rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k |
|---|---|---|
return wrapped.alphabet(); | return this.getSource().alphabet(); | public Alphabet alphabet() { return wrapped.alphabet(); } |
return wrapped.getAdvance(); | return this.getSource().getAdvance(); | public int [] getAdvance() { return wrapped.getAdvance(); } |
return wrapped.getName() + "-f"; | return super.getName() + "-f"; | public String getName() { return wrapped.getName() + "-f"; } |
return wrapped; | return this.getSource(); | public State getWrapped() { return wrapped; } |
this.transFrom = new HashMap(); this.transTo = new HashMap(); this.transModelTrans = new HashMap(); | public FlatModel(MarkovModel model) throws IllegalResidueException, IllegalAlphabetException { this.source = model; this.stateAlpha = new SimpleAlphabet(); this.transFrom = new HashMap(); this.transTo = new HashMap(); this.transModelTrans = new HashMap(); stateAlpha.setName("flat " + model.stat... | |
transFrom.put(s, new HashSet()); transTo.put(s, new HashSet()); | super.addState(s); | private void addAState(State s) { //System.out.println("Adding state: " + s.getName()); try { stateAlpha.addResidue(s); transFrom.put(s, new HashSet()); transTo.put(s, new HashSet()); } catch (Exception e) { throw new BioError(e, "Something got stuffed up while adding state " + s.getName(... |
private void createTransition( State from, State to, MarkovModel within, State source, State dest ) { try { ModelTransition mt = getMT(from, to); if(mt == null) { transModelTrans.put( new Transition(from, to), new ModelTransition(within, source, dest) ); } Set f = (Set) transFrom.get(from); Set t = (Set) transTo.get(t... | public void createTransition(State from, State to) throws IllegalResidueException, UnsupportedOperationException { Alphabet a = stateAlphabet(); a.validate(from); a.validate(to); throw new UnsupportedOperationException("createTransition not supported by FlatModel"); | private void createTransition( State from, State to, MarkovModel within, State source, State dest ) { //System.out.println("Adding: " + from.getName() + " -> " + to.getName()); try { ModelTransition mt = getMT(from, to); if(mt == null) { transModelTrans.put( new Transition(from,... |
public IllegalResidueException(Residue res, String message) { super(message); this.res = res; | public IllegalResidueException(String message) { this(null, null, message); | public IllegalResidueException(Residue res, String message) { super(message); this.res = res; } |
public IllegalTransitionException(State from, State to) { this(from, to, ""); | public IllegalTransitionException(State from, State to, String message) { super(message + "[" + from.getName() + " -> " + to.getName() + "]"); this.from = from; this.to = to; | public IllegalTransitionException(State from, State to) { this(from, to, ""); } |
public SeqException(Exception ex, String message) { super(ex, message); | public SeqException(String message) { super(message); | public SeqException(Exception ex, String message) { super(ex, message); } |
public RagbagSequence(String name, String urn, SequenceBuilder builder) | public RagbagSequence(String name, String urn) | public RagbagSequence(String name, String urn, SequenceBuilder builder) { this.builder = builder; this.name = name; this.urn = urn; } |
this.builder = builder; this.name = name; this.urn = urn; | builder = new SimpleSequenceBuilder(); this.name = name; this.urn = urn; System.out.println("RagbagSequence constructor: " + name + " " + urn); | public RagbagSequence(String name, String urn, SequenceBuilder builder) { this.builder = builder; this.name = name; this.urn = urn; } |
setFeatureProperty("sequence.id", s); | ComponentFeatureHandler.this.setFeatureProperty("sequence.id", s); | protected StAXContentHandler getComponentIDHandler() { return new StringElementHandlerBase() { protected void setStringValue(String s) throws SAXException { try { setFeatureProperty("sequence.id", s); } catch (Exception ex) { throw new SAXException("Couldn't set property", ex); } } }... |
