rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k |
|---|---|---|
subSeqBox.setRect(seqBox.getX() + offset, seqBox.getY(), | subSeqBox.setRect(seqBox.getX(), seqBox.getY(), | public void paint(Graphics2D g, SequenceRenderContext ctx, Rectangle2D seqBox) { double offset = 0.0; Rectangle2D subSeqBox = new Rectangle2D.Double(); for (Iterator i = renderList.iterator(); i.hasNext(); ) { LabelAndRenderer lar = (LabelAndRenderer) i.next(); SequenceRenderContext subctx ... |
((changeType == null) || (changeType.isMatchingType(Annotation.PROPERTY))) && | (Annotation.PROPERTY.isMatchingType(changeType) || changeType.isMatchingType(Annotation.PROPERTY)) && | protected ChangeSupport getChangeSupport(ChangeType changeType) { ChangeSupport changeSupport = super.getChangeSupport(changeType); if( ((changeType == null) || (changeType.isMatchingType(Annotation.PROPERTY))) && (propertyForwarder == null) ) { propertyForwarder = new PropertyForwarder( ... |
this.depth = 0; | public Indexer(File file, IndexStore indexStore) throws FileNotFoundException { this.file = new RAF(file, "r"); this.reader = new CountedBufferedReader(new FileReader(file)); this.indexStore = indexStore; this.seccondaryKeys = new SmallMap(); } | |
depth--; if(depth == 0) { | public void endRecord() throws ParserException { //try { if(primaryKey == null) { throw new NullPointerException("No primary key"); } int length = (int) (reader.getFilePointer() - offset); indexStore.writeRecord( file, offset, length, primaryKey, secc... | |
} | public void endRecord() throws ParserException { //try { if(primaryKey == null) { throw new NullPointerException("No primary key"); } int length = (int) (reader.getFilePointer() - offset); indexStore.writeRecord( file, offset, length, primaryKey, secc... | |
offset = reader.getFilePointer(); primaryKey = null; for(Iterator i = seccondaryKeys.values().iterator(); i.hasNext(); ) { List list = (List) i.next(); list.clear(); | if(depth == 0) { offset = reader.getFilePointer(); primaryKey = null; for(Iterator i = seccondaryKeys.values().iterator(); i.hasNext(); ) { List list = (List) i.next(); list.clear(); } | public void startRecord() { offset = reader.getFilePointer(); primaryKey = null; for(Iterator i = seccondaryKeys.values().iterator(); i.hasNext(); ) { List list = (List) i.next(); list.clear(); } } |
depth++; | public void startRecord() { offset = reader.getFilePointer(); primaryKey = null; for(Iterator i = seccondaryKeys.values().iterator(); i.hasNext(); ) { List list = (List) i.next(); list.clear(); } } | |
private static Location _union(List locList) { | protected static Location _union(List locList) { | private static Location _union(List locList) { // sort these blocks Collections.sort(locList, Location.naturalOrder); // merge into this list... List joinList = new ArrayList(); // start iterating over sorted list. // last is used as loop variable. We must be careful about zero lengthe... |
if(isDecorated(locA) || isDecorated(locB)) { handleDecorations(locA, locB); if(BetweenLocationTools.isBetween(locA) || (BetweenLocationTools.isBetween(locB))) { return BetweenLocationTools.union(locA, locB); } } | if(isDecorated(locA) || isDecorated(locB)) { handleDecorations(locA, locB); if(locA instanceof CircularLocation && locB instanceof CircularLocation){ return CircularLocationTools.union((CircularLocation)locA,(CircularLocation)locB); } if(BetweenLocationTools.isBetween(locA) || (BetweenLocationTools.isBetween(locB))) { ... | public static Location union(Location locA, Location locB) { if(isDecorated(locA) || isDecorated(locB)) { handleDecorations(locA, locB); if(BetweenLocationTools.isBetween(locA) || (BetweenLocationTools.isBetween(locB))) { return BetweenLocationTools.union(locA, locB); } } if( locA.isCont... |
System.err.println(filtClass); | 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... | |
