.startSequence(); // Pass name to listener listener.setName(seq.getName()); // Pass URN to listener listener.setURI(seq.getURN()); // Pass s... | |
try { String id = (String) i.next(); Sequence seq = sdb.getSequence(id); if(annotate(seq)) { hitDB.addSequence(id, seq); } } catch (SeqException se){ | String id = (String) i.next(); Sequence seq = sdb.getSequence(id); if(annotate(seq)) { hitDB.addSequence(id, seq); | public SequenceDB annotate(SequenceDB sdb) throws IllegalResidueException, SeqException { HashSequenceDB hitDB = new HashSequenceDB(null); for(Iterator i = sdb.ids().iterator(); i.hasNext(); ) { try { String id = (String) i.next(); Sequence seq = sdb.getSequence(id); if(annotate... |
throws IOException, BioException { this.location = location; metaData = new ConfigFile(BioStoreFactory.makeConfigFile(location)); idToList = new SmallMap(); primaryKey = (String) metaData.getProperty(BioStoreFactory.PRIMARY_KEY_NAME); String keyList = (String) metaData.getProperty(BioStoreFactory.KEYS); File plFile =... | throws IOException, BioException { this(location, cache, false); | public BioStore(File location, boolean cache) throws IOException, BioException { this.location = location; metaData = new ConfigFile(BioStoreFactory.makeConfigFile(location)); idToList = new SmallMap(); primaryKey = (String) metaData.getProperty(BioStoreFactory.PRIMARY_KEY_NAME); ... |
RAF[] tmpr = new RAF[indx]; | RAF[] tmpr = new RAF[indx+1]; | private void readFileIDs() throws IOException, BioException { fileIDToRAF = new RAF[5]; fileCount = 0; for (Iterator i = metaData.keys().iterator(); i.hasNext(); ) { String key = (String) i.next(); if (key.startsWith("fileid_")) { ... |
String name = enzyme.getName(); | public void run() { SymbolListCharSequence charSeq = new SymbolListCharSequence(target); try { Pattern [] patterns = RestrictionEnzymeManager.getPatterns(enzyme); String name = enzyme.getName(); int siteLen = enzyme.getRecognitionSite().length(); i... | |
listener.addSequenceProperty(key, a.getProperty(key)); | if ( key.equals(ReferenceAnnotation.class)) { ArrayList references = null; if (a.getProperty(key) instanceof ArrayList) { references = ((ArrayList)a.getProperty(key)); } if (references != null) { for ( int i = 0; i < references.size(); i++ ) { ReferenceAnnotation refAnnot = (ReferenceAnnotation)references.get(i); ... | void getSeqIOEvents(Sequence seq, SeqIOListener listener) { try { // Inform listener of sequence start listener.startSequence(); // Pass name to listener listener.setName(seq.getName()); // Pass URN to listener listener.setURI(seq.ge... |
URL mapURL = new URL(((Text) mapmaster.getFirstChild()).getData().trim()); | String mapURLString = ((Text) mapmaster.getFirstChild()).getData().trim(); if (! (mapURLString.charAt(mapURLString.length() - 1) == '/')) { mapURLString = mapURLString + '/'; } URL mapURL = new URL(mapURLString); | private void addDasURLImpl(URL dasURL) throws BioException, ChangeVetoException { try { URL dsnURL = new URL(dasURL, "dsn"); HttpURLConnection huc = (HttpURLConnection) dsnURL.openConnection(); huc.connect(); int status = DASSequenceDB.tolerantIntHeader(huc, "X-DAS-Status"); // int status... |
public String startElement(String string, Attributes attributes) | public String startElement(String string) | public String startElement(String string, Attributes attributes) { oElementStack.push(string); oStr.setLength(0); if (!tLastWritePCData) oStr.append(nl()); oStr.append(indent()); oStr.append("<"); oStr.append(string); int i = 0; oSpaceStore.setLe... |
int i = 0; oSpaceStore.setLength(0); oSpaceStore.append(indent()); for (i = 0; i <= string.length(); i++) oSpaceStore.append(" "); for (i = 0; i < attributes.getLength() - 1; i++) { oAttName = attributes.getLocalName(i); oAttValue = attributes.getValue(i); oStr.append(" "); if (i > 0) oStr.append(oSpaceStore.toString()... | public String startElement(String string, Attributes attributes) { oElementStack.push(string); oStr.setLength(0); if (!tLastWritePCData) oStr.append(nl()); oStr.append(indent()); oStr.append("<"); oStr.append(string); int i = 0; oSpaceStore.setLe... | |
List chains = getChains(modelnr); | public Group findGroup(String chainId, String pdbResnum, int modelnr) throws StructureException { // if structure is xray there will be only one "model". if ( modelnr > models.size()) throw new StructureException(" no model nr " + modelnr + " in this structu... | |
Iterator iter = chains.iterator(); while (iter.hasNext()){ Chain c = (Chain)iter.next(); boolean foundChain = false; if (c.getName().equals(chainId)) { foundChain = true; Chain newchain = new ChainImpl(); newchain.setName(c.getName()); | Chain c = findChain(chainId,modelnr); | public Group findGroup(String chainId, String pdbResnum, int modelnr) throws StructureException { // if structure is xray there will be only one "model". if ( modelnr > models.size()) throw new StructureException(" no model nr " + modelnr + " in this structu... |
Iterator giter = groups.iterator(); while (giter.hasNext()){ Group g = (Group) giter.next(); String rnum = g.getPDBCode(); | public Group findGroup(String chainId, String pdbResnum, int modelnr) throws StructureException { // if structure is xray there will be only one "model". if ( modelnr > models.size()) throw new StructureException(" no model nr " + modelnr + " in this structu... |
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