setFeatureProperty("sequence.id", s); | ComponentFeatureHandler.this.setFeatureProperty("sequence.id", s); | protected void setStringValue(String s) throws SAXException { try { setFeatureProperty("sequence.id", s); } catch (Exception ex) { throw new SAXException("Couldn't set property", ex); } } |
! (featC.isAssignableFrom(getClass())) && ! (getClass().isAssignableFrom(featC)); | ! (featC.isAssignableFrom(getTestClass())) && ! (getTestClass().isAssignableFrom(featC)); | public boolean isDisjoint(FeatureFilter feat) { if(feat instanceof ByClass) { Class featC = ((ByClass) feat).getClass(); return ! (featC.isAssignableFrom(getClass())) && ! (getClass().isAssignableFrom(featC)); } return (feat instanceof AcceptNoneFilter); } |
protected SimpleSymbol(char token, Annotation annotation) | protected SimpleSymbol(Annotation annotation) | protected SimpleSymbol(char token, Annotation annotation) { this.token = token; this.annotation = new SimpleAnnotation(annotation); } |
this.token = token; | protected SimpleSymbol(char token, Annotation annotation) { this.token = token; this.annotation = new SimpleAnnotation(annotation); } | |
for(int j = wordLength+2; j <= seq.length(); j++) { | for(int j = wordLength + 1; j <= seq.length(); j++) { | public DataStore buildDataStore( File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold ) throws IllegalAlphabetException, IOException, BioException { ByteArrayOutputStream packingStream = new ByteArrayOutputStream(); ObjectOutputStream packingSerializer = new... |
writeRecord(hashTable, hitTable, j - wordLength, seqNumber, word); | writeRecord(hashTable, hitTable, j - wordLength + 1, seqNumber, word); | public DataStore buildDataStore( File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold ) throws IllegalAlphabetException, IOException, BioException { ByteArrayOutputStream packingStream = new ByteArrayOutputStream(); ObjectOutputStream packingSerializer = new... |
private static Set fillSet(String [] tokenArray, Set set) | private static Set fillSet(final String [] tokenArray, final Set set) | private static Set fillSet(String [] tokenArray, Set set) { for (int i = 0; i < tokenArray.length; i++) set.add(tokenArray[i]); return set; } |
private Integer parseCoord(String line) | private Integer parseCoord(final String line) | private Integer parseCoord(String line) { int sepIndex = line.lastIndexOf(":"); String coord = line.substring(sepIndex + 1); return Integer.valueOf(coord.trim()); } |
private String parseDB(String line) | private String parseDB(final String line) | private String parseDB(String line) throws ParserException { StringTokenizer st = new StringTokenizer(line); String db; String previous = null; String current = null; // The database filename is the second-to-last token on the line while (st.hasMoreTokens()) { if (current == null) current = st.nextToken();... |
private String parseID(String line) | private String parseID(final String line) | private String parseID(String line) throws ParserException { StringTokenizer st = new StringTokenizer(line); String id; if (st.hasMoreTokens()) id = st.nextToken(); else throw new ParserException("Fasta parser failed to parse a sequence ID", null, lineNumber, line); // For Hit ... |
private boolean parseLine(String line, Set tokenSet, Map dataMap) | private boolean parseLine(final String line, final Set tokenSet, final Map dataMap) | private boolean parseLine(String line, Set tokenSet, Map dataMap) throws ParserException { int idTokenStart = line.indexOf(";"); int idTokenEnd = line.indexOf(":"); String idToken = line.substring(idTokenStart + 1, idTokenEnd); idToken = idToken.trim(); String idValue = line.substring(idTokenEnd +... |
public boolean parseSearch(BufferedReader reader, SearchContentHandler scHandler) | public boolean parseSearch(final BufferedReader reader, final SearchContentHandler scHandler) | public boolean parseSearch(BufferedReader reader, SearchContentHandler scHandler) throws IOException, BioException, ParserException { boolean foundQuerySeqID = false; lineNumber = 0; FastaSearchBuilder handler = (FastaSearchBuilder) scHandler; LINE: while ((line = reader.readLine()) != null) { ... |
