rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k |
|---|---|---|
queryText = "from SimpleNamespace as ns where ns.name = ?"; | queryText = "from Namespace as ns where ns.name = ?"; | public Object buildObject(Class clazz, Object[] params) { Object o = super.buildObject(clazz, params); String queryText; if (o instanceof SimpleNamespace) { queryText = "from SimpleNamespace as ns where ns.name = ?"; } else if (o instanceof SimpleComparableOntology) { ... |
queryText = "from SimpleComparableOntology as o where o.name = ?"; | queryText = "from Ontology as o where o.name = ?"; | public Object buildObject(Class clazz, Object[] params) { Object o = super.buildObject(clazz, params); String queryText; if (o instanceof SimpleNamespace) { queryText = "from SimpleNamespace as ns where ns.name = ?"; } else if (o instanceof SimpleComparableOntology) { ... |
queryText = "from SimpleNCBITaxon as o where o.NCBITaxID = ?"; | queryText = "from Taxon as o where o.NCBITaxID = ?"; | public Object buildObject(Class clazz, Object[] params) { Object o = super.buildObject(clazz, params); String queryText; if (o instanceof SimpleNamespace) { queryText = "from SimpleNamespace as ns where ns.name = ?"; } else if (o instanceof SimpleComparableOntology) { ... |
queryText = "from SimpleCrossRef as cr where cr.dbname = ? and cr.accession = ?"; | queryText = "from CrossRef as cr where cr.dbname = ? and cr.accession = ?"; | public Object buildObject(Class clazz, Object[] params) { Object o = super.buildObject(clazz, params); String queryText; if (o instanceof SimpleNamespace) { queryText = "from SimpleNamespace as ns where ns.name = ?"; } else if (o instanceof SimpleComparableOntology) { ... |
queryText = "from SimpleDocRef as cr where cr.authors = ? and cr.location = ?"; | queryText = "from DocRef as cr where cr.authors = ? and cr.location = ?"; | public Object buildObject(Class clazz, Object[] params) { Object o = super.buildObject(clazz, params); String queryText; if (o instanceof SimpleNamespace) { queryText = "from SimpleNamespace as ns where ns.name = ?"; } else if (o instanceof SimpleComparableOntology) { ... |
FeatureFilter.And ffa = (FeatureFilter.And) ff; | public void writeFilter(FeatureFilter ff, XMLWriter xw, XMLFilterWriter config) throws ClassCastException, IllegalArgumentException, IOException { FeatureFilter.And ffa = (FeatureFilter.And) ff; xw.openTag(XML_... | |
FeatureFilter.Or ffa = (FeatureFilter.Or) ff; | public void writeFilter(FeatureFilter ff, XMLWriter xw, XMLFilterWriter config) throws ClassCastException, IllegalArgumentException, IOException { FeatureFilter.Or ffa = (FeatureFilter.Or) ff; xw.openTag(XML_FI... | |
public KeyedWeakReference(Object key, Object ref, ReferenceQueue queue) { super(ref, queue); | public KeyedWeakReference(Object key, Object ref) { super(ref); | public KeyedWeakReference(Object key, Object ref, ReferenceQueue queue) { super(ref, queue); this.key = key; } |
numNs = Math.min(loc.getMin(), end) - pos; | numNs = Math.min(loc.getMin(), end + 1) - pos; | public String subStr(int start, int end) { if (start < 1 || end > length) { throw new IndexOutOfBoundsException("Range out of bounds: " + start + " - " + end); } StringBuffer sb = new StringBuffer(); int pos = start; while (pos <= end) { Location loc = locationOfPoint(pos); if (loc != null) { SymbolLis... |
catch (IOException iox) | catch (IOException ioe) | public boolean hasNext() { if (! moreSearchesAvailable) try { reader.close(); } catch (IOException iox) { iox.printStackTrace(); } return moreSearchesAvailable; } |
iox.printStackTrace(); | ioe.printStackTrace(); | public boolean hasNext() { if (! moreSearchesAvailable) try { reader.close(); } catch (IOException iox) { iox.printStackTrace(); } return moreSearchesAvailable; } |
catch (ParserException pex) | catch (ParserException pe) | public Object next() throws NoSuchElementException { if (! moreSearchesAvailable) throw new NoSuchElementException("Attempt to read search result from empty stream"); try { moreSearchesAvailable = parser.parseSearch(reader, handler); return handler.makeSearchResult(); } catch (ParserException pex) { ... |
+ pex.getLineNumber() | + pe.getLineNumber() | public Object next() throws NoSuchElementException { if (! moreSearchesAvailable) throw new NoSuchElementException("Attempt to read search result from empty stream"); try { moreSearchesAvailable = parser.parseSearch(reader, handler); return handler.makeSearchResult(); } catch (ParserException pex) { ... |