System.err.println("\t" + m); | 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... | |
bodyIV.add(ByteCode.make_aload((LocalVariable) wrappedLVs.get(ai+1))); | bodyIV.add(ByteCode.make_aload((LocalVariable) wrappedLVs.get(ai-1))); | 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... |
public ValueChanger() { super(); | public ValueChanger(TagValueListener delegate) { super(delegate); | public ValueChanger() { super(); } |
this.changer = changeTable.getChanger(tag); this.splitter = changeTable.getSplitter(tag); | if(changeTable != null) { this.changer = changeTable.getChanger(tag); this.splitter = changeTable.getSplitter(tag); } else { this.changer = null; this.splitter = null; } | public void startTag(Object tag) throws ParserException { this.changer = changeTable.getChanger(tag); this.splitter = changeTable.getSplitter(tag); if(this.changer == null) { this.changer = defaultC; } if(this.splitter == null) { this.splitter = defaultS; } super.startTag(t... |
((changeType == null) || (changeType == SymbolList.EDIT)) && | (SymbolList.EDIT.isMatchingType(changeType) || changeType.isMatchingType(SymbolList.EDIT)) && | protected ChangeSupport getChangeSupport(ChangeType changeType) { ChangeSupport cs = super.getChangeSupport(changeType); if( ((changeType == null) || (changeType == SymbolList.EDIT)) && (editTranslater == null) ) { editTranslater = new EditTranslater(this, cs, start, end); ... |
if(a.equals(b)) { return false; } if(a instanceof OptimizableFilter) { return ((OptimizableFilter) a).isDisjoint(b); } return false; | return areDisjointOneWay(a, b) || areDisjointOneWay(b, a); | public static boolean areDisjoint(FeatureFilter a, FeatureFilter b) { if(a.equals(b)) { return false; } if(a instanceof OptimizableFilter) { return ((OptimizableFilter) a).isDisjoint(b); } return false; } |
String qualifier = SeqFormatTools.formatQualifier(key, vi.next()); stream.println(SeqFormatTools.formatQualifierBlock(qualifier, leader, 80)); | StringBuffer sb = formatQualifierBlock(new StringBuffer(), formatQualifier(key, vi.next()), leader, 80); stream.println(sb); | public void addFeatureProperty(Object key, Object value) throws ParseException { // There are 21 spaces in the leader String leader = " "; // Don't print internal data structures if (key.equals(Feature.PROPERTY_DATA_KEY)) return; // The value may be a collection if several qualifiers of... |
String qualifier = SeqFormatTools.formatQualifier(key, value); stream.println(SeqFormatTools.formatQualifierBlock(qualifier, leader, 80)); | StringBuffer sb = formatQualifierBlock(new StringBuffer(), formatQualifier(key, value), leader, 80); stream.println(sb); | public void addFeatureProperty(Object key, Object value) throws ParseException { // There are 21 spaces in the leader String leader = " "; // Don't print internal data structures if (key.equals(Feature.PROPERTY_DATA_KEY)) return; // The value may be a collection if several qualifiers of... |
sq.append(aCount + " t\nORIGIN\n"); | sq.append(aCount + " t"); sq.append(nl); sq.append("ORIGIN"); sq.append(nl); | 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; for (int i = 0; i < syms.length; i++) { char c = syms[i].getToken(); switch (c) {... |
String blocks = (SeqFormatTools.formatTokenBlock(sa, 10)).toString(); | String blocks = (formatTokenBlock(new StringBuffer(sa.length), sa, 10)).toString(); | 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; for (int i = 0; i < syms.length; i++) { char c = syms[i].getToken(); switch (c) {... |
StringBuffer lb = SeqFormatTools.formatLocationBlock(templ.location, strand, leader, 80); | StringBuffer lb = formatLocationBlock(new StringBuffer(leader), templ.location, strand, leader, 80); | public void startFeature(Feature.Template templ) throws ParseException { // There are 21 spaces in the leader String leader = " "; int strand = 0; if (templ instanceof StrandedFeature.Template) strand = ((StrandedFeature.Template) templ).strand.getValue(); StringBuffer lb = SeqFormatTo... |