private boolean parseSequence(String line, String name, Map dataMap) | private boolean parseSequence(final String line, final String name, final Map dataMap) | private boolean parseSequence(String line, String name, Map dataMap) { if (line.startsWith(";")) { // Check the sequence type given by the report if (line.equals("; sq_type: p")) { dataMap.put(name, "protein"); return true; } else if (line.equals("; sq_type: D")) { dataMap.put(name, "d... |
Feature f = new SimpleFeature(this, template); | Feature f = SimpleFeatureRealizer.DEFAULT.realizeFeature(this, template); | public AceSequence(AceObject seqObj) throws AceException, BioException { this.name = seqObj.getName(); this.fHolder = new SimpleMutableFeatureHolder(); try { // load in relevent ACeDB object & construct annotation wrapper annotation = new AceAnnotation(seqObj); // load in the corresp... |
return "urn: | return "urn:sequence/acedb:" + getName(); | public String getURN() { return "urn://sequence:acedb/" + getName(); } |
public RichStreamReader(BufferedReader reader, | public RichStreamReader(InputStream is, | public RichStreamReader(BufferedReader reader, RichSequenceFormat format, SymbolTokenization symParser, RichSequenceBuilderFactory sf, Namespace ns) { this.reader = reader; this.format = format; this.symParser = symParser; this.sf = sf; ... |
this.reader = reader; this.format = format; this.symParser = symParser; this.sf = sf; this.ns = ns; | this(new BufferedReader(new InputStreamReader(is)), format,symParser,sf,ns); | public RichStreamReader(BufferedReader reader, RichSequenceFormat format, SymbolTokenization symParser, RichSequenceBuilderFactory sf, Namespace ns) { this.reader = reader; this.format = format; this.symParser = symParser; this.sf = sf; ... |
this.annotation = (annotation == null ? new SimpleAnnotation() : annotation); | this.annotation = annotation; this.sequenceDB.addChangeListener(ChangeListener.ALWAYS_VETO); this.querySeq.addChangeListener(ChangeListener.ALWAYS_VETO); this.annotation.addChangeListener(ChangeListener.ALWAYS_VETO); | public SequenceDBSearchResult(SequenceDB sequenceDB, Map searchParameters, SymbolList querySeq, Annotation annotation, List hits) { Contract.pre(querySeq != null, "querySeq was null"); Contract.pre(sequenceDB != null, "sequenceDB was null"); // searchParameters may be null Cont... |
throw new AlreadyExistsException("Ontology " + getName() + " already contains " + name); | throw new AlreadyExistsException("Ontology " + getName() + " already contains " + t.getName()); | private void addTerm(Term t) throws AlreadyExistsException, IllegalArgumentException, ChangeVetoException { if (terms.containsKey(t.getName())) { throw new AlreadyExistsException("Ontology " + getName() + " already contains " + name); } ... |
public RemoteTerm importTerm(Term t, String name) | public Term importTerm(Term t, String name) | public RemoteTerm importTerm(Term t, String name) throws IllegalArgumentException, ChangeVetoException { RemoteTerm rt = (RemoteTerm) remoteTerms.get(t); if (rt == null) { rt = new RemoteTerm.Impl(this, t, name); try { addTerm(rt); } catch (AlreadyExistsExceptio... |
while(t instanceof RemoteTerm) { t = ((RemoteTerm) t).getRemoteTerm(); } if(t.getOntology() == this) { return t; } | public RemoteTerm importTerm(Term t, String name) throws IllegalArgumentException, ChangeVetoException { RemoteTerm rt = (RemoteTerm) remoteTerms.get(t); if (rt == null) { rt = new RemoteTerm.Impl(this, t, name); try { addTerm(rt); } catch (AlreadyExistsExceptio... | |
public RemoteTerm importTerm(Term t, String localName) | public Term importTerm(Term t, String localName) | public RemoteTerm importTerm(Term t, String localName) throws ChangeVetoException, IllegalArgumentException; |