catch (IOException iox) | catch (IOException ioe) | public Object next() throws NoSuchElementException { if (! moreSearchesAvailable) throw new NoSuchElementException("Attempt to read search result from empty stream"); try { moreSearchesAvailable = parser.parseSearch(reader, handler); return handler.makeSearchResult(); } catch (ParserException pex) { ... |
catch (BioException bex) | catch (BioException be) | public Object next() throws NoSuchElementException { if (! moreSearchesAvailable) throw new NoSuchElementException("Attempt to read search result from empty stream"); try { moreSearchesAvailable = parser.parseSearch(reader, handler); return handler.makeSearchResult(); } catch (ParserException pex) { ... |
+ bex.getMessage()); | + be.getMessage()); | public Object next() throws NoSuchElementException { if (! moreSearchesAvailable) throw new NoSuchElementException("Attempt to read search result from empty stream"); try { moreSearchesAvailable = parser.parseSearch(reader, handler); return handler.makeSearchResult(); } catch (ParserException pex) { ... |
public void postChangeTransitionScore(TransitionEvent te) { updateTransitions(); } | public void postChangeTransitionScore(TransitionEvent te) {} | public void postChangeTransitionScore(TransitionEvent te) { updateTransitions(); } |
public void postCreateTransition(TransitionEvent te) { updateTransitions(); } | public void postCreateTransition(TransitionEvent te) {} | public void postCreateTransition(TransitionEvent te) { updateTransitions(); } |
public void postDestroyTransition(TransitionEvent te) { updateTransitions(); } | public void postDestroyTransition(TransitionEvent te) {} | public void postDestroyTransition(TransitionEvent te) { updateTransitions(); } |
throws ModelVetoException {} | throws ModelVetoException { complain(te); } | public void preChangeTransitionScore(TransitionEvent te) throws ModelVetoException {} |
throws ModelVetoException {} | throws ModelVetoException { complain(te); } | public void preCreateTransition(TransitionEvent te) throws ModelVetoException {} |
throws ModelVetoException {} | throws ModelVetoException { complain(te); } | public void preDestroyTransition(TransitionEvent te) throws ModelVetoException {} |
HMMOrderByTransition(MarkovModel mm) { | private HMMOrderByTransition(MarkovModel mm) { | HMMOrderByTransition(MarkovModel mm) { this.mm = mm; } |
this.forwardTransitionScores = new HashMap(); this.backwardTransitionScores = new HashMap(); | public DP(MarkovModel model) throws IllegalSymbolException, IllegalTransitionException, BioException { this.model = model; updateTransitions(); model.addTransitionListener(UPDATER); } | |
public abstract double backward(SymbolList [] resList) | public abstract double backward(SymbolList [] resList, ScoreType scoreType) | public abstract double backward(SymbolList [] resList) throws IllegalSymbolException, IllegalAlphabetException, IllegalTransitionException; |
public abstract DPMatrix backwardMatrix(SymbolList [] resList) | public abstract DPMatrix backwardMatrix(SymbolList [] resList, ScoreType scoreType) | public abstract DPMatrix backwardMatrix(SymbolList [] resList) throws IllegalSymbolException, IllegalAlphabetException, IllegalTransitionException; |
int [][] transitions) throws IllegalSymbolException { | int [][] transitions, ScoreType scoreType ) throws IllegalSymbolException { | public static double [][] backwardTransitionScores(MarkovModel model, State [] states, int [][] transitions) throws IllegalSymbolException { int stateCount = states.length; double [][] scores = new double[stateCount][]; for (int i = 0; i < stateCount; i++) { State is = states[i]; scores[i] = ... |
scores[i][j] = model.getWeights(is).getWeight(states[transitions[i][j]]); | scores[i][j] = Math.log(scoreType.calculateScore( model.getWeights(is), states[transitions[i][j]] )); | public static double [][] backwardTransitionScores(MarkovModel model, State [] states, int [][] transitions) throws IllegalSymbolException { int stateCount = states.length; double [][] scores = new double[stateCount][]; for (int i = 0; i < stateCount; i++) { State is = states[i]; scores[i] = ... |
if (trans.contains(states[j])) | if (trans.contains(states[j])) { | public static int [][] backwardTransitions(MarkovModel model, State [] states) throws IllegalSymbolException { int stateCount = states.length; int [][] transitions = new int[stateCount][]; for (int i = 0; i < stateCount; i++) { int [] tmp = new int[stateCount]; int len = 0; FiniteAlphabet ... |