AnnotationType.Impl type = new AnnotationType.Impl(); type.setConstraints( key, new PropertyConstraint.ExactValue(value), CardinalityConstraint.ONE ); setType(type); | public ByAnnotation(Object key, Object value) { this.key = key; this.value = value; } | |
public ByAnnotationType(AnnotationType type) { this.type = type; | protected ByAnnotationType() { this(AnnotationType.ANY); | public ByAnnotationType(AnnotationType type) { this.type = type; } |
return true; | return false; | public boolean isDisjoint(FeatureFilter filter) { if(filter instanceof AcceptNoneFilter) { return true; } else if(filter instanceof ByAnnotationType) { // check for common property names ByAnnotationType that = (ByAnnotationType) filter; Set props = that.getType().getProperties... |
AnnotationType.Impl type = new AnnotationType.Impl(); type.setConstraints( key, PropertyConstraint.ANY, CardinalityConstraint.ANY ); setType(type); | public HasAnnotation(Object key) { this.key = key; } | |
public DASComponentFeature(FeatureHolder parent, ComponentFeature.Template temp) | public DASComponentFeature(DASSequence parent, Location loc, StrandedFeature.Strand strand, String id) | public DASComponentFeature(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."); } ... |
if (locationContent(temp.location) != locationContent(temp.componentLocation)) { throw new BioException("Component and container locations must contain an equal number of symbols."); } | public DASComponentFeature(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."); } ... | |
if (!temp.location.isContiguous() || temp.componentLocation.isContiguous()) { throw new BioException("Can only include contiguous segments in an assembly [may change in future]"); } | public DASComponentFeature(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."); } ... | |
this.location = temp.location; this.type = temp.type; this.source = temp.source; this.annotation = temp.annotation; | this.location = loc; this.strand = strand; this.componentID = id; | public DASComponentFeature(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."); } ... |
this.strand = temp.strand; this.componentSequence = temp.componentSequence; this.componentLocation = temp.componentLocation; if (temp.strand == StrandedFeature.NEGATIVE) { this.translation = temp.location.getMax() - temp.componentLocation.getMin() + 1; this.projectedFeatures = new ProjectedFeatureHolder(componentSequ... | if (strand != StrandedFeature.NEGATIVE && strand != StrandedFeature.POSITIVE) { | public DASComponentFeature(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."); } ... |
return componentSequence.countFeatures(); | return getComponentSequence().countFeatures(); | public int countFeatures() { return componentSequence.countFeatures(); } |
return annotation; | return Annotation.EMPTY_ANNOTATION; | public Annotation getAnnotation() { return annotation; } |
return componentLocation; | return new RangeLocation(1, location.getMax() - location.getMin() + 1); | public Location getComponentLocation() { return componentLocation; } |
if (componentSequence == null) { try { componentSequence = new DASSequence(parent.getParentDB(), parent.getDataSourceURL(), componentID, parent.getName()); } catch (Exception ex) { throw new BioError(ex, "Couldn't create child DAS sequence"); } } | public Sequence getComponentSequence() { return componentSequence; } | |
if (projectedFeatures == null) { if (strand == StrandedFeature.NEGATIVE) { int translation = location.getMax() + 1; this.projectedFeatures = new ProjectedFeatureHolder(getComponentSequence(), this, translation, true); } else if (strand == StrandedFeature.POSITIVE) { int translation = location.getMin() - 1; this.projec... | protected FeatureHolder getProjectedFeatures() {// if (projectedFeatures == null) {// projectedFeatures = new ProjectedFeatureHolder(componentSequence,// this, translation);// } return projectedFeatures; } | |