public SimpleSymbol( char token, String name, Annotation annotation, Set bases | protected SimpleSymbol( char token, String name, Annotation annotation | public SimpleSymbol( char token, String name, Annotation annotation, Set bases ) { this.token = token; this.name = name; this.annotation = new SimpleAnnotation(annotation); if(bases == null) { this.bases = null; } else { this.bases = Collections.unmodifiableSet(bases); } } |
if(bases == null) { this.bases = null; } else { this.bases = Collections.unmodifiableSet(bases); } | public SimpleSymbol( char token, String name, Annotation annotation, Set bases ) { this.token = token; this.name = name; this.annotation = new SimpleAnnotation(annotation); if(bases == null) { this.bases = null; } else { this.bases = Collections.unmodifiableSet(bases); } } | |
Set bases = getBases(); Set mat = new HashSet(); for(Iterator i = bases.iterator(); i.hasNext(); ) { BasisSymbol bs = (BasisSymbol) i.next(); if(bs instanceof AtomicSymbol) { mat.add(bs); } else { FiniteAlphabet ma = (FiniteAlphabet) bs.getMatches(); for(Iterator j = ma.iterator(); j.hasNext(); ) { mat.add((AtomicSymbo... | throw new BioError("Assertion Failure: Matches alphabet is null"); | protected Alphabet createMatches() { Set bases = getBases(); Set mat = new HashSet(); for(Iterator i = bases.iterator(); i.hasNext(); ) { BasisSymbol bs = (BasisSymbol) i.next(); if(bs instanceof AtomicSymbol) { mat.add(bs); } else { FiniteAlphabet ma = (FiniteAlphabet) bs.getMat... |
dp.setFeature("http: | static DOMParser nonvalidatingParser() { DOMParser dp = new DOMParser(); 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-grammar"... | |
try { componentID = (String) temp.annotation.getProperty("sequence.id"); } catch (NoSuchElementException ex) { throw new BioRuntimeException("No sequence.id property"); | componentID = temp.componentSequenceName; if (componentID == null) { try { componentID = (String) temp.annotation.getProperty("sequence.id"); } catch (NoSuchElementException ex) { throw new BioRuntimeException("No sequence.id property"); } | public DASComponentFeature(DASSequence 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."); } ... |
public Ticket requestFeatures(String id, SeqIOListener l, String type, String category) { Ticket t = new Ticket(id, l, type, category); openTickets.add(t); return t; | public Ticket requestFeatures(String id, SeqIOListener l) { return requestFeatures(id, l, null, null); | public Ticket requestFeatures(String id, SeqIOListener l, String type, String category) { Ticket t = new Ticket(id, l, type, category); openTickets.add(t); return t; } |
public DNANoAmbPack(Symbol placeHolderSymbol) { this.placeHolder = pack(placeHolderSymbol); | public DNANoAmbPack(byte placeHolder) { this.placeHolder = placeHolder; | public DNANoAmbPack(Symbol placeHolderSymbol) { this.placeHolder = pack(placeHolderSymbol); } |
Element segment = null; | public Set ids() { if (rootIDs == null) { try { DAS.startedActivity(this); Set ids = new HashSet(); URL epURL = new URL(dataSourceURL, "entry_points"); HttpURLConnection huc = (HttpURLConnection) epURL.openConnection(); try... | |
Map seqMap = new HashMap(); | Map seqMap = new LinkedHashMap(); | public Alignment read(BufferedReader br) { try { SequenceIterator seqs = null; br.mark(200); String line = br.readLine(); line = br.readLine(); br.reset(); for (int i = 0; i < line.length(); i++) { if (Character.toUpperCase(line... |
public void addSequence(Sequence seq) { sequenceByID.put(idMaker.calcID(seq), seq); | public void addSequence(String id, Sequence seq) { sequenceByID.put(id, seq); | public void addSequence(Sequence seq) { sequenceByID.put(idMaker.calcID(seq), seq); } |
if (!(value instanceof String)) value = value.toString(); | if ((value != null) && !(value instanceof String)) value = value.toString(); | public void addFeatureProperty(Object key, Object value) throws ParseException { if (this.featureStack.size() == 0) throw new ParseException("Assertion failed: Not within a feature"); if (!(key instanceof ComparableTerm)) key = RichObjectFactory.getDefaultOntology().getOrCreateTerm(key.toString()); ... |