for (int j = 0; j < len; j++) | for (int j = 0; j < len; j++) { | public static int [][] backwardTransitions(MarkovModel model, State [] states) throws IllegalSymbolException { int stateCount = states.length; int [][] transitions = new int[stateCount][]; for (int i = 0; i < stateCount; i++) { int [] tmp = new int[stateCount]; int len = 0; FiniteAlphabet ... |
} | public static int [][] backwardTransitions(MarkovModel model, State [] states) throws IllegalSymbolException { int stateCount = states.length; int [][] transitions = new int[stateCount][]; for (int i = 0; i < stateCount; i++) { int [] tmp = new int[stateCount]; int len = 0; FiniteAlphabet ... | |
System.out.println("Got state " + s + " with name " + s.getName()); | public static MarkovModel flatView(MarkovModel model) throws IllegalAlphabetException, IllegalSymbolException { for(Iterator i = model.stateAlphabet().iterator(); i.hasNext(); ) { State s = (State) i.next(); if( !(s instanceof DotState) && !(s instanceof EmissionState) ) { Syst... | |
public abstract double forward(SymbolList [] resList) | public abstract double forward(SymbolList [] resList, ScoreType scoreType) | public abstract double forward(SymbolList [] resList) throws IllegalSymbolException, IllegalAlphabetException, IllegalTransitionException; |
public abstract DPMatrix forwardMatrix(SymbolList [] resList) | public abstract DPMatrix forwardMatrix(SymbolList [] resList, ScoreType scoreType) | public abstract DPMatrix forwardMatrix(SymbolList [] resList) throws IllegalSymbolException, IllegalAlphabetException, IllegalTransitionException; |
int [][] transitions | int [][] transitions, ScoreType scoreType | public static double [][] forwardTransitionScores( MarkovModel model, State [] states, int [][] transitions ) throws IllegalSymbolException { int stateCount = states.length; double [][] scores = new double[stateCount][]; for (int i = 0; i < stateCount; i++) { State is = states[i]; scores[... |
scores[i][j] = model.getWeights(states[transitions[i][j]]).getWeight(is); | scores[i][j] = Math.log(scoreType.calculateScore( model.getWeights(states[transitions[i][j]]), is )); | public static double [][] forwardTransitionScores( MarkovModel model, State [] states, int [][] transitions ) throws IllegalSymbolException { int stateCount = states.length; double [][] scores = new double[stateCount][]; for (int i = 0; i < stateCount; i++) { State is = states[i]; scores[... |
for (int j = 0; j < len; j++) | for (int j = 0; j < len; j++) { | public static int [][] forwardTransitions( MarkovModel model, State [] states ) throws IllegalSymbolException { int stateCount = states.length; int [][] transitions = new int[stateCount][]; for (int i = 0; i < stateCount; i++) { int [] tmp = new int[stateCount]; int len = 0; FiniteAlpha... |
} | public static int [][] forwardTransitions( MarkovModel model, State [] states ) throws IllegalSymbolException { int stateCount = states.length; int [][] transitions = new int[stateCount][]; for (int i = 0; i < stateCount; i++) { int [] tmp = new int[stateCount]; int len = 0; FiniteAlpha... | |
public DPMatrix forwardsBackwards(SymbolList [] resList) | public DPMatrix forwardsBackwards(SymbolList [] resList, ScoreType scoreType) | public DPMatrix forwardsBackwards(SymbolList [] resList) throws BioException { try { System.out.println("Making backward matrix"); final DPMatrix bMatrix = backwardMatrix(resList); System.out.println("Making forward matrix"); final DPMatrix fMatrix = forwardMatrix(resList); System.out... |
final DPMatrix bMatrix = backwardMatrix(resList); | final DPMatrix bMatrix = backwardMatrix(resList, scoreType); | public DPMatrix forwardsBackwards(SymbolList [] resList) throws BioException { try { System.out.println("Making backward matrix"); final DPMatrix bMatrix = backwardMatrix(resList); System.out.println("Making forward matrix"); final DPMatrix fMatrix = forwardMatrix(resList); System.out... |
final DPMatrix fMatrix = forwardMatrix(resList); | final DPMatrix fMatrix = forwardMatrix(resList, scoreType); | public DPMatrix forwardsBackwards(SymbolList [] resList) throws BioException { try { System.out.println("Making backward matrix"); final DPMatrix bMatrix = backwardMatrix(resList); System.out.println("Making forward matrix"); final DPMatrix fMatrix = forwardMatrix(resList); System.out... |