FeatureHolder fh = parent; while (fh instanceof Feature) fh = ((Feature) fh).getParent(); return (Sequence) fh; | return parent; | public Sequence getSequence() { FeatureHolder fh = parent; while (fh instanceof Feature) fh = ((Feature) fh).getParent(); return (Sequence) fh; } |
return source; | return "Dazzle_Client"; | public String getSource() { return source; } |
SymbolList syms = componentLocation.symbols(componentSequence); | SymbolList syms = getComponentSequence(); | public SymbolList getSymbols() { SymbolList syms = componentLocation.symbols(componentSequence); if (strand == StrandedFeature.NEGATIVE) { try { syms = DNATools.reverseComplement(syms); } catch (IllegalAlphabetException ex) { throw new BioError(ex); } } return syms; } |
return type; | return "SubSequence"; | public String getType() { return type; } |
private ArrayList getIntervals() | ArrayList getIntervals() | private ArrayList getIntervals() { return new ArrayList( m_intervals ); } |
private String getAccession() | String getAccession() | private String getAccession() { return m_accession; } |
private String getFrom() | String getFrom() | private String getFrom() { return m_from; } |
private String getPoint() | String getPoint() | private String getPoint() { return m_point; } |
private String getTo() | String getTo() | private String getTo() { return m_to; } |
private String getConsortium() | String getConsortium() | private String getConsortium() { return m_consortium; } |
private String getRemark() | String getRemark() | private String getRemark() { return m_remark; } |
private String getContig() | String getContig() | private String getContig() { return m_contig; } |
private String getCreateDate() | String getCreateDate() | private String getCreateDate() { return m_createDate; } |
private String getCreateRelease() | String getCreateRelease() | private String getCreateRelease() { return m_createRelease; } |
private String getDatabaseReference() | String getDatabaseReference() | private String getDatabaseReference() { return m_databaseReference; } |
private String getEntryVersion() | String getEntryVersion() | private String getEntryVersion() { return m_entryVersion; } |
private String getPrimary() | String getPrimary() | private String getPrimary() { return m_primary; } |
private ArrayList getSecondaryAccessions() | ArrayList getSecondaryAccessions() | private ArrayList getSecondaryAccessions() { return new ArrayList( m_secondaryAccessions ); } |
private String getSegment() | String getSegment() | private String getSegment() { return m_segment; } |
private String getSourceDb() | String getSourceDb() | private String getSourceDb() { return m_sourceDb; } |
private String getUpdateRelease() | String getUpdateRelease() | private String getUpdateRelease() { return m_updateRelease; } |
(ct == null || ct == Annotatable.ANNOTATION)){ | Annotatable.ANNOTATION.isMatchingType(ChangeType.UNKNOWN)) { | protected ChangeSupport getChangeSupport(ChangeType ct){ ChangeSupport cs = super.getChangeSupport(ct); if(annotationForwarder == null && (ct == null || ct == Annotatable.ANNOTATION)){ annotationForwarder = new Annotatable.AnnotationForwarder( this, cs); getAnnotation().addChang... |
public SimpleBasisSymbol( | protected SimpleBasisSymbol( | public SimpleBasisSymbol( char token, String name, Annotation annotation, List symbols ) throws IllegalSymbolException { this(token, name, annotation); if(symbols == null) { throw new NullPointerException("symbols can't be null"); } if(symbols.size() == 0) { throw new IllegalSymbolExcepti... |