} catch (IllegalAlphabetException iae) { | } catch (IllegalResidueException iae) { | public Residue residueAt(int index) throws IndexOutOfBoundsException { if(index < 1 || index > length()) { throw new IndexOutOfBoundsException( "index must be within (1 .. " + length() + "), not " + index ); } index = (index-1)*width + 1; try { return alpha.getResidue... |
throws IllegalAlphabetException; | throws IllegalResidueException; | public CrossProductResidue getResidue(List rl) throws IllegalAlphabetException; |
this(fh, null, parent, translation, oppositeStrand); | this.wrapped = fh; this.parent = parent; this.translate = translation; this.oppositeStrand = oppositeStrand; this.filter = filter; underlyingFeaturesChange = new ChangeListener() { public void preChange(ChangeEvent e) throws ChangeVetoException { if (changeSupport != null) { changeSupport.firePreChangeEvent(new Change... | public ProjectedFeatureHolder(FeatureHolder fh, FeatureHolder parent, int translation, boolean oppositeStrand) { this(fh, null, parent, translation, oppositeStrand); } |
return new PointLocation(this.point + dist); | if (dist == 0) return this; return new PointLocation(this.point + dist); | public Location translate(int dist) { return new PointLocation(this.point + dist); } |
this.alfa = alfa; | public Search(FiniteAlphabet alfa) { this.alfa = alfa; factory = PatternFactory.makeFactory(alfa); } | |
public org.biojava.utils.regex.Matcher reset(SymbolList sl) | public org.biojava.utils.regex.Matcher reset() | public org.biojava.utils.regex.Matcher reset(SymbolList sl) { this.sl = sl; matcher = matcher.reset(new SymbolListCharSequence(sl)); return this; } |
this.sl = sl; matcher = matcher.reset(new SymbolListCharSequence(sl)); | matcher = matcher.reset(); | public org.biojava.utils.regex.Matcher reset(SymbolList sl) { this.sl = sl; matcher = matcher.reset(new SymbolListCharSequence(sl)); return this; } |
public boolean find(int start) throws IndexOutOfBoundsException { return matcher.find(start); } | public boolean find() { return matcher.find(); } | public boolean find(int start) throws IndexOutOfBoundsException { return matcher.find(start); } |
public int start() { return matcher.start(); } | public int start() { return matcher.start() + 1; } | public int start() { return matcher.start(); } |
public int end() { return matcher.end(); } | public int end() { return matcher.end() + 1; } | public int end() { return matcher.end(); } |
for(Iterator i = alphabet.iterator(); i.hasNext(); ) { weight.put(i.next(), new Double(Double.NaN)); } | public SimpleDistribution(FiniteAlphabet alphabet) { this.alphabet = alphabet; this.weight = new HashMap(); for(Iterator i = alphabet.iterator(); i.hasNext(); ) { weight.put(i.next(), new Double(Double.NaN)); } try { setNullModel(new UniformDistribution(alphabet)); } catch (Exception e) { ... | |
for(Iterator i = ((FiniteAlphabet) sym.getMatches()).iterator(); i.hasNext(); ) { | FiniteAlphabet matches = (FiniteAlphabet) sym.getMatches(); if(matches.size() == 0) { if(sym.equals(AlphabetManager.getGapSymbol())) { return true; } else if(sym instanceof BasisSymbol) { if(((BasisSymbol) sym).getSymbols().size() == getAlphabets().size()) { return true; } } return true; } for(Iterator i = matches.... | public final boolean contains(Symbol sym) { if(sym instanceof AtomicSymbol) { return containsImpl((AtomicSymbol) sym); } else { if(sym == null) { throw new NullPointerException("Symbols can't be null"); } for(Iterator i = ((FiniteAlphabet) sym.getMatches()).iterator(); i.hasNext(); ) ... |
Iterator i = iterator(); | /*Iterator i = iterator(); | public final void validate(Symbol sym) throws IllegalSymbolException { if(!contains(sym)) { StringBuffer sb = new StringBuffer("{"); Iterator i = iterator(); if(i.hasNext()) { sb.append(((Symbol) i.next()).getToken()); } while(i.hasNext()) { sb.append(','); sb.append(... |
sb.append(((Symbol) i.next()).getToken()); | sb.append(((Symbol) i.next()).getName()); | public final void validate(Symbol sym) throws IllegalSymbolException { if(!contains(sym)) { StringBuffer sb = new StringBuffer("{"); Iterator i = iterator(); if(i.hasNext()) { sb.append(((Symbol) i.next()).getToken()); } while(i.hasNext()) { sb.append(','); sb.append(... |
