public String getValueString(double position, WindowFunction windowFunction) { // //LOG.info("getValueString"); MutableString buffer = new MutableString(); buffer.append(entry.toString()); buffer.replace("\n", "<br>"); if (this.isPaired()) { buffer.append("----------------------" + "<br>"); buffer.append("Pair start = " + getMate().positionString() + "<br>"); buffer.append("Pair is mapped = " + (getMate().isMapped() ? "yes" : "no") + "<br>"); // buf.append("Pair is proper = " + (getProperPairFlag() ? "yes" : "no") + "<br>"); if (getChr().equals(getMate().getChr())) { buffer.append("Insert size = " + getInferredInsertSize() + "<br>"); } if (getPairOrientation().length() > 0) { buffer.append("Pair orientation = " + getPairOrientation() + "<br>"); } if (isFirstOfPair()) { buffer.append("First of pair <br>"); } if (isSecondOfPair()) { buffer.append("Second of pair <br>"); } } return buffer.toString(); }
protected void ensureParsed_(Iterator<Relation> relations) throws IOException { objects.clear(); predicates.clear(); contexts.clear(); subjectTokens.clear(); // Index subject tokens // We index the BNode id. Do we need it? String subject = getSubject(); FastBufferedReader fbr; // remove http/https or _: int startAt = subject.indexOf(':'); if (startAt < 0) { fbr = new FastBufferedReader(subject.toCharArray()); } else { startAt++; fbr = new FastBufferedReader(subject.toCharArray(), startAt, subject.length() - startAt); } MutableString word = new MutableString(); MutableString nonWord = new MutableString(); while (fbr.next(word, nonWord)) { if (word != null && !word.equals("")) { if (CombinedTermProcessor.getInstance().processTerm(word)) { subjectTokens.add(word.toString().toLowerCase()); } } } fbr.close(); while (relations.hasNext()) { Relation relation = relations.next(); String predicate = relation.getPredicate().toString(); // Check if prefix is on blacklist if (RDFDocumentFactory.isOnPredicateBlacklist(predicate.toLowerCase())) { factory.incrementCounter(RdfCounters.BLACKLISTED_TRIPLES, 1); continue; } String predicateId = factory.lookupResource(predicate, false); if (predicateId == null) { throw new IllegalStateException( "Predicate " + predicate + " not in resources hash function!"); } String contextId = NO_CONTEXT; if (factory.isWithContexts() && relation.getContext() != null) { if (relation.getContext() instanceof Resource) { contextId = factory.lookupResource(relation.getContext().toString(), false); if (contextId == null) { throw new IllegalStateException( "Context " + relation.getContext() + " not in resources hash function!"); } } else { throw new IllegalStateException( "Context " + relation.getContext() + " is not a Resource."); } } if (relation.getObject() instanceof Resource) { if (predicate.equals(RDF.TYPE.toString())) { factory.incrementCounter(RdfCounters.RDF_TYPE_TRIPLES, 1); objects.add(relation.getObject().toString()); } else { String objectId = factory.lookupResource(relation.getObject().toString(), true); if (objectId == null) { throw new IllegalStateException( "Object " + relation.getObject() + " not in resources hash function!"); } objects.add(objectId); } predicates.add(predicateId); contexts.add(contextId); } else if (relation.getObject() instanceof BNode) { String objectId = factory.lookupResource(relation.getObject().toString(), false); if (objectId == null) { throw new IllegalStateException( "Object " + relation.getObject() + " not in resources hash function!"); } objects.add(objectId); predicates.add(predicateId); contexts.add(contextId); } else { String object = relation.getObject().toString(); // Iterate over the words of the value fbr = new FastBufferedReader(object.toCharArray()); while (fbr.next(word, nonWord)) { if (word != null && !word.equals("")) { if (CombinedTermProcessor.getInstance().processTerm(word)) { // Lowercase terms objects.add(word.toString()); // Preserve casing for properties and // contexts predicates.add(predicateId); contexts.add(contextId); } } } fbr.close(); } factory.incrementCounter(RdfCounters.INDEXED_TRIPLES, 1); } }