doIsaTest(OntoTools.EQUIVALENCE, OntoTools.PARTIAL_ORDER, true); | doIsaTest(OntoTools.EQUIVALENCE, OntoTools.PARTIAL_ORDER, false); | public void testCoreISA() throws OntologyException { Ontology onto = OntoTools.getCoreOntology(); doIsaTest(OntoTools.IS_A, OntoTools.IS_A, true); doIsaTest(OntoTools.HAS_A, OntoTools.IS_A, false); doIsaTest(OntoTools.RELATION, OntoTools.ANY, true); doIsaTest(OntoTools.REFLEXIVE, O... |
b.append(RichSequenceFormat.Tools.rightPad(key, indent)); String[] lines = RichSequenceFormat.Tools.writeWordWrap(text, sep, this.getLineWidth()-indent); | b.append(StringTools.rightPad(key, indent)); String[] lines = StringTools.writeWordWrap(text, sep, this.getLineWidth()-indent); | private void _writeWrappedLine(String key, int indent, String text, PrintStream os, String sep) throws IOException { text = text.trim(); StringBuffer b = new StringBuffer(); b.append(RichSequenceFormat.Tools.rightPad(key, indent)); String[] lines = RichSequenceFormat.Tools.writeWordWrap(... |
else b.append(RichSequenceFormat.Tools.leftIndent(lines[i],indent)); | else b.append(StringTools.leftIndent(lines[i],indent)); | private void _writeWrappedLine(String key, int indent, String text, PrintStream os, String sep) throws IOException { text = text.trim(); StringBuffer b = new StringBuffer(); b.append(RichSequenceFormat.Tools.rightPad(key, indent)); String[] lines = RichSequenceFormat.Tools.writeWordWrap(... |
if (key.equals("REMARK")) authors = val; | if (key.equals("REMARK")) remark = val; | public boolean readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) throws IllegalSymbolException, IOException, ParseException { String line; boolean hasAnotherSequence = true; boolean has... |
if (src.getDirection() == src.HORIZONTAL) { | if (src.getDirection() == SequenceRenderContext.HORIZONTAL) { | public void renderFeature( Graphics2D g, Feature f, SequenceRenderContext src ) { Shape s = null; Location loc = f.getLocation(); float depth = (float) (arrowSize + 2.0 * arrowScoop); double minD, maxD; if (src.getScale() > 1.0) { minD = src.sequenceToGraphics(loc.getMin()); maxD = src.seque... |
ReferenceServer ds = new ReferenceServer(dsURL, sourceText, descrText); | private void addDasURLImpl(URL dasURL) throws BioException, ChangeVetoException { try { URL dsnURL = new URL(dasURL, "dsn"); DAS.startedActivity(dsnURL); HttpURLConnection huc = (HttpURLConnection) dsnURL.openConnection(); huc.connect(); int status = DASSequenceDB.tolerantIntHeader(huc, "... | |
for(Iterator ai = master.getAnnotaters().iterator(); ai.hasNext(); ) { ds.addAnnotator( (DataSource) ai.next() ); } } dataSources.put(dsURL, ds); | master.setName(sourceText); master.setDescription(descrText); } else { ReferenceServer ds = new ReferenceServer(dsURL, sourceText, descrText); dataSources.put(dsURL, ds); } | private void addDasURLImpl(URL dasURL) throws BioException, ChangeVetoException { try { URL dsnURL = new URL(dasURL, "dsn"); DAS.startedActivity(dsnURL); HttpURLConnection huc = (HttpURLConnection) dsnURL.openConnection(); huc.connect(); int status = DASSequenceDB.tolerantIntHeader(huc, "... |
List l = Collections.nCopies(2,DNATools.getDNA()); | List l = Collections.nCopies(3,DNATools.getDNA()); | protected void setUp() { // create distributions try { dist = DistributionFactory.DEFAULT.createDistribution(DNATools.getDNA()); uniform = new UniformDistribution(DNATools.getDNA()); gap = new GapDistribution(DNATools.getDNA()); pair = new PairDistribution(dist,gap); List l = Collectio... |
System.out.println("ConditionedDistClass = "+orderN.getDistribution(s).getClass().getName()); | public void testOrderNSerialization()throws Exception{ File f = File.createTempFile("DistSerTest",".tmp"); ObjectOutputStream oos = new ObjectOutputStream(new BufferedOutputStream(new FileOutputStream(f))); oos.writeObject(orderN); oos.flush(); oos.close(); ObjectInputStream ois = new ... | |
