rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k |
|---|---|---|
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testCircularBoundedPointRangedPointRangedLocationGenbank() { String expected = "<94..(200.250)"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mCircularBoundedPointRangedPointRangedLocation, PLUS).toString(); this.assertEquals(expected, actual); ... |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testCircularBoundedRangedLocationGenbank() { String expected = "<345..500"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mCircularBoundedRangedLocation, PLUS).toString(); this.assertEquals(expected, actual); } |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testCircularRangedPointRangedPointRangedLocationGenbank() { String expected = "(122.133)..(204.221)"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mCircularRangedPointRangedPointRangedLocation, PLUS).toString(); this.assertEquals(expected, actua... |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testCircularRangedPointSimplePointRangedLocationGenbank() { String expected = "(23.45)..600"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mCircularRangedPointSimplePointRangedLocation, PLUS).toString(); this.assertEquals(expected, actual); } |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testCircularSimpleRangedLocationGenbank() { String expected = "340..565"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mCircularSimpleRangedLocation, PLUS).toString(); this.assertEquals(expected, actual); } |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testComplementBoundedPointLocationGenbank() { String expected = "complement(>12)"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mBoundedPointLocation, MINUS).toString(); this.assertEquals(expected, actual); } |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testComplementBoundedPointRangedPointRangedLocationGenbank() { String expected = "complement(<94..(200.250))"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mBoundedPointRangedPointRangedLocation, MINUS).toString(); this.assertEquals(expected, ac... |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testComplementBoundedRangedLocationGenbank() { String expected = "complement(<345..500)"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mBoundedRangedLocation, MINUS).toString(); this.assertEquals(expected, actual); } |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testComplementCircularBoundedPointRangedPointRangedLocationGenbank() { String expected = "complement(<94..(200.250))"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mCircularBoundedPointRangedPointRangedLocation, MINUS).toString(); this.assertEqu... |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testComplementCircularBoundedRangedLocationGenbank() { String expected = "complement(<345..500)"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mCircularBoundedRangedLocation, MINUS).toString(); this.assertEquals(expected, actual); } |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testComplementCircularRangedPointRangedPointRangedLocationGenbank() { String expected = "complement((122.133)..(204.221))"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mCircularRangedPointRangedPointRangedLocation, MINUS).toString(); this.asser... |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testComplementCircularRangedPointSimplePointRangedLocationGenbank() { String expected = "complement((23.45)..600)"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mCircularRangedPointSimplePointRangedLocation, MINUS).toString(); this.assertEquals(... |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testComplementCircularSimpleRangedLocationGenbank() { String expected = "complement(340..565)"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mCircularSimpleRangedLocation, MINUS).toString(); this.assertEquals(expected, actual); } |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testComplementRangedPointLocationGenbank() { String expected = "complement((102.110))"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mRangedPointLocation, MINUS).toString(); this.assertEquals(expected, actual); } |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testComplementRangedPointRangedPointRangedLocationGenbank() { String expected = "complement((122.133)..