rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k |
|---|---|---|
alpha = am.alphabetForName("RNA"); | alpha = am.getGappedAlphabet(am.alphabetForName("RNA")); | public SymbolListAdapter(AnonymousSeq anonymousSeq) throws IllegalAlphabetException, IllegalSymbolException, BioException { AlphabetManager am = AlphabetManager.instance(); Alphabet alpha = null; SeqType type = anonymousSeq.type(); if(type == SeqType.DNA) { alpha = am.alphabetForName("DNA"); } el... |
alpha = am.alphabetForName("PROTEIN"); | alpha = am.getGappedAlphabet(ProteinTools.getXAlphabet()); | public SymbolListAdapter(AnonymousSeq anonymousSeq) throws IllegalAlphabetException, IllegalSymbolException, BioException { AlphabetManager am = AlphabetManager.instance(); Alphabet alpha = null; SeqType type = anonymousSeq.type(); if(type == SeqType.DNA) { alpha = am.alphabetForName("DNA"); } el... |
FiniteAlphabet aaAlfa = ProteinTools.getTAlphabet(); | private void preparePrefsByResidue() throws IllegalSymbolException { try { codonPrefByResidue = new HashMap(); // what we want is to create residue-specific distributions FiniteAlphabet aaAlfa = ProteinTools.getTAlphabet(); for (Iterator residueI = Protei... | |
FiniteAlphabet aaAlfa = ProteinTools.getTAlphabet(); | private void preparePrefsByWobble() throws IllegalSymbolException { try { wobbleDistributions = new HashMap(); // what we want is to create residue-specific distributions FiniteAlphabet aaAlfa = ProteinTools.getTAlphabet(); FiniteAlphabet nonWobbleAlfa = ... | |
if (! (s.startsWith("BLAST") || s.startsWith("TBLAST"))) | String program = context.getProgram().toUpperCase(); if (program.indexOf("BLAST") == -1 ) | private void setStringValue(String s) throws SAXException { // Check that we are dealing with Blast output if (! (s.startsWith("BLAST") || s.startsWith("TBLAST"))) return; StringTokenizer st = new StringTokenizer(s); String query = null; String database = null; ... |
StringTokenizer st = new StringTokenizer(s); | StringTokenizer st = new StringTokenizer(s.trim()); | private void setStringValue(String s) throws SAXException { // Check that we are dealing with Blast output if (! (s.startsWith("BLAST") || s.startsWith("TBLAST"))) return; StringTokenizer st = new StringTokenizer(s); String query = null; String database = null; ... |
for(int i = 1; i <= gl.length(); i++) { System.out.println(gl.viewToSource(i)); } | public static void main(String [] args) { try { SymbolList res = Tools.createSymbolList(10); final int trials = 10; System.out.println("Starting with:\n" + res.seqString()); GappedSymbolList gl = new GappedSymbolList(res); System.out.println("Gapped version:\n" + gl.seqString()); gl.dumpBlock... | |
this.symbols = new ArrayList(); | protected GenbankContext(SymbolTokenization theSymbolParser, SeqIOListener theListener) { this.symbols = new ArrayList(); this.status = HEADER; this.listener = theListener; this.symParser = theSymbolParser; this.streamParser = symParser.parseStream(listener); if (this.listener instanceof ParseErro... | |
assert(LocationTools.areEqual(r1, r1)); assert(LocationTools.areEqual(r1, new RangeLocation(1, 100))); | assertTrue(LocationTools.areEqual(r1, r1)); assertTrue(LocationTools.areEqual(r1, new RangeLocation(1, 100))); | public void testAreEqual() { assert(LocationTools.areEqual(r1, r1)); assert(LocationTools.areEqual(r1, new RangeLocation(1, 100))); } |
assert(LocationTools.contains(r3, r4)); assert(! LocationTools.contains(r4, r3)); | assertTrue(LocationTools.contains(r3, r4)); assertTrue(! LocationTools.contains(r4, r3)); | public void testContains() { assert(LocationTools.contains(r3, r4)); assert(! LocationTools.contains(r4, r3)); assert(r1.contains(1)); assert(r1.contains(100)); assert(! r1.contains(101)); } |
assert(r1.contains(1)); assert(r1.contains(100)); assert(! r1.contains(101)); | assertTrue(r1.contains(1)); assertTrue(r1.contains(100)); assertTrue(! r1.contains(101)); | public void testContains() { assert(LocationTools.contains(r3, r4)); assert(! LocationTools.contains(r4, r3)); assert(r1.contains(1)); assert(r1.contains(100)); assert(! r1.contains(101)); } |
assert(LocationTools.overlaps(r1, r1)); assert(LocationTools.overlaps(r2, r2)); assert(LocationTools.overlaps(r1, r2)); assert(LocationTools.overlaps(r2, r1)); | assertTrue(LocationTools.overlaps(r1, r1)); assertTrue(LocationTools.overlaps(r2, r2)); assertTrue(LocationTools.overlaps(r1, r2)); assertTrue(LocationTools.overlaps(r2, r1)); | public void testOverlaps() { assert(LocationTools.overlaps(r1, r1)); assert(LocationTools.overlaps(r2, r2)); assert(LocationTools.overlaps(r1, r2)); assert(LocationTools.overlaps(r2, r1)); assert(! LocationTools.overlaps(r1, r3)); } |