sb.append("}"); | sb.append("}");*/ | public final void validate(Symbol sym) throws IllegalSymbolException { if(!contains(sym)) { StringBuffer sb = new StringBuffer("{"); Iterator i = iterator(); if(i.hasNext()) { sb.append(((Symbol) i.next()).getToken()); } while(i.hasNext()) { sb.append(','); sb.append(... |
static public Symbol createSymbol( char token, Annotation annotation, Set symSet, Alphabet alpha ) throws IllegalSymbolException { if(symSet.size() == 0) { return getGapSymbol(); } Set asSet = new HashSet(); int len = -1; for( Iterator i = symSet.iterator(); i.hasNext(); ) { Symbol s = (Symbol) i.next(); if(s instanceo... | static public AtomicSymbol createSymbol( char token, String name, Annotation annotation ) { AtomicSymbol as = new FundamentalAtomicSymbol(name, token, annotation); return as; | static public Symbol createSymbol( char token, Annotation annotation, Set symSet, Alphabet alpha ) throws IllegalSymbolException { if(symSet.size() == 0) { return getGapSymbol(); } Set asSet = new HashSet(); int len = -1; for( Iterator i = symSet.iterator(); i.hasNext(); ) { ... |
public void add(LabelIncrementer labelIncrementer) { this.labelIncrementer = labelIncrementer; | public void add(CCDateFormat dateFormat) { this.dateFormat = dateFormat; | public void add(LabelIncrementer labelIncrementer) { this.labelIncrementer = labelIncrementer; } |
int stateCount = states.length; | private void forward_recurse(DPCursor dpCursor, ScoreType scoreType) throws IllegalSymbolException { State [] states = getStates(); int stateCount = states.length; int [][] transitions = getForwardTransitions(); double [][] transitionScore = getForwardTransitionScores(scoreType); // int _index = 0; ... | |
char [] emptyLine = new char [80]; | public void addSymbols(Alphabet alpha, Symbol [] syms, int start, int length) throws IllegalAlphabetException { int aCount = 0; int cCount = 0; int gCount = 0; int tCount = 0; int oCount = 0; int end = start + length - 1; for (int i = start; i <= end; i++) { char c = syms[i].getTo... | |
Contract.pre(queryStrand != null, "queryStrand was null"); Contract.pre(subjectStrand != null, "subjectStrand was null"); | public SimpleSeqSimilaritySearchSubHit(double score, double eValue, double pValue, int queryStart, int queryEnd, Strand queryStrand, int subjectStart, int subjectEnd, Strand subjectStran... | |
throw new IllegalAlphabetException(); | throw new IllegalAlphabetException( "Unable to find CrossProduct residue for " + l + " in alphabet " + getName() ); | public CrossProductResidue getResidue(List l) throws IllegalAlphabetException { gopher.l = l; CrossProductResidue r = (CrossProductResidue) ourResidues.get(gopher); if (r == null) { throw new IllegalAlphabetException(); } return r; } |
int end) | int length) | public void characters(char[] ch, int start, int end) throws SAXException { } |
if(pos > symList.size()) { | if(pos > symList.length()) { | public int end() { if(pos == 0) { throw new IllegalStateException("Can't call end() before find()"); } if(pos > symList.size()) { throw new IllegalStateException("Can't call end() after find() has returned false"); } return pos + length - 1; } |
pos = symList.size() + 1; | pos = symList.length() + 1; | public boolean find() { try { // are we doing the 1st find? if(pos == 0) { // can't find an n-long sub-sequence of a <n-long super-sequence if(length > symList.length()) { return false; } // getting the initial counts for(int i = 1; i <= length; i++) { ... |
if(pos > symList.size()) { | if(pos > symList.length()) { | public SymbolList group() { if(pos == 0) { throw new IllegalStateException("Can't call group() before find()"); } if(pos > symList.size()) { throw new IllegalStateException("Can't call group() after find() has returned false"); } return symList.subList(pos, pos + length - 1); } |