System.out.println("Testing post Ser vs post Ser"); | public void testOrderNSerialization()throws Exception{ File f = File.createTempFile("DistSerTest",".tmp"); ObjectOutputStream oos = new ObjectOutputStream(new BufferedOutputStream(new FileOutputStream(f))); oos.writeObject(orderN); oos.flush(); oos.close(); ObjectInputStream ois = new ... | |
System.out.println("ConditionedDistClass = "+((OrderNDistribution)dist2).getDistribution(s).getClass().getName()); | public void testOrderNSerialization()throws Exception{ File f = File.createTempFile("DistSerTest",".tmp"); ObjectOutputStream oos = new ObjectOutputStream(new BufferedOutputStream(new FileOutputStream(f))); oos.writeObject(orderN); oos.flush(); oos.close(); ObjectInputStream ois = new ... | |
System.out.println("Testing pre Ser vs post Ser"); | public void testOrderNSerialization()throws Exception{ File f = File.createTempFile("DistSerTest",".tmp"); ObjectOutputStream oos = new ObjectOutputStream(new BufferedOutputStream(new FileOutputStream(f))); oos.writeObject(orderN); oos.flush(); oos.close(); ObjectInputStream ois = new ... | |
private static void doIndex(File index, Set seqFiles, int seqType) | private static void doIndex(String dbName, File index, Set seqFiles, int seqType) | private static void doIndex(File index, Set seqFiles, int seqType) throws Exception { if (index.exists()) { File [] indexedFiles = index.listFiles(); for (int i = 0; i < indexedFiles.length; i++) { if (indexedFiles[i].canWrite()) ... |
IndexTools.indexFasta(index, files, alphaType); | IndexTools.indexFasta(dbName, index, files, alphaType); | private static void doIndex(File index, Set seqFiles, int seqType) throws Exception { if (index.exists()) { File [] indexedFiles = index.listFiles(); for (int i = 0; i < indexedFiles.length; i++) { if (indexedFiles[i].canWrite()) ... |
IndexTools.indexEmbl(index, files, alphaType); | IndexTools.indexEmbl(dbName, index, files, alphaType); | private static void doIndex(File index, Set seqFiles, int seqType) throws Exception { if (index.exists()) { File [] indexedFiles = index.listFiles(); for (int i = 0; i < indexedFiles.length; i++) { if (indexedFiles[i].canWrite()) ... |
IndexTools.indexGenbank(index, files, alphaType); | IndexTools.indexGenbank(dbName, index, files, alphaType); | private static void doIndex(File index, Set seqFiles, int seqType) throws Exception { if (index.exists()) { File [] indexedFiles = index.listFiles(); for (int i = 0; i < indexedFiles.length; i++) { if (indexedFiles[i].canWrite()) ... |
IndexTools.indexSwissprot(index, files); | IndexTools.indexSwissprot(dbName, index, files); | private static void doIndex(File index, Set seqFiles, int seqType) throws Exception { if (index.exists()) { File [] indexedFiles = index.listFiles(); for (int i = 0; i < indexedFiles.length; i++) { if (indexedFiles[i].canWrite()) ... |
throw new BioException(nsee, "Malformed OBDA index " + "does not indicate sequence format"); | throw new BioException("Malformed OBDA index " + "does not indicate sequence format", nsee); | private static LifeScienceIdentifier getFormatSpec(Annotation config) throws BioException { LifeScienceIdentifier format; try { String lsid = (String) config.getProperty("format"); format = LifeScienceIdentifier.valueOf(lsid); } catch (NoSuchElement... |
throw new BioException(lse, "Malformed OBDA index " + "has a format identifier which is not a valid LSID"); | throw new BioException("Malformed OBDA index " + "has a format identifier which is not a valid LSID", lse); | private static LifeScienceIdentifier getFormatSpec(Annotation config) throws BioException { LifeScienceIdentifier format; try { String lsid = (String) config.getProperty("format"); format = LifeScienceIdentifier.valueOf(lsid); } catch (NoSuchElement... |
doIndex(index, seqFiles, seqType); | doIndex(dbName, index, seqFiles, seqType); | public static void main(String [] argv) throws Exception { Options opts = createOptions(); try { CommandLine cmd = new GnuParser().parse(opts, argv); String alphabet = ""; String format = ""; String dbName = ""; String location = "";... |