assert(! LocationTools.overlaps(r1, r3)); | assertTrue(! LocationTools.overlaps(r1, r3)); | public void testOverlaps() { assert(LocationTools.overlaps(r1, r1)); assert(LocationTools.overlaps(r2, r2)); assert(LocationTools.overlaps(r1, r2)); assert(LocationTools.overlaps(r2, r1)); assert(! LocationTools.overlaps(r1, r3)); } |
if(tv.isNewTag() || !tv.getTag().equals(frame.tag)) { | if( tv.isNewTag() || (tv.getTag() != null && !tv.getTag().equals(frame.tag)) ) { | public boolean read( BufferedReader reader, TagValueParser parser, TagValueListener listener ) throws IOException, ParserException { final List stack = new ArrayList(); push(stack, new Frame(parser, listener, null)); Context ctxt = new Context(); listener.startRecord(); for... |
throws IllegalResidueException, IllegalAlphabetException { | throws IllegalResidueException, IllegalAlphabetException, SeqException { | public static WeightMatrix readMatrix(Element root) throws IllegalResidueException, IllegalAlphabetException { Element alphaE = (Element) root.getElementsByTagName("alphabet").item(0); Alphabet sa = AlphabetManager.instance().alphabetForName( alphaE.getAttribute("name")); if(! (sa instanceof FiniteAlph... |
ResidueParser symParser = seqAlpha.getParser("symbol"); | public static MarkovModel readModel(Element root) throws SeqException, IllegalResidueException, IllegalAlphabetException { if(root.getTagName().equals("WeightMatrix")) { return new WMAsMM(readMatrix(root)); } int heads = Integer.parseInt(root.getAttribute("heads")); Element alphaE = (Element) ro... | |
if(resName.length() > 1) res = nameParser.parseToken(resName); else res = symParser.parseToken(resName); | res = nameParser.parseToken(resName); | public static MarkovModel readModel(Element root) throws SeqException, IllegalResidueException, IllegalAlphabetException { if(root.getTagName().equals("WeightMatrix")) { return new WMAsMM(readMatrix(root)); } int heads = Integer.parseInt(root.getAttribute("heads")); Element alphaE = (Element) ro... |
registerFeatureFetchers(new Object()); | registerFeatureFetchers(null); | public Iterator features() { try { registerFeatureFetchers(new Object()); return features.features(); } catch (BioException be) { throw new BioRuntimeException(be, "Couldn't create features iterator"); } } |
numComponents = registerFeatureFetchers(ffl, new Object()); | numComponents = registerFeatureFetchers(ffl, ff); | public FeatureHolder filter(FeatureFilter ff, boolean recurse) { try { // // We optimise for the case of just wanting `structural' features, // which improves the scalability of the Dazzle server (and probably // other applications, too) // FeatureHolder structure = getStructure(); ... |
numComponents = registerFeatureFetchers(new Object()); | numComponents = registerFeatureFetchers(ff); | public FeatureHolder filter(FeatureFilter ff, boolean recurse) { try { // // We optimise for the case of just wanting `structural' features, // which improves the scalability of the Dazzle server (and probably // other applications, too) // FeatureHolder structure = getStructure(); ... |
registerLocalFeatureFetchers(ffl, new Object()); | registerLocalFeatureFetchers(ffl, ff); | public FeatureHolder filter(FeatureFilter ff, boolean recurse) { try { // // We optimise for the case of just wanting `structural' features, // which improves the scalability of the Dazzle server (and probably // other applications, too) // FeatureHolder structure = getStructure(); ... |
registerLocalFeatureFetchers(new Object()); | registerLocalFeatureFetchers(ff); | public FeatureHolder filter(FeatureFilter ff, boolean recurse) { try { // // We optimise for the case of just wanting `structural' features, // which improves the scalability of the Dazzle server (and probably // other applications, too) // FeatureHolder structure = getStructure(); ... |
if (f instanceof StrandedFeature) { rft.strand = ((StrandedFeature) f).getStrand(); } else { rft.strand = StrandedFeature.UNKNOWN; } | protected FeatureHolder createFeatureHolder() { ProjectionContext pc = new ProjectionContext() { public FeatureHolder getParent(Feature f) { return featureParent; } public Sequence getSequence(Feature f) { return SubSequence.this; } public Location getLocation(Feature f) { return f.getLocation(... | |