(204.221))"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mRangedPointRangedPointRangedLocation, MINUS).toString(); this.assertEquals(expected... |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testComplementRangedPointSimplePointRangedLocationGenbank() { String expected = "complement((23.45)..600)"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mRangedPointSimplePointRangedLocation, MINUS).toString(); this.assertEquals(expected, actual... |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testComplementSimplePointLocationGenbank() { String expected = "complement(467)"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mSimplePointLocation, MINUS).toString(); this.assertEquals(expected, actual); } |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testComplementSimpleRangedLocationGenbank() { String expected = "complement(340..565)"; sb.delete(0, sb.length() ); String actual = fileFormer.formatLocation(sb, mSimpleRangedLocation, MINUS).toString(); this.assertEquals(expected, actual); } |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testRangedPointLocationGenbank() { String expected = "(102.110)"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mRangedPointLocation, PLUS).toString(); this.assertEquals(expected, actual); } |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testRangedPointRangedPointRangedLocationGenbank() { String expected = "(122.133)..(204.221)"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mRangedPointRangedPointRangedLocation, PLUS).toString(); this.assertEquals(expected, actual); } |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testRangedPointSimplePointRangedLocationGenbank() { String expected = "(23.45)..600"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mRangedPointSimplePointRangedLocation, PLUS).toString(); this.assertEquals(expected, actual); } |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testSimplePointLocationGenbank() { String expected = "467"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mSimplePointLocation, PLUS).toString(); this.assertEquals(expected, actual); } |
this.assertEquals(expected, actual); | assertEquals(expected, actual); | public void testSimpleRangedLocationGenbank() { String expected = "340..565"; sb.delete(0, sb.length()); String actual = fileFormer.formatLocation(sb, mSimpleRangedLocation, PLUS).toString(); this.assertEquals(expected, actual); } |
return u; | return RNATools.u(); | public Symbol translate(Symbol s) throws IllegalSymbolException { if(s == DNATools.t()) { return u; } DNATools.getDNA().validate(s); return s; } |
if(s == u) { | if(s == RNATools.u()) { | public Symbol untranslate(Symbol s) throws IllegalSymbolException { if(s == u) { return DNATools.t(); } rna.validate(s); return s; } |
rna.validate(s); | RNATools.getRNA().validate(s); | public Symbol untranslate(Symbol s) throws IllegalSymbolException { if(s == u) { return DNATools.t(); } rna.validate(s); return s; } |
assert(LocationTools.areEqual(r1, r1)); assert(LocationTools.areEqual(r1, new PointLocation(1))); | assertTrue(LocationTools.areEqual(r1, r1)); assertTrue(LocationTools.areEqual(r1, new PointLocation(1))); | public void testAreEqual() { assert(LocationTools.areEqual(r1, r1)); assert(LocationTools.areEqual(r1, new PointLocation(1))); } |
assert(LocationTools.contains(r1, new PointLocation(1))); assert(! LocationTools.contains(r1, r2)); | assertTrue(LocationTools.contains(r1, new PointLocation(1))); assertTrue(! LocationTools.contains(r1, r2)); | public void testContains() { assert(LocationTools.contains(r1, new PointLocation(1))); assert(! LocationTools.contains(r1, r2)); assert(r1.contains(1)); assert(! r1.contains(2)); } |
assert(r1.contains(1)); assert(! r1.contains(2)); | assertTrue(r1.contains(1)); assertTrue(! r1.contains(2)); | public void testContains() { assert(LocationTools.contains(r1, new PointLocation(1))); assert(! LocationTools.contains(r1, r2)); assert(r1.contains(1)); assert(! r1.contains(2)); } |
assert(r1.isContiguous()); | assertTrue(r1.isContiguous()); | public void testIsContiguous() { assert(r1.isContiguous()); } |
assert(LocationTools.overlaps(r1, r1)); assert(! LocationTools.overlaps(r1, r2)); | assertTrue(LocationTools.overlaps(r1, r1)); assertTrue(! LocationTools.overlaps(r1, r2)); | public void testOverlaps() { assert(LocationTools.overlaps(r1, r1)); assert(! LocationTools.overlaps(r1, r2)); } |