super( '-', "gap", Annotation.EMPTY_ANNOTATION, Alphabet.EMPTY_ALPHABET ); } | } | public GapSymbol() { super( '-', "gap", Annotation.EMPTY_ANNOTATION, Alphabet.EMPTY_ALPHABET ); } |
super(token, name, a); | super(name, token, a); | public WellKnownSymbol(WellKnownAlphabet alpha, char token, String name, Annotation a) { super(token, name, a); this.alpha = alpha; } |
"Got symbol ref to " + refName + " but it doesn't match anythin" | "Got symbol ref to " + refName + " but it doesn't match anything" | static private Symbol ambiguityFromXML( Alphabet alpha, Element symE, Map nameToSym ) throws IllegalSymbolException { char token = '\0'; String name = null; String description = null; Set syms = new HashSet(); NodeList children = symE.getChildNodes(); for(int i = 0; i < children.getLength();... |
token, name, Annotation.EMPTY_ANNOTATION, | token, Annotation.EMPTY_ANNOTATION, | static private Symbol ambiguityFromXML( Alphabet alpha, Element symE, Map nameToSym ) throws IllegalSymbolException { char token = '\0'; String name = null; String description = null; Set syms = new HashSet(); NodeList children = symE.getChildNodes(); for(int i = 0; i < children.getLength();... |
AtomicSymbol as = new SimpleAtomicSymbol(token, name, annotation); | AtomicSymbol as = new FundamentalAtomicSymbol(name, token, annotation); | static public AtomicSymbol createSymbol( char token, String name, Annotation annotation ) { AtomicSymbol as = new SimpleAtomicSymbol(token, name, annotation); return as; } |
alpha, token, name, Annotation.EMPTY_ANNOTATION | alpha, token, name, new SimpleAnnotation() | static private AtomicSymbol symbolFromXML( Element symE, WellKnownAlphabet alpha ) { char token = '\0'; String name = null; String description = null; NodeList children = symE.getChildNodes(); for(int i = 0; i < children.getLength(); i++) { Node n = children.item(i); if (! (n instanceof E... |
return new IndexedNthOrderDistribution(alpha, df); } else { return new GeneralNthOrderDistribution(alpha, df); | return new IndexedNthOrderDistribution(alpha, df); } else { Alphabet conditioned = (Alphabet)aList.get(aList.size()-1); Alphabet conditioning = AlphabetManager.getCrossProductAlphabet(aList.subList(0,aList.size()-1)); List l = new ArrayList(); l.add(conditioning); l.add(conditioned); alpha = AlphabetManager.getCrossPr... | public Distribution createDistribution(Alphabet alpha) throws IllegalAlphabetException { List aList = alpha.getAlphabets(); if ( aList.size() == 2 && aList.get(0) == org.biojava.bio.seq.DNATools.getDNA() ) { return new IndexedNthOrderDistribution(alpha, df); } else { retur... |
currentVal.append(line.substring(8)); | currentVal.append(line.substring(8).trim()); | private List readSection(BufferedReader br) throws ParseException { List section = new ArrayList(); String line; String currKey = null; StringBuffer currVal = new StringBuffer(); boolean done = false; int linecount = 0; // while not done try { ... |
if (currentTag!=null) section.add(new String[]{currentTag,currentVal.toString()}); | private List readSection(BufferedReader br) throws ParseException { List section = new ArrayList(); String line; String currKey = null; StringBuffer currVal = new StringBuffer(); boolean done = false; int linecount = 0; // while not done try { ... | |
assertEquals(be.COMMENT, ce.getType()); | assertEquals(BioEntry.COMMENT, ce.getType()); | public void testAddComment() { System.out.println("testAddComment"); //should not be able to add null try{ be.addComment(null); fail("Expected IllegalArgumentException"); }catch(IllegalArgumentException ex){} catch(Exception ex){ fail("No... |