public double [][] getBackwardTransitionScores() { return backwardTransitionScores; | public double [][] getBackwardTransitionScores(ScoreType scoreType) { double [][] ts = (double [][]) backwardTransitionScores.get(scoreType); if(ts == null) { try { backwardTransitionScores.put(scoreType, ts = backwardTransitionScores( getModel(), getStates(), backwardTransitions, scoreType )); } catch (IllegalSymbolEx... | public double [][] getBackwardTransitionScores() { return backwardTransitionScores; } |
public double [][] getForwardTransitionScores() { return forwardTransitionScores; | public double [][] getForwardTransitionScores(ScoreType scoreType) { double [][] ts = (double [][]) forwardTransitionScores.get(scoreType); if(ts == null) { try { forwardTransitionScores.put(scoreType, ts = forwardTransitionScores( getModel(), getStates(), forwardTransitions, scoreType )); } catch (IllegalSymbolExcepti... | public double [][] getForwardTransitionScores() { return forwardTransitionScores; } |
for (int c = 0; c < cols; c++) | for (int c = 0; c < cols; c++) { | public static double scoreWeightMatrix( WeightMatrix matrix, SymbolList symList, int start) throws IllegalSymbolException { double score = 0; int cols = matrix.columns(); for (int c = 0; c < cols; c++) score += Math.log(matrix.getColumn(c).getWeight(symList.symbolAt(c + start))); return score; } |
} | public static double scoreWeightMatrix( WeightMatrix matrix, SymbolList symList, int start) throws IllegalSymbolException { double score = 0; int cols = matrix.columns(); for (int c = 0; c < cols; c++) score += Math.log(matrix.getColumn(c).getWeight(symList.symbolAt(c + start))); return score; } | |
this.forwardTransitionScores = forwardTransitionScores( model, states, forwardTransitions ); | this.forwardTransitionScores.clear(); | public void updateTransitions() { try { this.states = stateList(model); this.forwardTransitions = forwardTransitions(model, states); this.forwardTransitionScores = forwardTransitionScores( model, states, forwardTransitions ); this.backwardTransitions = backwardTransitions(mod... |
this.backwardTransitionScores = backwardTransitionScores( model, states, backwardTransitions ); | this.backwardTransitionScores.clear(); | public void updateTransitions() { try { this.states = stateList(model); this.forwardTransitions = forwardTransitions(model, states); this.forwardTransitionScores = forwardTransitionScores( model, states, forwardTransitions ); this.backwardTransitions = backwardTransitions(mod... |
public abstract StatePath viterbi(SymbolList [] resList) | public abstract StatePath viterbi(SymbolList [] resList, ScoreType scoreType) | public abstract StatePath viterbi(SymbolList [] resList) throws IllegalSymbolException, IllegalArgumentException, IllegalAlphabetException, IllegalTransitionException; |
for (Iterator ai = ((List) value).iterator(); ai.hasNext();) | List l; if(value instanceof List){ l = (List)value; }else{ l = new ArrayList(); l.add(value); } for (Iterator ai = l.iterator(); ai.hasNext();) | public void addSequenceProperty(Object key, Object value) throws ParseException { if (key.equals("LOCUS")) { idb.setLength(0); idb.append("LOCUS " + (String) value); } else if (key.equals("TYPE")) { typeb.append(value); } else if (k... |
System.out.println("Stream read interupted"); | System.out.println("Stream read interrupted"); | public void parse(InputSource poSource ) throws IOException,SAXException { BufferedReader oContents; String oLine = null; //Use method form superclass oContents = this.getContentStream(poSource); // loop over file try { // loop over file oLine = oContents.readLine(); while... |
public OverlayMap(Map parent) { | public OverlayMap(Map parent, Map overlay) { | public OverlayMap(Map parent) { super(); this.parent = parent; this.overlay = new HashMap(); } |
this.overlay = new HashMap(); | this.overlay = overlay; | public OverlayMap(Map parent) { super(); this.parent = parent; this.overlay = new HashMap(); } |
public Segment(String id, int start, int stop) { | public Segment(String id) { | public Segment(String id, int start, int stop) { this.id = id; this.start = start; this.stop = stop; } |
this.start = start; this.stop = stop; | this.start = this.stop = -1; | public Segment(String id, int start, int stop) { this.id = id; this.start = start; this.stop = stop; } |
void registerFeatureFetcher(Object regKey) { | private void registerFeatureFetcher(int tileNum, Object regKey) { | void registerFeatureFetcher(Object regKey) { Location[] tiles = getTiles(); for (int t = 0; t < tiles.length; ++t) { registerFeatureFetcher(t, regKey); } } |