if(pos > symList.size()) { | if(pos > symList.length()) { | public int start() { if(pos == 0) { throw new IllegalStateException("Can't call start() before find()"); } if(pos > symList.size()) { throw new IllegalStateException("Can't call start() after find() has returned false"); } return pos; } |
public SimpleXMLEmitter(boolean flag) | public SimpleXMLEmitter() | public SimpleXMLEmitter(boolean flag) { oXMLWriter = new BaseXMLWriter(); tEmitQNames = true; setEmitQNames(flag); System.out.println("<?xml version=\"1.0\"?>"); } |
setEmitQNames(flag); | public SimpleXMLEmitter(boolean flag) { oXMLWriter = new BaseXMLWriter(); tEmitQNames = true; setEmitQNames(flag); System.out.println("<?xml version=\"1.0\"?>"); } | |
StrandedFeature.Template t = new StrandedFeature.Template(); | RestrictionSite.Template t = new RestrictionSite.Template(); | public void run() { SymbolListCharSequence charSeq = new SymbolListCharSequence(target); try { Pattern [] patterns = RestrictionEnzymeManager.getPatterns(enzyme); String name = enzyme.getName(); int siteLen = enzyme.getRecognitionSite().length(); i... |
t.enzyme = enzyme; | public void run() { SymbolListCharSequence charSeq = new SymbolListCharSequence(target); try { Pattern [] patterns = RestrictionEnzymeManager.getPatterns(enzyme); String name = enzyme.getName(); int siteLen = enzyme.getRecognitionSite().length(); i... | |
if (accept(property)) { | if (accept(value)) { | public void setProperty(Annotation ann, Object property, Object value) throws ChangeVetoException { if (accept(property)) { ann.setProperty(property, value); } else { throw new ChangeVetoException("Value not accepted"); } } |
this.matches = getInstance().getSubAlphabet(minVal, maxVal); | this.matches = DoubleAlphabet.getSubAlphabet(minVal, maxVal); | protected DoubleRange(double minVal, double maxVal) { this.minVal = minVal; this.maxVal = maxVal; this.matches = getInstance().getSubAlphabet(minVal, maxVal); } |
throw new BioRuntimeException(ex, "Assertion failure: trivial URI manipulation failed"); | throw new BioException(ex, "Assertion failure: trivial URI manipulation failed"); | public DASSequenceDB(URL dataSourceURL) throws BioException { String s = dataSourceURL.toString(); if (! (s.endsWith("/"))) { try { dataSourceURL = new URL(s + "/"); } catch (MalformedURLException ex) { throw new BioRuntimeException(ex, "Assertion failure: trivial URI manipulation failed"); } } t... |
int lead = (int) (leadingPixles / src.getScale()); int trail = (int) (trailingPixles / src.getScale()); | protected List doLayer(SequenceRenderContext src, FeatureFilter filt) { FeatureHolder features = src.getFeatures(); List layers = new ArrayList(); List layerLocs = new ArrayList(); for( Iterator fi = features.filter( filt, false ).features(); fi.hasNext(); ) { Feature f =... | |
if(!fLoc.isContiguous()) { fLoc = new RangeLocation(fLoc.getMin(), fLoc.getMax()); } | fLoc = new RangeLocation(fLoc.getMin() - lead, fLoc.getMax() + trail); | protected List doLayer(SequenceRenderContext src, FeatureFilter filt) { FeatureHolder features = src.getFeatures(); List layers = new ArrayList(); List layerLocs = new ArrayList(); for( Iterator fi = features.filter( filt, false ).features(); fi.hasNext(); ) { Feature f =... |
public SequenceRendererWrapper(SequenceRenderer renderer) { this.renderer = renderer; } | public SequenceRendererWrapper() {} | public SequenceRendererWrapper(SequenceRenderer renderer) { this.renderer = renderer; } |
dotStates.add(0, state); | dotStates.add(state); | public static State[] stateList(MarkovModel mm) throws IllegalResidueException, IllegalTransitionException { Alphabet alpha = mm.stateAlphabet(); List emissionStates = new ArrayList(); HMMOrderByTransition comp = new HMMOrderByTransition(mm); List dotStates = new LinkedList(); for (Iterator addStates = alpha.res... |
public void addFeatureProperty(final Object key, final Object value) | public void addFeatureProperty(Object key, Object value) | public void addFeatureProperty(final Object key, final Object value) throws ParseException { // There are 19 spaces in the leader String leader = "FT "; // Don't print internal data structures if (key.equals(Feature.PROPERTY_DATA_KEY)) return; // The value may be... |