assertEquals(be.RANKEDCROSSREF, ce.getType()); | assertEquals(BioEntry.RANKEDCROSSREF, ce.getType()); | public void testAddRankedCrossRef() { System.out.println("testAddRankedCrossRef"); //should not be able to add null try{ be.addRankedCrossRef(null); fail("Expected IllegalArgumentException"); }catch(IllegalArgumentException ex){} catch(Exception ex){... |
assertEquals(be.RANKEDDOCREF, ce.getType()); | assertEquals(BioEntry.RANKEDDOCREF, ce.getType()); | public void testAddRankedDocRef() { System.out.println("testAddRankedDocRef"); //should not be able to add null try{ be.addRankedDocRef(null); fail("Expected IllegalArgumentException"); }catch(IllegalArgumentException ex){} catch(Exception ex){ ... |
assertEquals(be.RELATIONS, ce.getType()); | assertEquals(BioEntry.RELATIONS, ce.getType()); | public void testAddRelationship() { System.out.println("testAddRelationship"); //should not be able to add null try{ be.addRelationship(null); fail("Expected IllegalArgumentException"); }catch(IllegalArgumentException ex){} catch(Exception ex){ ... |
assertEquals(be.COMMENT, ce.getType()); | assertEquals(BioEntry.COMMENT, ce.getType()); | public void testRemoveComment() { System.out.println("testRemoveComment"); //should not be able to remove null try{ be.removeComment(null); fail("Expected IllegalArgumentException"); }catch(IllegalArgumentException ex){} catch(Exception ex){ ... |
assertEquals(be.RANKEDCROSSREF, ce.getType()); | assertEquals(BioEntry.RANKEDCROSSREF, ce.getType()); | public void testRemoveRankedCrossRef() { System.out.println("testRemoveRankedCrossRef"); //first add one RankedCrossRef xref = new SimpleRankedCrossRef( new SimpleCrossRef("dbname", "AC123456", 1), 0); try{ be.addRankedCrossRef(xref); } ca... |
assertEquals(be.RANKEDDOCREF, ce.getType()); | assertEquals(BioEntry.RANKEDDOCREF, ce.getType()); | public void testRemoveRankedDocRef() { System.out.println("testRemoveRankedDocRef"); //should not be able to remove null try{ be.removeRankedDocRef(null); fail("Expected IllegalArgumentException"); }catch(IllegalArgumentException ex){} catch(Exceptio... |
assertEquals(be.RELATIONS, ce.getType()); | assertEquals(BioEntry.RELATIONS, ce.getType()); | public void testRemoveRelationship() { System.out.println("testRemoveRelationship"); //should not be able to remove null try{ be.removeRelationship(null); fail("Expected IllegalArgumentException"); }catch(IllegalArgumentException ex){} catch(Exceptio... |
assertEquals(be.DESCRIPTION, ce.getType()); | assertEquals(BioEntry.DESCRIPTION, ce.getType()); | public void testSetDescription() { System.out.println("testSetDescription"); String d = "new desc"; try{ be.setDescription(d); //should get back d assertEquals(d, be.getDescription()); //should have generated an event Ch... |
assertEquals(be.DIVISION, ce.getType()); | assertEquals(BioEntry.DIVISION, ce.getType()); | public void testSetDivision() { System.out.println("testSetDivision"); String div = "new div"; try{ be.setDivision(div); //should get back div assertEquals(div, be.getDivision()); //should have generated an event ChangeE... |
assertEquals(be.IDENTIFIER, ce.getType()); | assertEquals(BioEntry.IDENTIFIER, ce.getType()); | public void testSetIdentifier() { System.out.println("testSetIdentifier"); String id = "new id"; try{ be.setIdentifier(id); //should get back id assertEquals(id, be.getIdentifier()); //should have generated an event Chan... |
assertEquals(be.TAXON, cr.getEvent().getType()); | assertEquals(BioEntry.TAXON, cr.getEvent().getType()); | public void testSetTaxon() { System.out.println("testSetTaxon"); NCBITaxon tax = new SimpleNCBITaxon(1621); try{ be.addChangeListener(cr); be.setTaxon(tax); //should have fired an event; assertNotNull(cr.getEvent()); ... |
alpha = am.alphabetForName("DNA"); | alpha = am.getGappedAlphabet(DNATools.getAmbiguity()); | 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... |
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