for (int t = 0; t < tiles.length; ++t) { registerFeatureFetcher(t, regKey); | if (tileFeatures[tileNum] == null || tileFeatures[tileNum].get() == null) { if (featureTickets[tileNum] == null) { SeqIOListener listener = new DASFeatureSetPopulator(tileNum); FeatureRequestManager frm = refSequence.getParentDB().getFeatureRequestManager(); if (tiles.length > 1) { featureTickets[tileNum] = frm.request... | void registerFeatureFetcher(Object regKey) { Location[] tiles = getTiles(); for (int t = 0; t < tiles.length; ++t) { registerFeatureFetcher(t, regKey); } } |
if (Character.isDigit(nextCh)) return NUMERIC; | private int nextTokenType() { if (!hasNext()) return EOL; char nextCh = packedTxt.charAt(ptr); // symbol tokens assumed to be alphas. if (Character.isLetter(nextCh)) return SYMBOL_TOKEN; // now check for specific chars if (n... | |
StringBuffer numString = new StringBuffer(); | private Range getIterations() throws ParserException { Range range = new Range(); // consume the left brace toke.getToken(); // there can either be one or two numbers boolean onSecondArg = false; while (toke.hasNext()) { int tokenType = toke.nextTokenTy... | |
if (toke.getToken() == Tokenizer.LEFT_BRACE) { | if (toke.nextTokenType() == Tokenizer.LEFT_BRACE) { | public PatternSearch.Pattern parsePattern(String patternTxt, FiniteAlphabet alfa) throws BioException, IllegalSymbolException, IllegalAlphabetException, ParserException { toke = new Tokenizer(patternTxt); pattern = new PatternSearch.Pattern(patternTxt, alfa); symToke = alfa.getTokeniz... |
} catch (MappingException e) { throw new SQLException("Type mapping exception:".concat(e.getMessage())); | public boolean execute(String sql) throws SQLException { zeroLastResources(); checkIfClosed(); connection.checkClosed(); switch (getStatementType(sql)) { case type_select: lastActionResultSet = executeQuery(sql); case type_update: break; default: { SimpleSQL ssql = new SimpleSQL(); ssql.setClient(client... | |
byte[] cmsg = ((org.pgj.messages.Error) msg).getMessage().getBytes(); | byte[] cmsg = null; String mesg = ((org.pgj.messages.Error) msg).getMessage(); if(mesg == null ){ cmsg = new byte[0]; } else { cmsg = mesg.getBytes(); } | public void sendMessage(Message msg, PGStream stream) throws IOException { byte[] cname = ((org.pgj.messages.Error) msg).getExceptionClassName() .getBytes(); stream.SendInteger(cname.length, 4); stream.Send(cname); byte[] cmsg = ((org.pgj.messages.Error) msg).getMessage().getBytes(); stream.SendInteger(cmsg.le... |
rlistener.addSequenceProperty(getMolTypeTerm(),m.group(3)); rlistener.addSequenceProperty(getModificationTerm(),m.group(6)); | rlistener.addSequenceProperty(Terms.getMolTypeTerm(),m.group(3)); rlistener.addSequenceProperty(Terms.getModificationTerm(),m.group(6)); | public boolean readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) throws IllegalSymbolException, IOException, ParseException { String line; boolean hasAnotherSequence = true; boolea... |
if (stranded!=null) rlistener.addSequenceProperty(getStrandedTerm(),stranded); | if (stranded!=null) rlistener.addSequenceProperty(Terms.getStrandedTerm(),stranded); | public boolean readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) throws IllegalSymbolException, IOException, ParseException { String line; boolean hasAnotherSequence = true; boolea... |
rlistener.addSequenceProperty(getAccessionTerm(),accs[i].trim()); | rlistener.addSequenceProperty(Terms.getAccessionTerm(),accs[i].trim()); | public boolean readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) throws IllegalSymbolException, IOException, ParseException { String line; boolean hasAnotherSequence = true; boolea... |
rlistener.addSequenceProperty(getKeywordsTerm(), ((String[])section.get(0))[1]); | rlistener.addSequenceProperty(Terms.getKeywordsTerm(), ((String[])section.get(0))[1]); | public boolean readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) throws IllegalSymbolException, IOException, ParseException { String line; boolean hasAnotherSequence = true; boolea... |
pcr = (CrossRef)RichObjectFactory.getObject(SimpleCrossRef.class,new Object[]{"PUBMED", pubmed}); | pcr = (CrossRef)RichObjectFactory.getObject(SimpleCrossRef.class,new Object[]{Terms.PUBMED_KEY, pubmed}); | public boolean readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) throws IllegalSymbolException, IOException, ParseException { String line; boolean hasAnotherSequence = true; boolea... |