if (context.getDirection() == context.HORIZONTAL) | if (context.getDirection() == PairwiseRenderContext.HORIZONTAL) | public void paint(Graphics2D g2, PairwiseRenderContext context) { FeatureHolder fh; if (context.getDirection() == context.HORIZONTAL) { fh = context.getFeatures().filter(new FeatureFilter.And(new FeatureFilter.OverlapsLocation(context.getRange()), ... |
if (context.getDirection() == context.HORIZONTAL) | if (context.getDirection() == PairwiseRenderContext.HORIZONTAL) | public SequenceViewerEvent processMouseEvent(PairwiseRenderContext context, MouseEvent me, List path) { path.add(this); double gPos; if (context.getDirection() == conte... |
if (i.next() == MagicalState.MAGICAL_RESIDUE) { | if (o == MagicalState.MAGICAL_RESIDUE) { | private static Residue getResWrapper(CrossProductAlphabet a, List l) throws IllegalAlphabetException {// System.out.println(a.getName() + " getting:");// for (Iterator i = l.iterator(); i.hasNext(); ) {// Residue blah = (Residue) i.next();// System.out.println(blah.getName());... |
int iCurrentEnd = 0; | void drawCurrentAlignment( BlastLikeAlignment oAlignment ) { int iCurrentEnd = 0; int i = 0; int iCurrentQueryStart = Integer.parseInt ( oAlignment.oQuerySeq.startPosition ); int iCurrentHitStart = Integer.parseInt ( oAlignment.oHitSeq.startPosition ); int iQueryLen = oAlignment.oQuerySeq.seq.length(); int ... | |
if(nameParser != null) { sym = nameParser.parseToken(symName); } else { sym = symbolParser.parseToken(symName); | try { if(nameParser != null) { sym = nameParser.parseToken(symName); } else { sym = symbolParser.parseToken(symName); } } catch (IllegalSymbolException ise) { throw new BioException(ise, "Can't extract symbol from " + weightE + " in " + stateE); | public static MarkovModel readModel(Element root) throws BioException, IllegalSymbolException, IllegalAlphabetException { if(root.getTagName().equals("WeightMatrix")) { return new WMAsMM(readMatrix(root)); } int heads = Integer.parseInt(root.getAttribute("heads")); Element alphaE = (Element) roo... |
IWTimestamp fromStamp = new IWTimestamp(); IWTimestamp toStamp = new IWTimestamp(); String from = iwc.getParameter(PARAMETER_FROM_DATE); String to = iwc.getParameter(PARAMETER_TO_DATE); if (from != null) { fromStamp = new IWTimestamp(from); } else { fromStamp.addYears(-1); } if (to != null) { toStamp = new IWTimestamp(... | private Layer getStatementMovements(IWContext iwc, String communeNumber, String personalId, PaymentItem item) throws RemoteException { NumberFormat currencyFormat = NumberFormat.getCurrencyInstance(iwc .getCurrentLocale()); currencyFormat.setGroupingUsed(true); currencyFormat.setMaximumFractionDigits(0); curr... | |
if (odd) { row.setStyleClass("oddRow"); } else { row.setStyleClass("evenRow"); } odd = !odd; | private Layer getStatementMovements(IWContext iwc, String communeNumber, String personalId, PaymentItem item) throws RemoteException { NumberFormat currencyFormat = NumberFormat.getCurrencyInstance(iwc .getCurrentLocale()); currencyFormat.setGroupingUsed(true); currencyFormat.setMaximumFractionDigits(0); curr... | |
row = group.createRow(); if (odd) { row.setStyleClass("oddRow"); } else { row.setStyleClass("evenRow"); | Layer buttonLayer = new Layer(Layer.DIV); buttonLayer.setStyleClass("buttonLayer"); layer.add(buttonLayer); GenericButton backLink = new GenericButton("back", iwrb.getLocalizedString("back", "Back")); if (backPage != null) { backLink.setPageToOpen(backPage); | private Layer getStatementMovements(IWContext iwc, String communeNumber, String personalId, PaymentItem item) throws RemoteException { NumberFormat currencyFormat = NumberFormat.getCurrencyInstance(iwc .getCurrentLocale()); currencyFormat.setGroupingUsed(true); currencyFormat.setMaximumFractionDigits(0); curr... |
row.setStyleClass("lastRow"); Layer l = new Layer(Layer.DIV); l.setStyleClass("formSection"); layer.add(l); Form form = new Form(); l.add(form); DateInput inp = new DateInput(PARAMETER_FROM_DATE, true); inp.setDate(fromStamp.getDate()); inp.setStyleClass("dateInput"); DateInput toInp = new DateInput(PARAMETER_TO_DAT... | buttonLayer.add(backLink); | private Layer getStatementMovements(IWContext iwc, String communeNumber, String personalId, PaymentItem item) throws RemoteException { NumberFormat currencyFormat = NumberFormat.getCurrencyInstance(iwc .getCurrentLocale()); currencyFormat.setGroupingUsed(true); currencyFormat.setMaximumFractionDigits(0); curr... |
else if (this.getTitle() != null && them.getTitle() == null) return 1; | public int compareTo(Object o) { if(o == this) return 0; // Hibernate comparison - we haven't been populated yet if (this.authors==null) return -1; // Normal comparison DocRef them = (DocRef)o; if (!this.getAuthors().equals(them.getAuthors())) return this.getAuthors().compa... | |