assertTrue(before.compareTo(ref) < 1); assertTrue(ref.compareTo(before) > 1); | assertTrue(before.compareTo(ref) < 0); assertTrue(ref.compareTo(before) > 0); | public void testCompareTo() { System.out.println("testCompareTo"); DocRef before = new SimpleDocRef(authors, "A", title); assertTrue(before.compareTo(ref) < 1); assertTrue(ref.compareTo(before) > 1); before = new SimpleDocRef(Collections.singletonList( new S... |
assertNull(ref.getTitle()); | assertEquals(this.title ,ref.getTitle()); | public void testGetTitle() { System.out.println("testGetTitle"); //should be null until set assertNull(ref.getTitle()); } |
if (context.getDirection() == context.HORIZONTAL) | if (context.getDirection() == SequenceRenderContext.HORIZONTAL) | public void renderImageMap(Graphics2D g2, Feature f, SequenceRenderContext context) { Rectangle bounds = g2.getDeviceConfiguration().getBounds(); // Safe to cast as bounds come from raster int ma... |
builder.startDB(); builder.startGroup(); inDB = inGroup = true; | public static void instantiateDB(URL url, HomologeneBuilder builder) throws OperationNotSupportedException, FileNotFoundException, IOException { boolean inDB = false; boolean inGroup = false; if (!url.getProtocol().equals("file")) throw new OperationNotSupportedException();... | |
Pattern orthoPattern = Pattern.compile("^\\s*(\\d+)\\s*\\|\\s*(\\d+)\\s*\\|([Bbc]{1})\\|(.*)\\|\\s*(\\d+)\\s*\\|(.*)\\|(.*)\\|\\s*(\\d+)\\s*\\|(.*)\\|(.*)"); | Pattern orthoPattern = Pattern.compile("^(\\d+)\\s*\\|\\s*(\\d+)\\s*\\|([Bbc]{1})\\|(.*)\\|\\s*(\\d+)\\s*\\|(.*)\\|(.*)\\|\\s*(\\d+)\\s*\\|(.*)\\|(.*)"); | public static void instantiateDB(URL url, HomologeneBuilder builder) throws OperationNotSupportedException, FileNotFoundException, IOException { boolean inDB = false; boolean inGroup = false; if (!url.getProtocol().equals("file")) throw new OperationNotSupportedException();... |
if (inGroup) builder.endGroup(); builder.startGroup(); | if (!inDB) { builder.startDB(); inDB = true; } if (inGroup) { builder.endGroup(); } builder.startGroup(); inGroup = true; | public static void instantiateDB(URL url, HomologeneBuilder builder) throws OperationNotSupportedException, FileNotFoundException, IOException { boolean inDB = false; boolean inGroup = false; if (!url.getProtocol().equals("file")) throw new OperationNotSupportedException();... |
if (!inDB) { builder.startDB(); inDB = true; } if (!inGroup) { builder.startGroup(); inGroup = true; } | public static void instantiateDB(URL url, HomologeneBuilder builder) throws OperationNotSupportedException, FileNotFoundException, IOException { boolean inDB = false; boolean inGroup = false; if (!url.getProtocol().equals("file")) throw new OperationNotSupportedException();... | |
nfe.printStackTrace(); | public static void instantiateDB(URL url, HomologeneBuilder builder) throws OperationNotSupportedException, FileNotFoundException, IOException { boolean inDB = false; boolean inGroup = false; if (!url.getProtocol().equals("file")) throw new OperationNotSupportedException();... | |
System.err.println("Removed old feature: " + feature); | public void testEditFeatures() throws Exception { String name = "dna_1"; Sequence seq = DNATools.createDNASequence("atgctgatgatgatg", name); assertTrue(!mSequenceDB.ids().contains(name)); mSequenceDB.addSequence(seq); assertTrue(mSequenceDB.ids().contains(name)); seq = mSeq... | |
ops = Collections.EMPTY_SET; | if(nodes.contains(arc.from) && nodes.contains(arc.to)) { ops = Collections.EMPTY_SET; } else { throw new NullPointerException("Can't find data for arc: " + arc); } | public Set getOperations(Arc arc) { Set ops = (Set) operationsToLabel.get(arc); if(ops == null) { ops = Collections.EMPTY_SET; } return ops; } |
String altLoc = line.substring (16, 17); | private void pdb_ATOM_Handler(String line) throws PDBParseException { //System.out.println(line); String recordName = line.substring (0, 6).trim (); // create new atom AtomImpl atom = new AtomImpl() ; int pdbnumber = Integer.parseInt (line.substring (6, 11)... | |