mcr = (CrossRef)RichObjectFactory.getObject(SimpleCrossRef.class,new Object[]{"MEDLINE", medline}); | mcr = (CrossRef)RichObjectFactory.getObject(SimpleCrossRef.class,new Object[]{Terms.MEDLINE_KEY, medline}); | public boolean readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) throws IllegalSymbolException, IOException, ParseException { String line; boolean hasAnotherSequence = true; boolea... |
templ.sourceTerm = getGenBankTerm(); | templ.sourceTerm = Terms.getGenBankTerm(); | public boolean readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) throws IllegalSymbolException, IOException, ParseException { String line; boolean hasAnotherSequence = true; boolea... |
return new SimpleSequence(resList, uri, name, annotation, realizer); | return new org.biojava.bio.seq.impl.SimpleSequence(resList, uri, name, annotation, realizer); | public Sequence createSequence(SymbolList resList, String uri, String name, Annotation annotation) { return new SimpleSequence(resList, uri, name, annotation, realizer); } |
throw new IndexOutOfBoundsException(); | throw new IndexOutOfBoundsException("Index out of range: " + pos); | public Symbol symbolAt(int pos) { if (pos < 1 || pos > length) throw new IndexOutOfBoundsException(); return array[offset + pos - 1]; } |
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+db+"&id="+id; retur... | 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 + db + "&id=" + id ... | 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+db+"&id="+id; ... |
public Sequence getSequence(String id) throws BioException { try { IOExceptionFound=false; ExceptionFound=false; URL queryURL = getAddress(id); SequenceFormat sFormat = getSequenceFormat(); SequenceBuilder sbuilder = new SimpleSequenceBuilder(); SequenceBuilderFactory sFact=new GenbankProcessor.Factory(SimpleSequenceB... | public Sequence getSequence(String id) throws BioException { try { IOExceptionFound = false; ExceptionFound = false; URL queryURL = getAddress(id); SequenceFormat sFormat = getSequenceFormat(); SequenceBuilder sbuilder = new SimpleSequenceBuilder(); SequenceBuilderFactory sFact = new GenbankProcessor.Factory( SimpleS... | 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 incoming se... |
hitQueryStart(), hitQueryEnd(), hitQueryStrand(), hitSubjectStart(), hitSubjectEnd(), hitSubjectStrand(), | subs[s].getQueryStart(), subs[e].getQueryEnd(), bestQueryStrand, subs[s].getSubjectStart(), subs[e].getSubjectEnd(), bestSubjectStrand, | private SeqSimilaritySearchHit makeHit() { double sc = Double.NaN; double ev = Double.NaN; double pv = Double.NaN; subs = (SeqSimilaritySearchSubHit []) subHits .toArray(new SeqSimilaritySearchSubHit [subHits.size() - 1]); // Sort to get highest score Arrays.s... |
int qStart = Integer.parseInt((String) subHitData.get("QuerySequenceStart")); int qEnd = Integer.parseInt((String) subHitData.get("QuerySequenceEnd")); int sStart = Integer.parseInt((String) subHitData.get("HitSequenceStart")); int sEnd = Integer.parseInt((String) subHitData.get("HitSequenceEnd")); Strand qStrand ... | private SeqSimilaritySearchSubHit makeSubHit() throws BioException { double sc = Double.NaN; double ev = Double.NaN; double pv = Double.NaN; if (subHitData.containsKey("score")) sc = Double.parseDouble((String) subHitData.get("score")); if (subHitData.containsKey("ex... | |
{ | private SeqSimilaritySearchSubHit makeSubHit() throws BioException { double sc = Double.NaN; double ev = Double.NaN; double pv = Double.NaN; if (subHitData.containsKey("score")) sc = Double.parseDouble((String) subHitData.get("score")); if (subHitData.containsKey("ex... | |
} | private SeqSimilaritySearchSubHit makeSubHit() throws BioException { double sc = Double.NaN; double ev = Double.NaN; double pv = Double.NaN; if (subHitData.containsKey("score")) sc = Double.parseDouble((String) subHitData.get("score")); if (subHitData.containsKey("ex... | |
this.annotation = (annotation == null ? new SimpleAnnotation() : annotation); | this.annotation = annotation; this.annotation.addChangeListener(ChangeListener.ALWAYS_VETO); | 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... |
this.alignment.addChangeListener(ChangeListener.ALWAYS_VETO); | public SequenceDBSearchSubHit(double score, double eValue, double pValue, Alignment alignment) { this.score = score; this.pValue = eValue; this.eValue = pValue; this.alignment = alignment; } | |