private void setCrossRef(CrossRef crossref) { this.crossref = crossref; } | void setCrossRef(CrossRef crossref) { this.crossref = crossref; } | private void setCrossRef(CrossRef crossref) { this.crossref = crossref; } |
"Can't parse " + token + " as it is not bracketed" | "Can't parse '" + token + "' as it is not bracketed" | public Symbol parseToken(String token) throws IllegalSymbolException { if(!token.startsWith("(") || !token.endsWith(")")) { throw new IllegalSymbolException( "Can't parse " + token + " as it is not bracketed" ); } token = token.substring(1, token.length()-1).trim(); List rList = ... |
int j = token.indexOf(", ", i); | int comma = token.indexOf(",", i); int space = token.indexOf(" ", i); int j; if(comma == -1) { j = space; } else if(space == -1) { j = comma; } else { j = Math.min(comma, space); } | public Symbol parseToken(String token) throws IllegalSymbolException { if(!token.startsWith("(") || !token.endsWith(")")) { throw new IllegalSymbolException( "Can't parse " + token + " as it is not bracketed" ); } token = token.substring(1, token.length()-1).trim(); List rList = ... |
token.substring(i) | token.substring(i).trim() | public Symbol parseToken(String token) throws IllegalSymbolException { if(!token.startsWith("(") || !token.endsWith(")")) { throw new IllegalSymbolException( "Can't parse " + token + " as it is not bracketed" ); } token = token.substring(1, token.length()-1).trim(); List rList = ... |
token.substring(i, j) | token.substring(i, j).trim() | public Symbol parseToken(String token) throws IllegalSymbolException { if(!token.startsWith("(") || !token.endsWith(")")) { throw new IllegalSymbolException( "Can't parse " + token + " as it is not bracketed" ); } token = token.substring(1, token.length()-1).trim(); List rList = ... |
i = j + ", ".length(); | i = j + 1; | public Symbol parseToken(String token) throws IllegalSymbolException { if(!token.startsWith("(") || !token.endsWith(")")) { throw new IllegalSymbolException( "Can't parse " + token + " as it is not bracketed" ); } token = token.substring(1, token.length()-1).trim(); List rList = ... |
FeatureHolder parent, Feature.Template template) throws IllegalArgumentException { if(template.location == null) { | FeatureHolder parent, Feature.Template template) { if (template.location == null) { | public SimpleFeature(Sequence sourceSeq, FeatureHolder parent, Feature.Template template) throws IllegalArgumentException { if(template.location == null) { throw new IllegalArgumentException( "Location can not be null. Did you mean Location.EMPT... |
if (this.type == null) { throw new NullPointerException("Either type or typeTerm must have a non-null value"); | if (this.type == null) { throw new NullPointerException("Either type or typeTerm must have a non-null value"); } if (this.source == null) { throw new NullPointerException("Either source or sourceTerm must have a non-null value"); } this.annotation = template.annotation != null ? new SimpleAnnotation(template.annotation... | public SimpleFeature(Sequence sourceSeq, FeatureHolder parent, Feature.Template template) throws IllegalArgumentException { if(template.location == null) { throw new IllegalArgumentException( "Location can not be null. Did you mean Location.EMPT... |
if (this.source == null) { throw new NullPointerException("Either source or sourceTerm must have a non-null value"); } this.annotation = (template.annotation == Annotation.EMPTY_ANNOTATION) ? new SimpleAnnotation() : template.annotation; } | public SimpleFeature(Sequence sourceSeq, FeatureHolder parent, Feature.Template template) throws IllegalArgumentException { if(template.location == null) { throw new IllegalArgumentException( "Location can not be null. Did you mean Location.EMPT... | |
if(assertion) { if(!isSane()) { throw new AssertionError("Data corrupted: " + blocks); } } | public void addGapsInSource(int pos, int length) { if(pos < 1 || pos > (length() + 1)) { throw new IndexOutOfBoundsException( "Attempted to add a gap outside of this sequence (1.." + length() + ") at " + pos ); } int i = blocks.size() / 2; int imin = 0; int imax = blocks.size() - 1... | |