this.translation = temp.location.getMin() - temp.componentLocation.getMin(); this.projectedFeatures = new ProjectedFeatureHolder(componentSequence, this, translation); | if (temp.strand == StrandedFeature.NEGATIVE) { this.translation = temp.location.getMax() - temp.componentLocation.getMin() + 1; this.projectedFeatures = new ProjectedFeatureHolder(componentSequence, this, translation, true); } else if (temp.strand == StrandedFeature.POSITIVE) { this.translation = temp.location.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."); } t... |
private String getAlphabetName() { return (this.symList==SymbolList.EMPTY_LIST?null:this.getAlphabetName()); } | private String getAlphabetName() { return (this.symList==SymbolList.EMPTY_LIST?null:this.symList.getAlphabet().getName()); } | private String getAlphabetName() { return (this.symList==SymbolList.EMPTY_LIST?null:this.getAlphabetName()); } |
SequenceFormat eFormat = new EmblFormat(); | SequenceFormat eFormat = new EmblLikeFormat(); | public static void main(String [] args) throws Exception { if(args.length != 3) { throw new Exception("Use: EmblToGffFasta emblFile fastaOut gffOut"); } try { // make the files early to get exceptions about stupid file names File emblFile = new File(args[0]); File fastaFile = new File... |
SequenceFactory sFact = new SimpleSequenceFactory(); | SequenceBuilderFactory sFact = new EmblProcessor.Factory(SimpleSequenceBuilder.FACTORY); | public static void main(String [] args) throws Exception { if(args.length != 3) { throw new Exception("Use: EmblToGffFasta emblFile fastaOut gffOut"); } try { // make the files early to get exceptions about stupid file names File emblFile = new File(args[0]); File fastaFile = new File... |
sym = new SimpleAtomicSymbol(token.charAt(0), token, null); | sym = AlphabetManager.createSymbol(token.charAt(0), token, null); | public SymbolParser getParser(String name) throws NoSuchElementException { if(name.equals("name")) { return new NameParser(nameToSymbol) { public Symbol parseToken(String token) throws IllegalSymbolException { Symbol sym = (Symbol) nameToSymbol.get(token); if(sym == null) { ... |
s = new SimpleAtomicSymbol(c, token, null); | s = AlphabetManager.createSymbol(c, token, null); | public SymbolParser getParser(String name) throws NoSuchElementException { if(name.equals("name")) { return new NameParser(nameToSymbol) { public Symbol parseToken(String token) throws IllegalSymbolException { Symbol sym = (Symbol) nameToSymbol.get(token); if(sym == null) { ... |
sym = new SimpleAtomicSymbol(token.charAt(0), token, null); | sym = AlphabetManager.createSymbol(token.charAt(0), token, null); | public Symbol parseToken(String token) throws IllegalSymbolException { Symbol sym = (Symbol) nameToSymbol.get(token); if(sym == null) { sym = new SimpleAtomicSymbol(token.charAt(0), token, null); try { addSymbol(sym); } catch (ChangeVetoException c... |
s = new SimpleAtomicSymbol(c, token, null); | s = AlphabetManager.createSymbol(c, token, null); | public Symbol parseToken(String token) throws IllegalSymbolException { char c = token.charAt(0); Character ch = new Character(c); Symbol s = (Symbol) tokenToSymbol.get(ch); if(s == null) { s = new SimpleAtomicSymbol(c, token, null); try { ... |
tokenSeed++, ""+tokenSeed, Annotation.EMPTY_ANNOTATION, s, this | tokenSeed++, Annotation.EMPTY_ANNOTATION, s, this | private AtomicSymbol putSymbol(List s) { AtomicSymbol ss; if(parent != null) { try { ss = (AtomicSymbol) parent.getSymbol(s); } catch (IllegalSymbolException ise) { throw new BioError(ise, "Balls up - couldn't fetch symbol from parent"); } } else { try { ss = (AtomicS... |
PaymentItem p1 = new PaymentItem(); | /*PaymentItem p1 = new PaymentItem(); | public Collection getPaymentItems(String communeNumber, String personalId, String endpoint) { Collection c = new Vector(); PaymentItem p1 = new PaymentItem(); p1.setName("Test type"); p1.setAmount(100.0d); p1.setEntryTypeId(1); p1.setLastDate(new IWTimestamp()); c.add(p1); return c; /* if (endpoint == ... |
return c; | return c;*/ | public Collection getPaymentItems(String communeNumber, String personalId, String endpoint) { Collection c = new Vector(); PaymentItem p1 = new PaymentItem(); p1.setName("Test type"); p1.setAmount(100.0d); p1.setEntryTypeId(1); p1.setLastDate(new IWTimestamp()); c.add(p1); return c; /* if (endpoint == ... |
/* | public Collection getPaymentItems(String communeNumber, String personalId, String endpoint) { Collection c = new Vector(); PaymentItem p1 = new PaymentItem(); p1.setName("Test type"); p1.setAmount(100.0d); p1.setEntryTypeId(1); p1.setLastDate(new IWTimestamp()); c.add(p1); return c; /* if (endpoint == ... | |
