public Range createRange(int beginFrom, int endFrom, int beginTo, int endTo) { Range range = new Range(institution, beginFrom, endTo, null); range.setFromIntervalStart(beginFrom); range.setFromIntervalEnd(endFrom); range.setToIntervalStart(beginTo); range.setToIntervalEnd(endTo); CvFuzzyType fuzzyType = createCvObject(CvFuzzyType.class, "MI:0339", CvFuzzyType.UNDETERMINED); range.setFromCvFuzzyType(fuzzyType); range.setToCvFuzzyType(fuzzyType); return range; }
range.setToIntervalEnd(0); } else if (endStatus.isNTerminal()) { range.setToIntervalStart(1); range.setToIntervalEnd(1); } else if (endStatus.isCTerminal()) { if (proteinSequence != null) { range.setToIntervalStart(proteinSequence.length()); range.setToIntervalEnd(proteinSequence.length()); } else { range.setToIntervalStart(0); range.setToIntervalEnd(0);
range.setToIntervalEnd(0); } else if (endStatus.isNTerminal()) { range.setToIntervalStart(1); range.setToIntervalEnd(1); } else if (endStatus.isCTerminal()) { if (proteinSequence != null) { range.setToIntervalStart(proteinSequence.length()); range.setToIntervalEnd(proteinSequence.length()); } else { range.setToIntervalStart(0); range.setToIntervalEnd(0);
if (toCvFuzzyType.isCTerminal() && toIntervalStart == 0 && toIntervalEnd == 0){ setToIntervalStart(sequence.length()); setToIntervalEnd(sequence.length());
if (toCvFuzzyType.isCTerminal() && toIntervalStart == 0 && toIntervalEnd == 0){ setToIntervalStart(sequence.length()); setToIntervalEnd(sequence.length());
protected Range cloneRange(Range range) throws IntactClonerException { if (range == null) { throw new IllegalArgumentException("You must give a non null range"); } Range clone = new Range(); clonerManager.addClone(range, clone); clone.setFromIntervalStart(range.getFromIntervalStart()); clone.setFromIntervalEnd(range.getFromIntervalEnd()); clone.setToIntervalStart(range.getToIntervalStart()); clone.setToIntervalEnd(range.getToIntervalEnd()); clone.setSequence(range.getSequence()); clone.setFullSequence(range.getFullSequence()); clone.setUpStreamSequence(range.getUpStreamSequence()); clone.setDownStreamSequence(range.getDownStreamSequence()); clone.setFromCvFuzzyType(clone(range.getFromCvFuzzyType())); clone.setToCvFuzzyType(clone(range.getToCvFuzzyType())); clone.setFeature(clone(range.getFeature())); return clone; }
protected Range cloneRange(Range range) throws IntactClonerException { if (range == null) { throw new IllegalArgumentException("You must give a non null range"); } Range clone = new Range(); clonerManager.addClone(range, clone); clone.setFromIntervalStart(range.getFromIntervalStart()); clone.setFromIntervalEnd(range.getFromIntervalEnd()); clone.setToIntervalStart(range.getToIntervalStart()); clone.setToIntervalEnd(range.getToIntervalEnd()); clone.setSequence(range.getSequence()); clone.setFullSequence(range.getFullSequence()); clone.setUpStreamSequence(range.getUpStreamSequence()); clone.setDownStreamSequence(range.getDownStreamSequence()); clone.setFromCvFuzzyType(clone(range.getFromCvFuzzyType())); clone.setToCvFuzzyType(clone(range.getToCvFuzzyType())); clone.setFeature(clone(range.getFeature())); return clone; }