Block b = (Block) blocks.get(i); return source.symbolAt(b.sourceStart - b.viewStart + indx); | try { Block b = (Block) blocks.get(i); return source.symbolAt(b.sourceStart - b.viewStart + indx); } catch (IndexOutOfBoundsException e) { throw new AssertionFailure( "Internal book-keeping error fetching index: " + indx + " of " + length() + " blocks: " + blocks, e); } | public Symbol symbolAt(int indx) throws IndexOutOfBoundsException { if(indx > length() || indx < 1) { throw new IndexOutOfBoundsException( "Attempted to read outside of this sequence (1.." + length() + ") at " + indx ); } int i = findViewBlock(indx); if(i < 0) { if( (indx < f... |
System.out.println("=======================orthology line: " + m.groupCount() + "====================="); | 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();... | |
String taxonID0 = m.group(1); System.out.println(taxonID0); String taxonID1 = m.group(2); System.out.println(taxonID1); String type = m.group(3); System.out.println(type); String locus0 = m.group(4); System.out.println(locus0); String homoID0 = m.group(5); System.out.println(homoID0); String access0 = m.group(6); Syste... | String taxonID0 = m.group(1).trim(); String taxonID1 = m.group(2).trim(); String type = m.group(3).trim(); String locus0 = m.group(4).trim(); String homoID0 = m.group(5).trim(); String access0 = m.group(6).trim(); String locus1 = m.group(7).trim(); String homoID1 = m.group(8).trim(); String access1 = m.group(9).trim();... | 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();... |
Integer.parseInt(finale); | Double.parseDouble(finale); | 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();... |
builder.endOrthology(); | 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();... | |
for ( Iterator i = ((FiniteAlphabet) state.alphabet()).residues().iterator(); i.hasNext(); ) { Residue r = (Residue) i.next(); addCount(r, Math.exp(nullModel.getWeight(r) + weight)); | if(nullModel != null) { for ( Iterator i = ((FiniteAlphabet) state.alphabet()).residues().iterator(); i.hasNext(); ) { Residue r = (Residue) i.next(); addCount(r, Math.exp(nullModel.getWeight(r) + weight)); } | public void train( EmissionState nullModel, double weight ) throws IllegalResidueException { for ( Iterator i = ((FiniteAlphabet) state.alphabet()).residues().iterator(); i.hasNext(); ) { Residue r = (Residue) i.next(); addCount(r, Math.exp(nullModel.getWeight(r) + weight)); } ... |
CodeMethod m_getFilter = IntrospectedCodeClass.forMethod(m); | CodeMethod m_getFilter = null; | private Class generateWalker(Class visitorClass) throws BioException { try { String vcn = visitorClass.getName().replaceAll("\\.", ""); String walkerClassName = "scratch_.walker_" + vcn; CodeClass c_Visitor = IntrospectedCodeClass.forClass(Visitor.class); CodeClass c_ourVisitor = IntrospectedC... |
CodeMethod ourMeth = IntrospectedCodeClass.forMethod(meth); | CodeMethod ourMeth = null; | private Class generateWalker(Class visitorClass) throws BioException { try { String vcn = visitorClass.getName().replaceAll("\\.", ""); String walkerClassName = "scratch_.walker_" + vcn; CodeClass c_Visitor = IntrospectedCodeClass.forClass(Visitor.class); CodeClass c_ourVisitor = IntrospectedC... |
"Utility program to convert the output from blast-like"); | "Utility program to convert descriptions of macromolecular "); | public static void main(String[] args) throws Exception { String oInput = null; String oMode = null; boolean tStrict = true; // Catch wrong number of arguments or help requests if ( ( (args.length != 1) && (args.length != 3) ) || (args[0].equals("-help")) || (args[0].equals("-h"... |
"software into an XML format that should validate correctly"); | "structures in formats resembline PDB format "); | public static void main(String[] args) throws Exception { String oInput = null; String oMode = null; boolean tStrict = true; // Catch wrong number of arguments or help requests if ( ( (args.length != 1) && (args.length != 3) ) || (args[0].equals("-help")) || (args[0].equals("-h"... |
"against the biojava BlastLikeDataSectCollection DTD."); | "into an XML format that should validate correctly"); System.out.println( "against the biojava MacromolecularStructureCollection DTD."); | public static void main(String[] args) throws Exception { String oInput = null; String oMode = null; boolean tStrict = true; // Catch wrong number of arguments or help requests if ( ( (args.length != 1) && (args.length != 3) ) || (args[0].equals("-help")) || (args[0].equals("-h"... |
"[-mode <strict|lazy>] <blast output file pathname>"); | "[-mode <strict|lazy>] <pdb file pathname>"); | public static void main(String[] args) throws Exception { String oInput = null; String oMode = null; boolean tStrict = true; // Catch wrong number of arguments or help requests if ( ( (args.length != 1) && (args.length != 3) ) || (args[0].equals("-help")) || (args[0].equals("-h"... |