return c;*/ | return c; | public Collection getPaymentItems(String communeNumber, String personalId, String endpoint) { Collection c = new Vector(); PaymentItem p1 = new PaymentItem(); p1.setName("Test type"); p1.setAmount(100.0d); p1.setEntryTypeId(1); p1.setLastDate(new IWTimestamp()); c.add(p1); return c; /* if (endpoint == ... |
StatementItem s1 = new StatementItem(); | /* StatementItem s1 = new StatementItem(); | public Collection getStatementItems(String communeNumber, String personalId, PaymentItem pType, IWTimestamp fromStamp, IWTimestamp toStamp, String endpoint) { Collection c = new Vector(); StatementItem s1 = new StatementItem(); s1.setName("Statement type 1"); s1.setAmount(50.0d); s1.setLastDate(new IWTimestam... |
return c; | return c;*/ | public Collection getStatementItems(String communeNumber, String personalId, PaymentItem pType, IWTimestamp fromStamp, IWTimestamp toStamp, String endpoint) { Collection c = new Vector(); StatementItem s1 = new StatementItem(); s1.setName("Statement type 1"); s1.setAmount(50.0d); s1.setLastDate(new IWTimestam... |
/*if (endpoint == null) { | if (endpoint == null) { | public Collection getStatementItems(String communeNumber, String personalId, PaymentItem pType, IWTimestamp fromStamp, IWTimestamp toStamp, String endpoint) { Collection c = new Vector(); StatementItem s1 = new StatementItem(); s1.setName("Statement type 1"); s1.setAmount(50.0d); s1.setLastDate(new IWTimestam... |
return c;*/ | return c; | public Collection getStatementItems(String communeNumber, String personalId, PaymentItem pType, IWTimestamp fromStamp, IWTimestamp toStamp, String endpoint) { Collection c = new Vector(); StatementItem s1 = new StatementItem(); s1.setName("Statement type 1"); s1.setAmount(50.0d); s1.setLastDate(new IWTimestam... |
if (this.taxon!=null) throw new ParseException("Current BioEntry already has a taxon"); | if (this.taxon!=null){ if(! this.taxon.equals(taxon)){ throw new ParseException("Current BioEntry already has a taxon"); } return; } | public void setTaxon(NCBITaxon taxon) throws ParseException { if (taxon==null) throw new ParseException("Taxon cannot be null"); if (this.taxon!=null) throw new ParseException("Current BioEntry already has a taxon"); this.taxon = taxon; } |
invalid=invalid==null?null:invalid; | public void testGetEnzyme() { RestrictionEnzyme ecoRI = RestrictionEnzymeManager.getEnzyme("EcoRI"); assertEquals("EcoRI", ecoRI.getName()); try { RestrictionEnzyme invalid = RestrictionEnzymeManager.getEnzyme("xxxx"); } catch (IllegalArgumentException iae) ... | |
invalid=invalid==null?null:invalid; | public void testGetIsoschizomers() { Set isoAvaI = RestrictionEnzymeManager.getIsoschizomers("AvaI"); assertEquals(1, isoAvaI.size()); Set isoAvrI = RestrictionEnzymeManager.getIsoschizomers("AvrI"); assertEquals(1, isoAvrI.size()); RestrictionEnzyme avaI = RestrictionEnzymeMan... | |
String rebaseDataFileName = "/org/biojava/bio/molbio/rebase.dat"; | String rebaseDataFileName = "org/biojava/bio/molbio/rebase.dat"; | public void testloadEnzymeFile() { String rebaseDataFileName = "/org/biojava/bio/molbio/rebase.dat"; InputStream is = getClass().getClassLoader().getResourceAsStream(rebaseDataFileName); RestrictionEnzymeManager.loadEnzymeFile(is,true); Set re = RestrictionEnzymeManager.getAllEnzymes(); ... |
if(properties.containsKey(key)) | if(this.getProperties().containsKey(key)) | public void setProperty(Object key, Object value) throws ChangeVetoException { // This mess is to handle cases where there is already a value associated // with the key. Object newValue; Object oldValue = null; try { if(properties.containsKey(key)) { oldValue = this.getProperty(key); // If the old value is alr... |
String returnFormat = seqURL.getReturnFormat(); | protected URL getAddress(String id) throws MalformedURLException { String defaultReturnFormat = "text"; FetchURL seqURL = new FetchURL(DBName, defaultReturnFormat); String baseurl = seqURL.getbaseURL(); String db = seqURL.getDB(); String returnFormat = seqURL.getReturnFormat(); String url = baseurl ... | |