if(sequence == null) { | if( (sequence == null) || (renderer == null) ) { | public void paintComponent(Graphics g) { if(sequence == null) { return; } Graphics2D g2 = (Graphics2D) g; Rectangle2D currentClip = g2.getClip().getBounds2D(); double minPos; double maxPos; if(direction == HORIZONTAL) { minPos = currentClip.getMinY(); maxPos = currentClip.getMa... |
LineInfo currentLI; | public void paintComponent(Graphics g) { if(sequence == null) { return; } Graphics2D g2 = (Graphics2D) g; Rectangle2D currentClip = g2.getClip().getBounds2D(); double minPos; double maxPos; if(direction == HORIZONTAL) { minPos = currentClip.getMinY(); maxPos = currentClip.getMa... | |
for(int l = minOffset; l < lineInfos.size(); l++) { | for(int l = minOffset; l < realLines; l++) { | public void paintComponent(Graphics g) { if(sequence == null) { return; } Graphics2D g2 = (Graphics2D) g; Rectangle2D currentClip = g2.getClip().getBounds2D(); double minPos; double maxPos; if(direction == HORIZONTAL) { minPos = currentClip.getMinY(); maxPos = currentClip.getMa... |
currentLI = (LineInfo) lineInfos.get(l); | public void paintComponent(Graphics g) { if(sequence == null) { return; } Graphics2D g2 = (Graphics2D) g; Rectangle2D currentClip = g2.getClip().getBounds2D(); double minPos; double maxPos; if(direction == HORIZONTAL) { minPos = currentClip.getMinY(); maxPos = currentClip.getMa... | |
for (Iterator i = views.iterator(); i.hasNext(); ) { SequenceRenderer r = (SequenceRenderer) i.next(); double depth = currentLI.getDepth(r); if (direction == HORIZONTAL) { clip.height = depth; } else { clip.width = depth; } Shape oldClip = g2.getClip(); g2.clip(clip); r.paint(g2, this, min, max); g2.setClip(oldClip); ... | double depth = offsets[l] - spacer; if(l != 0) { depth -= offsets[l-1]; | public void paintComponent(Graphics g) { if(sequence == null) { return; } Graphics2D g2 = (Graphics2D) g; Rectangle2D currentClip = g2.getClip().getBounds2D(); double minPos; double maxPos; if(direction == HORIZONTAL) { minPos = currentClip.getMinY(); maxPos = currentClip.getMa... |
g2.translate(-alongDim, spacer); | clip.height = depth; | public void paintComponent(Graphics g) { if(sequence == null) { return; } Graphics2D g2 = (Graphics2D) g; Rectangle2D currentClip = g2.getClip().getBounds2D(); double minPos; double maxPos; if(direction == HORIZONTAL) { minPos = currentClip.getMinY(); maxPos = currentClip.getMa... |
g2.translate(spacer, -alongDim); | clip.width = depth; } Shape oldClip = g2.getClip(); renderer.paint(g2, this, min, max); if (direction == HORIZONTAL) { g2.translate(-alongDim, spacer + depth); } else { g2.translate(spacer + depth, -alongDim); | public void paintComponent(Graphics g) { if(sequence == null) { return; } Graphics2D g2 = (Graphics2D) g; Rectangle2D currentClip = g2.getClip().getBounds2D(); double minPos; double maxPos; if(direction == HORIZONTAL) { minPos = currentClip.getMinY(); maxPos = currentClip.getMa... |
if(offsets[l] > maxPos) { | if( (min > sequence.length()) || (offsets[l] > maxPos)) { | public void paintComponent(Graphics g) { if(sequence == null) { return; } Graphics2D g2 = (Graphics2D) g; Rectangle2D currentClip = g2.getClip().getBounds2D(); double minPos; double maxPos; if(direction == HORIZONTAL) { minPos = currentClip.getMinY(); maxPos = currentClip.getMa... |
int realLines; | public void resizeAndValidate() { System.out.println("resizeAndValidate starting"); Dimension d = null; int realLines; double acrossDim; if(sequence == null) { System.out.println("No sequence"); // no sequence - collapse down to no size at all alongDim = 0.0; acrossDim = 0.0; ... | |
if(sequence == null) { | if( (sequence == null) || (renderer == null) ) { | public void resizeAndValidate() { System.out.println("resizeAndValidate starting"); Dimension d = null; int realLines; double acrossDim; if(sequence == null) { System.out.println("No sequence"); // no sequence - collapse down to no size at all alongDim = 0.0; acrossDim = 0.0; ... |
double insetBefore = 0.0; double insetAfter = 0.0; for (Iterator i = views.iterator(); i.hasNext(); ) { SequenceRenderer r = (SequenceRenderer) i.next(); System.out.println("Renderer: " + r); insetBefore = Math.max(insetBefore, r.getMinimumLeader(this)); insetAfter = Math.max(insetAfter, r.getMinimumTrailer(this)); } | double insetBefore = renderer.getMinimumLeader(this); double insetAfter = renderer.getMinimumTrailer(this); | public void resizeAndValidate() { System.out.println("resizeAndValidate starting"); Dimension d = null; int realLines; double acrossDim; if(sequence == null) { System.out.println("No sequence"); // no sequence - collapse down to no size at all alongDim = 0.0; acrossDim = 0.0; ... |