qb.setLength(0); ub.setLength(0); StringBuffer fb = formatQualifierBlock(qb, formatQualifier(ub, key, vi.next()).toString(), leader, 80); | qb.setLength(0); ub.setLength(0); StringBuffer fb = formatQualifierBlock(qb, formatQualifier(ub, key, vi.next()).substring(0), leader, 80); | public void addFeatureProperty(final Object key, final Object value) throws ParseException { // There are 19 spaces in the leader String leader = "FT "; // Don't print internal data structures if (key.equals(Feature.PROPERTY_DATA_KEY)) return; // The value may be... |
StringBuffer fb = formatQualifierBlock(qb, formatQualifier(ub, key, value).toString(), leader, 80); | StringBuffer fb = formatQualifierBlock(qb, formatQualifier(ub, key, value).substring(0), leader, 80); | public void addFeatureProperty(final Object key, final Object value) throws ParseException { // There are 19 spaces in the leader String leader = "FT "; // Don't print internal data structures if (key.equals(Feature.PROPERTY_DATA_KEY)) return; // The value may be... |
public void addSequenceProperty(final Object key, final Object value) | public void addSequenceProperty(Object key, Object value) | public void addSequenceProperty(final Object key, final Object value) throws ParseException { if (key.equals("ID")) { idb.setLength(0); idb.append("ID " + (String) value); } else if (key.equals("DT") || key.equals("MDAT")) { dtb = new StringBuffer(se... |
public void addSymbols(final Alphabet alpha, final Symbol [] syms, final int start, final int length) | public void addSymbols(Alphabet alpha, Symbol [] syms, int start, int length) | 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... |
for (int i = start; i <= end; i++) { char c = dnaTokenization.tokenizeSymbol(syms[i]).charAt(0); | switch (c) { case 'a': case 'A': aCount++; break; case 'c': case 'C': cCount++; break; case 'g': case 'G': gCount++; break; case 't': case 'T': tCount++; break; | 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... |
switch (c) { case 'a': case 'A': aCount++; break; case 'c': case 'C': cCount++; break; case 'g': case 'G': gCount++; break; case 't': case 'T': tCount++; break; default: oCount++; } } | default: oCount++; } } | 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... |
Arrays.fill(lineLens, 60); lineLens[lineCount - 1] = partLine; | Arrays.fill(lineLens, 60); | 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... |
char [] emptyLine = new char [80]; | if (partLine > 0) lineLens[lineCount - 1] = partLine; | 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... |
for (int i = 0; i < lineLens.length; i++) { sq.setLength(0); ub.setLength(0); | char [] emptyLine = new char [80]; | 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... |
int len = lineLens[i]; | for (int i = 0; i < lineLens.length; i++) { sq.setLength(0); ub.setLength(0); | 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... |
Arrays.fill(emptyLine, ' '); sq.append(emptyLine); | int len = lineLens[i]; | 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... |
Symbol [] sa = new Symbol [len]; | Arrays.fill(emptyLine, ' '); sq.append(emptyLine); | 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... |
System.arraycopy(syms, start + (i * 60), sa, 0, len); | Symbol [] sa = new Symbol [len]; | 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... |
String blocks = (formatTokenBlock(ub, sa, 10, dnaTokenization)).toString(); | System.arraycopy(syms, start + (i * 60), sa, 0, len); | 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... |
sq.replace(5, blocks.length() + 5, blocks); | String blocks = (formatTokenBlock(ub, sa, 10, dnaTokenization)).toString(); | 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... |
String count = Integer.toString((i * 60) + len); sq.replace((80 - count.length()), 80, count); | sq.replace(5, blocks.length() + 5, blocks); | 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... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.