SequenceFormat sFormat = getSequenceFormat(); SequenceBuilder sbuilder = new SimpleSequenceBuilder(); SequenceBuilderFactory sFact = new GenbankProcessor.Factory( SimpleSequenceBuilder.FACTORY); Alphabet alpha = getAlphabet(); SymbolTokenization rParser = alpha.getTokenization("token"); | public Sequence getSequence(String id) throws BioException { try { IOExceptionFound = false; ExceptionFound = false; URL queryURL = getAddress(id); //achieve URL based on ID // System.err.println("query is "+ queryURL.toString()); SequenceFormat sFormat = getSequenceFormat(); //get incom... | |
} else if (CostMatrix[i][j] == CostMatrix[i-1][j-1] - matchReplace(query, subject, i, j)) { | } else if ((CostMatrix[i][j] == CostMatrix[i-1][j-1] - matchReplace(query, subject, i, j)) && !(gap_extend[0] || gap_extend[1])) { | public double pairwiseAlignment(Sequence query, Sequence subject) throws BioRuntimeException { if (query.getAlphabet().equals(subject.getAlphabet()) && query.getAlphabet().equals(subMatrix.getAlphabet())) { long time = System.currentTimeMillis(); int i, j; this.CostMatrix = new double[query.l... |
} else if (CostMatrix[i][j] == E[i][j]) { | } else if (CostMatrix[i][j] == E[i][j] || gap_extend[0]) { gap_extend[0] = (E[i][j] != CostMatrix[i][j-1] + insert + gapExt); | public double pairwiseAlignment(Sequence query, Sequence subject) throws BioRuntimeException { if (query.getAlphabet().equals(subject.getAlphabet()) && query.getAlphabet().equals(subMatrix.getAlphabet())) { long time = System.currentTimeMillis(); int i, j; this.CostMatrix = new double[query.l... |
gap_extend[1] = (F[i][j] != CostMatrix[i-1][j] + delete + gapExt); | public double pairwiseAlignment(Sequence query, Sequence subject) throws BioRuntimeException { if (query.getAlphabet().equals(subject.getAlphabet()) && query.getAlphabet().equals(subMatrix.getAlphabet())) { long time = System.currentTimeMillis(); int i, j; this.CostMatrix = new double[query.l... | |
if(max > min) throw new IllegalArgumentException("min must be less than max: "+min+" : "+max); | if(max < min) throw new IllegalArgumentException("min must be less than max: "+min+" : "+max); | SubIntegerAlphabet(int min, int max) throws IllegalArgumentException{ if(max > min) throw new IllegalArgumentException("min must be less than max: "+min+" : "+max); this.min = min; this.max = max; for(int i = min; i <= max; i++){ try{ this.addSymbol(new IntegerSymbol(i)); ... |
if(AlphabetManager.alphabetForName(name) == null){ FiniteAlphabet a = new SubIntegerAlphabet(min, max); AlphabetManager.registerAlphabet(a.getName(),a); } | FiniteAlphabet a = new SubIntegerAlphabet(min, max); AlphabetManager.registerAlphabet(a.getName(),a); | public static FiniteAlphabet getSubAlphabet(int min, int max)throws IllegalArgumentException{ String name = "SubIntegerAlphabet["+min+".."+max+"]"; if(AlphabetManager.alphabetForName(name) == null){ FiniteAlphabet a = new SubIntegerAlphabet(min, max); AlphabetManager.registerAlphabet(a.getName(),a); ... |
public SequenceDBSearchHit(String sequenceID, double score, double eValue, double pValue, List subHits, Annotation annotation) | public SequenceDBSearchHit(final String sequenceID, final double score, final double eValue, final double pValue, final List subHits, final Annotation annotation) | public SequenceDBSearchHit(String sequenceID, double score, double eValue, double pValue, List subHits, Annotation annotation) { Contract.pre(sequenceID != null, "sequenceID was null"); Contract.pre(! Double.isNaN(score), "score was NaN"); // pVa... |
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 SequenceDBSearchHit that = (SequenceDBSearchHit) other; if (! Obj... |
idLine = id; | public void setName(String id) throws ParseException { idLine = id; } | |
setIntValue(Integer.parseInt(data.toString())); | setIntValue(Integer.parseInt((data.toString()).trim())); | public void endElement( String nsURI, String localName, String qName, StAXContentHandler handler ) throws SAXException { level--; if (level == 0) { try { setIntValue(Integer.parseInt(data.toString())); } catch (NumberFormatException nfe) { throw new SAXException(nfe); }... |
min = Integer.parseInt(numString.toString()); | if (numString.length() > 0) min = Integer.parseInt(numString.toString()); else min = 0; | private Range getIterations() throws AutomatonException { int min = 0; int max = 0; // consume the left brace toke.getToken(); // there can either be one or two numbers boolean onSecondArg = false; StringBuffer numString = new StringBuffer(); while (... |