lineInfos.clear(); | this.offsets = new double[realLines]; int li = 0; double totDepth = 0.0; | public void resizeAndValidate() { System.out.println("resizeAndValidate starting"); Dimension d = null; int realLines; double acrossDim; if(sequence == null) { System.out.println("No sequence"); // no sequence - collapse down to no size at all alongDim = 0.0; acrossDim = 0.0; ... |
LineInfo li = new LineInfo(); | public void resizeAndValidate() { System.out.println("resizeAndValidate starting"); Dimension d = null; int realLines; double acrossDim; if(sequence == null) { System.out.println("No sequence"); // no sequence - collapse down to no size at all alongDim = 0.0; acrossDim = 0.0; ... | |
for(Iterator i = views.iterator(); i.hasNext(); ) { SequenceRenderer sr = (SequenceRenderer) i.next(); li.setDepth(sr, sr.getDepth(this, min, max)); } acrossDim += li.getTotalDepth(); lineInfos.add(li); | double depth = renderer.getDepth(this, min, max); acrossDim += depth + spacer; offsets[li] = totDepth; | public void resizeAndValidate() { System.out.println("resizeAndValidate starting"); Dimension d = null; int realLines; double acrossDim; if(sequence == null) { System.out.println("No sequence"); // no sequence - collapse down to no size at all alongDim = 0.0; acrossDim = 0.0; ... |
} offsets = new double[lineInfos.size()]; { int i = 0; double totDepth = 0.0; Iterator lii = lineInfos.iterator(); while(lii.hasNext()) { LineInfo li = (LineInfo) lii.next(); totDepth += li.getTotalDepth(); totDepth += spacer; offsets[i] = totDepth; i++; } | li++; | public void resizeAndValidate() { System.out.println("resizeAndValidate starting"); Dimension d = null; int realLines; double acrossDim; if(sequence == null) { System.out.println("No sequence"); // no sequence - collapse down to no size at all alongDim = 0.0; acrossDim = 0.0; ... |
public SuffixNode getChild(SuffixNode node, int i) { if(!node.hasChild(i)) { node.addChild(this, i, new SimpleNode(alphabet.size())); | public SuffixNode getChild(SuffixNode node, Symbol r) { if(!alphabet().contains(r)) { return null; | public SuffixNode getChild(SuffixNode node, int i) { if(!node.hasChild(i)) { node.addChild(this, i, new SimpleNode(alphabet.size())); } return node.getChild(i); } |
return node.getChild(i); | int index = indexForRes(r); return getChild(node, index); | public SuffixNode getChild(SuffixNode node, int i) { if(!node.hasChild(i)) { node.addChild(this, i, new SimpleNode(alphabet.size())); } return node.getChild(i); } |
((EmblCDROMIndexStore) emblCDIndexStore).setPathPrefix(entryNamIdx.getParentFile().getAbsoluteFile()); sequenceDB = new IndexedSequenceDB(emblCDIndexStore); | protected void setUp() throws Exception { URL divURL = EmblCDROMIndexStoreTest.class.getResource("emblcd/division.lkp"); URL entURL = EmblCDROMIndexStoreTest.class.getResource("emblcd/entrynam.idx"); File divisionLkp = new File(divURL.getFile()); File entryNamIdx = new File(entURL.get... | |
public void testFetch() throws BioException, IllegalIDException | public void testFetch() throws Exception | public void testFetch() throws BioException, IllegalIDException { // Fetch from file 1 Index i1 = emblCDIndexStore.fetch("NMA0007"); // Fetch from file 2 Index i2 = emblCDIndexStore.fetch("NMA0020"); // Fetch from file 3 Index i3 = emblCDIndexStore.fetch("NMA0030"); ... |
Sequence seq = sequenceDB.getSequence("NMA0007"); assertEquals("NMA0007", seq.getName()); assertEquals(235, seq.length()); seq = sequenceDB.getSequence("NMA0020"); assertEquals("NMA0020", seq.getName()); assertEquals(494, seq.length()); seq = sequenceDB.getSequence("NMA0030"); assertEquals("NMA0030", seq.getName()); ... | public void testFetch() throws BioException, IllegalIDException { // Fetch from file 1 Index i1 = emblCDIndexStore.fetch("NMA0007"); // Fetch from file 2 Index i2 = emblCDIndexStore.fetch("NMA0020"); // Fetch from file 3 Index i3 = emblCDIndexStore.fetch("NMA0030"); ... | |
SimpleOrthoPairCollection(Set groups) | public SimpleOrthoPairCollection() | SimpleOrthoPairCollection(Set groups) { this.groups = groups; } |
this.groups = groups; | groups = new HashSet(); | SimpleOrthoPairCollection(Set groups) { this.groups = groups; } |
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