public Collection getPaymentItems(String kt) { | public Collection getPaymentItems(String communeNumber, String personalId) { | public Collection getPaymentItems(String kt) { Collection c = new Vector(); PaymentItem p1 = new PaymentItem(); p1.setName("Fasteignagjld"); p1.setAmount(45346); p1.setLastDate( new IWTimestamp() ); PaymentItem p2 = new PaymentItem(); p2.setName("Leiksklagjld"); p2.setAmount(12234); p2.setLastDate( new IWTi... |
public Collection getStatementItems(String kt, PaymentItem pType, IWTimestamp fromStamp, IWTimestamp toStamp) { | public Collection getStatementItems(String communeNumber, String personalId, PaymentItem pType, IWTimestamp fromStamp, IWTimestamp toStamp) { | public Collection getStatementItems(String kt, PaymentItem pType, IWTimestamp fromStamp, IWTimestamp toStamp) { Collection c = new Vector(); StatementItem s1 = new StatementItem(); s1.setName("Upphafsstaa"); s1.setAmount(0); s1.setLastDate( new IWTimestamp() ); StatementItem s2 = new StatementItem(); s2.setNa... |
Dimension d = null; | Dimension mind = null; Dimension maxd = null; | public void resizeAndValidate() { //System.out.println("resizeAndValidate starting"); Dimension d = null; if(!isActive()) { // System.out.println("No sequence"); // no sequence - collapse down to no size at all leadingBorder.setSize(0.0); trailingBorder.setSize(0.0); d = new Dime... |
d = new Dimension(0, 0); | mind = maxd = new Dimension(0, 0); | public void resizeAndValidate() { //System.out.println("resizeAndValidate starting"); Dimension d = null; if(!isActive()) { // System.out.println("No sequence"); // no sequence - collapse down to no size at all leadingBorder.setSize(0.0); trailingBorder.setSize(0.0); d = new Dime... |
d = new Dimension((int) Math.ceil(alongDim), (int) Math.ceil(depth)); | mind = new Dimension((int) Math.ceil(alongDropDim), (int) Math.ceil(depth)); maxd = new Dimension((int) Math.ceil(alongDim), (int) Math.ceil(depth)); | public void resizeAndValidate() { //System.out.println("resizeAndValidate starting"); Dimension d = null; if(!isActive()) { // System.out.println("No sequence"); // no sequence - collapse down to no size at all leadingBorder.setSize(0.0); trailingBorder.setSize(0.0); d = new Dime... |
d = new Dimension((int) Math.ceil(depth), (int) Math.ceil(alongDim)); | mind = new Dimension((int) Math.ceil(depth), (int) Math.ceil(alongDropDim)); maxd = new Dimension((int) Math.ceil(depth), (int) Math.ceil(alongDim)); | public void resizeAndValidate() { //System.out.println("resizeAndValidate starting"); Dimension d = null; if(!isActive()) { // System.out.println("No sequence"); // no sequence - collapse down to no size at all leadingBorder.setSize(0.0); trailingBorder.setSize(0.0); d = new Dime... |
setMinimumSize(d); setPreferredSize(d); setMaximumSize(d); | setMinimumSize(mind); setPreferredSize(maxd); setMaximumSize(maxd); | public void resizeAndValidate() { //System.out.println("resizeAndValidate starting"); Dimension d = null; if(!isActive()) { // System.out.println("No sequence"); // no sequence - collapse down to no size at all leadingBorder.setSize(0.0); trailingBorder.setSize(0.0); d = new Dime... |
parent = t.getParentNCBITaxID(); } else parent = null; | if (t.getParentNCBITaxID().equals(new Integer(t.getNCBITaxID()))) parent = null; else parent = t.getParentNCBITaxID(); } else parent = null; | public String getNameHierarchy() { StringBuffer sb = new StringBuffer(); boolean first = true; Integer parent = this.getParentNCBITaxID(); while (parent!=null) { NCBITaxon t = (NCBITaxon)RichObjectFactory.getObject(SimpleNCBITaxon.class, new Object[]{parent}); Set s... |
private String getLocationText() { | String getLocationText() { | private String getLocationText() {// System.out.println("SimpleRichLocation.getLocationText-returns: ["+GenbankLocationParser.writeLocation(new SimpleRichLocation(getMinPosition(), getMaxPosition(), getRank()))+"], this: ["+this+"]"); return GenbankLocationParser.writeLocation(new SimpleRichLocation(getMin... |
private int getStrandNum() { return this.strand.intValue(); } | int getStrandNum() { return this.strand.intValue(); } | private int getStrandNum() { return this.strand.intValue(); } |
private void setLocationText(final String theLocation) throws ParseException { | void setLocationText(final String theLocation) throws ParseException { | private void setLocationText(final String theLocation) throws ParseException {// System.out.println("SimpleRichLocation.setLocationText-theLocation: ["+theLocation+"]"); if (theLocation == null) { setMinPosition(RichLocation.EMPTY_LOCATION.getMinPosition()); setMaxPosition(RichLocation.EMPTY_LOCAT... |