toke.getToken(); | Range parseIterations() throws AutomatonException { int tokenType = toke.nextTokenType(); switch (tokenType) { case Tokenizer.LEFT_BRACE: return getIterations(); case Tokenizer.PLUS: toke.getToken(); return new Range(1, Integ... | |
else toke.getToken(); | NfaSubModel parseSubPattern(NfaBuilder delegate) throws AutomatonException { NfaSubModel returnSubModel; // consume the left bracket toke.getToken(); returnSubModel = parse(delegate); // consume the right bracket if (toke.nextTokenType() != Tokenizer.RIGHT_BRACKET... | |
returnSubModel.addTransition(pre, post, sym); returnSubModel.addEpsilonTransition(returnSubModel.getStart(), pre); returnSubModel.addEpsilonTransition(post, returnSubModel.getEnd()); | if (sym instanceof AtomicSymbol) { returnSubModel.addTransition(pre, post, sym); returnSubModel.addEpsilonTransition(returnSubModel.getStart(), pre); returnSubModel.addEpsilonTransition(post, returnSubModel.getEnd()); } else { for (Iterator symI = ((FiniteAlphabet) sym.getMatches()).iterator(); symI.hasNext(); ) { Symb... | NfaSubModel parseSymbol(NfaBuilder delegate) throws AutomatonException { NfaSubModel returnSubModel = new NfaSubModel(delegate); Symbol sym; try { sym = symtoke.parseToken(Character.toString(toke.getToken())); } catch (IllegalSymbolException ise) { ... |
private String getTaxonHiddenChar() { | String getTaxonHiddenChar() { | private String getTaxonHiddenChar() { return isTaxonHidden()?TAXONISHIDDEN:null; } |
private void setNCBITaxID(int NCBITaxID) { this.NCBITaxID = NCBITaxID; } | void setNCBITaxID(int NCBITaxID) { this.NCBITaxID = NCBITaxID; } | private void setNCBITaxID(int NCBITaxID) { this.NCBITaxID = NCBITaxID; } |
private void setNameSet(Set names) { | void setNameSet(Set names) { | private void setNameSet(Set names) { this.names = names; // original for Hibernate // convert set to map this.namesMap.clear(); for (Iterator i = names.iterator(); i.hasNext(); ) { SimpleNCBITaxonName n = (SimpleNCBITaxonName)i.next(); try { this.addN... |
private void setTaxonHiddenChar(final String isHiddenChar) throws ChangeVetoException { | void setTaxonHiddenChar(final String isHiddenChar) throws ChangeVetoException { | private void setTaxonHiddenChar(final String isHiddenChar) throws ChangeVetoException { setTaxonHidden(isHiddenChar!=null || (isHiddenChar!=null && isHiddenChar.length() > 0));// any character will set } |
this.fetchEncoding = fetchEncoding; | public DASSegmentHandler(SeqIOListener siol, String fetchEncoding) { this.siol = siol; this.fetchEncoding = fetchEncoding; } | |
long startFetch = (new Date()).getTime(); | public void runFetch() throws BioException, ParseException { // get time long startFetch = (new Date()).getTime(); DAS.startedActivity(this); URL fURL = null; try { String fetchEncoding = "dasgff"; if (DASCapabilities.checkCapable(new URL(dataSource, "../"), DASCapabilities.CAPABIL... | |
while (!reachedEnd && parseStart < bytesRead) { | while (!reachedEnd && parseStart < bytesRead && cache[parseStart] != '>') { | private boolean readSequenceData(BufferedReader r, SymbolParser parser, SeqIOListener listener) throws IOException, IllegalSymbolException { char[] cache = new char[256]; boolean reachedEnd = false, seenEOF = false; StreamParser sparser = parser.parseStream(listener); while (!reachedEnd) ... |
if (parseStart < bytesRead && cache[parseStart] == '>') { r.reset(); if (r.skip(parseStart) != parseStart) throw new IOException("Couldn't reset to start of next sequence"); reachedEnd = true; } | } if (parseStart < bytesRead && cache[parseStart] == '>') { r.reset(); if (r.skip(parseStart) != parseStart) throw new IOException("Couldn't reset to start of next sequence"); reachedEnd = true; | private boolean readSequenceData(BufferedReader r, SymbolParser parser, SeqIOListener listener) throws IOException, IllegalSymbolException { char[] cache = new char[256]; boolean reachedEnd = false, seenEOF = false; StreamParser sparser = parser.parseStream(listener); while (!reachedEnd) ... |
public ProjectedFeatureHolder(FeatureHolder fh, | public ProjectedFeatureHolder(FeatureHolder fh, FeatureFilter filter, | public ProjectedFeatureHolder(FeatureHolder fh, FeatureHolder parent, int translation, boolean oppositeStrand) { this.wrapped = fh; this.parent = parent; this.translate = translation; this.oppositeStrand = oppositeStrand; underlyingFeaturesChange = new ChangeListener() { public void preChan... |