private void setMax(int max) { this.max = new SimplePosition(false,false,max); } | void setMax(int max) { this.max = new SimplePosition(false,false,max); } | private void setMax(int max) { this.max = new SimplePosition(false,false,max); } |
private void setMin(int min) { this.min = new SimplePosition(false,false,min); } | void setMin(int min) { this.min = new SimplePosition(false,false,min); } | private void setMin(int min) { this.min = new SimplePosition(false,false,min); } |
private void setStrandNum(int token) { this.strand = Strand.forValue(token); } | void setStrandNum(int token) { this.strand = Strand.forValue(token); } | private void setStrandNum(int token) { this.strand = Strand.forValue(token); } |
description = s.trim(); | protected void setStringValue(String s) { description = s.trim(); } | |
seqName = s.trim(); | protected void setStringValue(String s) { seqName = s.trim(); } | |
if (state != IN_HIT) parsingError= true; | public void addHitProperty(Object key, Object value) { if (skipHits) return; if (state != IN_HIT) parsingError= true; hitProperty.put(key, value); } | |
if (state != IN_SEARCH) parsingError= true; | public void addSearchProperty(Object key, Object value) { if (state != IN_SEARCH) parsingError= true; searchProperty.put(key, value); } | |
if (state != IN_SUBHIT) parsingError= true; | public void addSubHitProperty(Object key, Object value) { if (skipSubHits) return; if (state != IN_SUBHIT) parsingError= true; subHitProperty.put(key, value); } | |
state = UNINITTED; | public void endHeader() { state = UNINITTED; delegate.endHeader(); } | |
state = OUT_HIT; | public void endHit() { state = OUT_HIT; if (emittedStartHit) { delegate.endHit(); emittedStartHit = false; } } | |
state = UNINITTED; | public void endSearch() { state = UNINITTED; if (emittedStartSearch) { delegate.endSearch(); emittedStartSearch = false; } } | |
state = OUT_SUBHIT; | public void endSubHit() { state = OUT_SUBHIT; // test filter at subhit level here // this will be a decision on whether to emit events or not if (!skipSubHits) { for (Iterator subHitFilterI = subHitFilters.iterator(); subHitFilterI.hasNext();) { BlastLikeSear... | |
if (state != IN_HEADER) parsingError= true; databaseId = id; | public void setDatabaseID(String id) { if (state != IN_HEADER) parsingError= true; databaseId = id; delegate.setDatabaseID(id); emittedStartHeader =false; } | |
emittedStartHeader =false; | public void setDatabaseID(String id) { if (state != IN_HEADER) parsingError= true; databaseId = id; delegate.setDatabaseID(id); emittedStartHeader =false; } | |
if (state != IN_SEARCH) parsingError= true; | public void setQueryID(String queryID) { if (state != IN_SEARCH) parsingError= true; addSearchProperty(BlastLikeSearchFilter.KEY_QUERY_ID, queryID); } | |
state = IN_HEADER; | public void startHeader() { state = IN_HEADER; delegate.startHeader(); } | |
state = IN_HIT; | public void startHit() { state = IN_HIT; emittedStartHit = false; firstSubHit = true; // determine if anything at the search level // will cause the rest of the hits/subhits // in this search to be skipped. // do only for first hit in a search if (firstHit)... | |
state = IN_SEARCH; | public void startSearch() { state = IN_SEARCH; emittedStartSearch = false; firstHit = true; } | |
state = IN_SUBHIT; emittedStartSubHit = false; | public void startSubHit() { if (skipSubHits) return; state = IN_SUBHIT; emittedStartSubHit = false; // clear outcomes that depend on the properties // of this subhit for (Iterator subHitFilterI = hitFilters.iterator(); subHitFilterI.hasNext();) { BlastLikeSear... | |
if(changeSupport == null) { changeSupport = new ChangeSupport(); } | generateChangeSupport(null); | public void addChangeListener(ChangeListener cl) { if(changeSupport == null) { changeSupport = new ChangeSupport(); } synchronized(changeSupport) { changeSupport.addChangeListener(cl); } } |
DocRef dr = (DocRef)RichObjectFactory.getObject(SimpleDocRef.class,new Object[]{currRefAuthors,currRefJournal, new Integer(0)}); | DocRef dr = (DocRef)RichObjectFactory.getObject(SimpleDocRef.class,new Object[]{currRefAuthors,currRefJournal}); | public void endElement(String uri, String localName, String qName) throws SAXException { String val = this.m_currentString.toString().trim(); try { if (qName.equals(LOCUS_TAG)) rlistener.setName(val); else if (qName.equals(ACCESS... |