this.filter = filter; | public ProjectedFeatureHolder(FeatureHolder fh, FeatureHolder parent, int translation, boolean oppositeStrand) { this.wrapped = fh; this.parent = parent; this.translate = translation; this.oppositeStrand = oppositeStrand; underlyingFeaturesChange = new ChangeListener() { public void preChan... | |
return wrapped.countFeatures(); | return getProjectedFeatures().countFeatures(); | public int countFeatures() { return wrapped.countFeatures(); } |
for (Iterator i = wrapped.features(); i.hasNext(); ) { | for (Iterator i = toProject.features(); i.hasNext(); ) { | protected FeatureHolder getProjectedFeatures() { if (projectedFeatures == null) { SimpleFeatureHolder sfh = new SimpleFeatureHolder(); for (Iterator i = wrapped.features(); i.hasNext(); ) { Feature f = (Feature) i.next(); Feature wf = projectFeature(f); try { sfh.addFeature(wf); } catch (ChangeVeto... |
System.err.println("*** Generating " + pclass.getName()); | private static Class getProjectionClass(Class face) { Class projection = (Class) _projectionClasses.get(face); if (projection == null) { try { Class baseClass = ProjectedFeatureWrapper.class; if (StrandedFeature.class.isAssignableFrom(face)) baseClass = ProjectedStrandedFeatureWrapper.class; StringTok... | |
Annotation oba = annf.makeAnnotation(matrix) ; | Annotation oba = AnnotationFactory.makeAnnotation(matrix) ; | private void MATRIXhandler(Attributes atts) { HashMap matrix = new HashMap() ; //String intObjectId = atts.getValue("intObjectId"); matrix.put("intObjectId" ,intObjectId); for ( int x=1; x<=3; x++){ for ( int y=1; y<=3; y++){ String mat = "mat"+x+y... |
Annotation s = annf.makeAnnotation(score); | Annotation s = AnnotationFactory.makeAnnotation(score); | private void SCOREhandler(Attributes atts) { System.out.println("SCOREhandler not implemented,yet..."); HashMap score = new HashMap() ; String metnam = atts.getValue("methodName"); String value = atts.getValue("value"); score.put("methodName",metnam); score... |
Annotation oba = annf.makeAnnotation(vector) ; | Annotation oba = AnnotationFactory.makeAnnotation(vector) ; | private void VECTORhandler(Attributes atts) { //System.out.println("VECTORhandler"); //String intObjectId = atts.getValue("intObjectId"); String xs = atts.getValue("x"); String ys = atts.getValue("y"); String zs = atts.getValue("z"); AtomImpl atom = new AtomImp... |
Annotation oba = annf.makeAnnotation(current_object) ; | Annotation oba = AnnotationFactory.makeAnnotation(current_object) ; | public void endElement (String uri, String name, String qName){ //System.out.println("endElement >" + qName + "< >" + name + "<") ; if (qName.equals("geo3D")) { intObjectId = null ; } if (qName.equals("alignObject")) { try { Annotation oba = ... |
Annotation sega = annf.makeAnnotation(current_segment); | Annotation sega = AnnotationFactory.makeAnnotation(current_segment); | public void endElement (String uri, String name, String qName){ //System.out.println("endElement >" + qName + "< >" + name + "<") ; if (qName.equals("geo3D")) { intObjectId = null ; } if (qName.equals("alignObject")) { try { Annotation oba = ... |
Annotation bloa = annf.makeAnnotation(current_block); | Annotation bloa = AnnotationFactory.makeAnnotation(current_block); | public void endElement (String uri, String name, String qName){ //System.out.println("endElement >" + qName + "< >" + name + "<") ; if (qName.equals("geo3D")) { intObjectId = null ; } if (qName.equals("alignObject")) { try { Annotation oba = ... |
Annotation a = annf.makeAnnotation(detail); | Annotation a = AnnotationFactory.makeAnnotation(detail); | public void endElement (String uri, String name, String qName){ //System.out.println("endElement >" + qName + "< >" + name + "<") ; if (qName.equals("geo3D")) { intObjectId = null ; } if (qName.equals("alignObject")) { try { Annotation oba = ... |
in.mark(120); | in.mark(MAX_LINELENGTH); | public Sequence readSequence(StreamReader.Context context, SymbolParser resParser, SequenceFactory sf) throws IllegalSymbolException, IOException { final BufferedReader in = context.getReader(); StringBuffer sb = new StringBuffer(); String l... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.