return this.symList.subList(start, end); | if (this.getCircular()) { try { int modStart = RichLocation.Tools.modulateCircularIndex(start,this.length()); int modEnd = RichLocation.Tools.modulateCircularIndex(end,this.length()); int modLength = (Math.max(start,end)-Math.min(start,end))+1; int seqLength = this.length(); ChunkedSymbolListFactory symsf = new Chunke... | public SymbolList subList(int start, int end) throws IndexOutOfBoundsException { return this.symList.subList(start, end); } |
public String subStr(int start, int end) throws IndexOutOfBoundsException { return this.symList.subStr(start, end); } | public String subStr(int start, int end) throws IndexOutOfBoundsException { return this.symList.subList(start, end).seqString(); } | public String subStr(int start, int end) throws IndexOutOfBoundsException { return this.symList.subStr(start, end); } |
public Symbol symbolAt(int index) throws IndexOutOfBoundsException { return this.symList.symbolAt(index); } | public Symbol symbolAt(int index) throws IndexOutOfBoundsException { if (this.getCircular()) index = RichLocation.Tools.modulateCircularIndex(index,this.length()); return this.symList.symbolAt(index); } | public Symbol symbolAt(int index) throws IndexOutOfBoundsException { return this.symList.symbolAt(index); } |
int realSymsPerGap = src.graphicsToSequence(50.0); System.out.println("Real syms: " + realSymsPerGap); | int realSymsPerGap = src.graphicsToSequence(40.0); | public void paint( Graphics2D g, SequenceRenderContext src, int min, int max ) { double minX = src.sequenceToGraphics(min); double maxX = src.sequenceToGraphics(max); double scale = src.getScale(); double halfScale = scale * 0.5; Line2D line; if(src.getDirection() == src.HORIZONTAL) { ... |
System.out.println("Snapped syms: " + snapSymsPerGap); | public void paint( Graphics2D g, SequenceRenderContext src, int min, int max ) { double minX = src.sequenceToGraphics(min); double maxX = src.sequenceToGraphics(max); double scale = src.getScale(); double halfScale = scale * 0.5; Line2D line; if(src.getDirection() == src.HORIZONTAL) { ... | |
StringBuffer sb = new StringBuffer(); | void readBlastMatrix( String poFileName ) throws IOException { BufferedReader in = null; try { File oFile = new File( poFileName ); FileReader oFileReader = new FileReader( oFile ); in = new BufferedReader( oFileReader ); StringBuffer sb = new StringBuffer(); String oLine = in.readLine()... | |
SymbolTokenization toke = null; | public void write(OutputStream os, Alignment align, int fileType) throws BioException, IllegalSymbolException { PrintStream out = new PrintStream(os); Iterator labels = align.getLabels().listIterator(); Object curLabel = null; SymbolList curSeq = null; int lineWidth = 60; S... | |
toke = DNATools.getDNA().getTokenization("token"); | public void write(OutputStream os, Alignment align, int fileType) throws BioException, IllegalSymbolException { PrintStream out = new PrintStream(os); Iterator labels = align.getLabels().listIterator(); Object curLabel = null; SymbolList curSeq = null; int lineWidth = 60; S... | |
toke = ProteinTools.getTAlphabet().getTokenization("token"); | public void write(OutputStream os, Alignment align, int fileType) throws BioException, IllegalSymbolException { PrintStream out = new PrintStream(os); Iterator labels = align.getLabels().listIterator(); Object curLabel = null; SymbolList curSeq = null; int lineWidth = 60; S... | |
validate(s); | this.validate(s); | protected AtomicSymbol getSymbolImpl(List symL) throws IllegalSymbolException { if (symL.size() != 1) { throw new IllegalSymbolException( "SubDoubleAlphabet is one-dimensional: " + this.getName() + " : " + symL); } AtomicSymbol s = (AtomicSymbol) symL.get(0); ... |
super.addHandler(new ElementRecognizer.ByLocalName("seq"), GAMESeqHandler.GAME_SEQ_HANDLER_FACTORY); | GAMEFeatureSetHandler(StAXFeatureHandler staxenv) { // setup environment super(staxenv); // setup handlers // <name> super.addHandler(new ElementRecognizer.ByLocalName("name"), new StAXHandlerFactory() { public StAXContentHandler getHandler(StAXFeatureHan... | |
public void addEpsilonTransition(Node start, Node end) | public Transition addEpsilonTransition(Node start, Node end) | public void addEpsilonTransition(Node start, Node end) { addTransition(start, end, EPSILON); } |
addTransition(start, end, EPSILON); | return addTransition(start, end, EPSILON); | public void addEpsilonTransition(Node start, Node end) { addTransition(start, end, EPSILON); } |
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