public Range(CvFuzzyType fromStatus, int fromStart, int fromEnd, CvFuzzyType toStatus, int toStart, int toEnd, String seq){ super(); if (fromStatus == null){ throw new IllegalArgumentException("The start range status cannot be null."); } if (toStatus == null){ throw new IllegalArgumentException("The end range status cannot be null."); } setFromCvFuzzyType(fromStatus); setToCvFuzzyType(toStatus); setRangePositions(fromStart, fromEnd, toStart, toEnd, seq); if (seq != null){ if (seq.trim().length() > 0){ prepareSequence(seq); } } }
public Range(CvFuzzyType fromStatus, int fromStart, int fromEnd, CvFuzzyType toStatus, int toStart, int toEnd, String seq){ super(); if (fromStatus == null){ throw new IllegalArgumentException("The start range status cannot be null."); } if (toStatus == null){ throw new IllegalArgumentException("The end range status cannot be null."); } setFromCvFuzzyType(fromStatus); setToCvFuzzyType(toStatus); setRangePositions(fromStart, fromEnd, toStart, toEnd, seq); if (seq != null){ if (seq.trim().length() > 0){ prepareSequence(seq); } } }
public Range createRangeCTerminal() { Range range = new Range(institution, 0, 0, null); final CvFuzzyType fuzzyType = createCvObject(CvFuzzyType.class, CvFuzzyType.C_TERMINAL_MI_REF, CvFuzzyType.C_TERMINAL); range.setFromCvFuzzyType(fuzzyType); range.setToCvFuzzyType(fuzzyType); return range; }
public Range createRangeCTerminal(int beginFrom, int endFrom, int beginTo, int endTo) { Range range = new Range(institution, beginFrom, endFrom, beginTo, endTo, null); final CvFuzzyType fuzzyType = createCvObject(CvFuzzyType.class, CvFuzzyType.C_TERMINAL_MI_REF, CvFuzzyType.C_TERMINAL); range.setFromCvFuzzyType(fuzzyType); range.setToCvFuzzyType(fuzzyType); return range; }
public Range createRangeUndetermined() { Range range = new Range(institution, 0, 0, null); CvFuzzyType fuzzyType = createCvObject(CvFuzzyType.class, CvFuzzyType.UNDETERMINED_MI_REF, CvFuzzyType.UNDETERMINED); range.setFromCvFuzzyType(fuzzyType); range.setToCvFuzzyType(fuzzyType); return range; }
public Range createRangeUndetermined() { Range range = new Range(institution, 0, 0, null); CvFuzzyType fuzzyType = createCvObject(CvFuzzyType.class, CvFuzzyType.UNDETERMINED_MI_REF, CvFuzzyType.UNDETERMINED); range.setFromCvFuzzyType(fuzzyType); range.setToCvFuzzyType(fuzzyType); return range; }
public Range createRangeCTerminal(int beginFrom, int endFrom, int beginTo, int endTo) { Range range = new Range(institution, beginFrom, endFrom, beginTo, endTo, null); final CvFuzzyType fuzzyType = createCvObject(CvFuzzyType.class, CvFuzzyType.C_TERMINAL_MI_REF, CvFuzzyType.C_TERMINAL); range.setFromCvFuzzyType(fuzzyType); range.setToCvFuzzyType(fuzzyType); return range; }
public Range createRangeCTerminal() { Range range = new Range(institution, 0, 0, null); final CvFuzzyType fuzzyType = createCvObject(CvFuzzyType.class, CvFuzzyType.C_TERMINAL_MI_REF, CvFuzzyType.C_TERMINAL); range.setFromCvFuzzyType(fuzzyType); range.setToCvFuzzyType(fuzzyType); return range; }
/** * This is a convenient constructor to create Range with from and end values. * * @param fromStart The starting point of the 'from' interval for the Range. The 'from' end value is set to this * value. * @param toStart The starting point of the 'to' interval of the Range. The 'to' end value is set to this value. * @param seq The sequence - maximum of 100 characters (null allowed) * @deprecated the range status is mandatory in PSI MI. It is not possible to extract properly a feature sequence without this range status. * Here by default, the range status will be set to 'certain' */ @Deprecated public Range( int fromStart, int toStart, String seq ) { super(); CvFuzzyType certain = new CvFuzzyType(null, CvFuzzyType.CERTAIN); certain.setIdentifier(CvFuzzyType.CERTAIN_MI_REF); setFromCvFuzzyType(certain); setToCvFuzzyType(certain); setRangePositions(fromStart, fromStart, toStart, toStart, seq); if (seq != null){ if (seq.trim().length() > 0){ prepareSequence(seq); } } }
/** * This is a convenient constructor to create Range with from and end values. * * @param fromStart The starting point of the 'from' interval for the Range. The 'from' end value is set to this * value. * @param toStart The starting point of the 'to' interval of the Range. The 'to' end value is set to this value. * @param seq The sequence - maximum of 100 characters (null allowed) * @deprecated the range status is mandatory in PSI MI. It is not possible to extract properly a feature sequence without this range status. * Here by default, the range status will be set to 'certain' */ @Deprecated public Range( int fromStart, int toStart, String seq ) { super(); CvFuzzyType certain = new CvFuzzyType(null, CvFuzzyType.CERTAIN); certain.setIdentifier(CvFuzzyType.CERTAIN_MI_REF); setFromCvFuzzyType(certain); setToCvFuzzyType(certain); setRangePositions(fromStart, fromStart, toStart, toStart, seq); if (seq != null){ if (seq.trim().length() > 0){ prepareSequence(seq); } } }
public Range createRange(int beginFrom, int endFrom, int beginTo, int endTo) { if( beginFrom == 0 && endFrom == 0 && beginTo == 0 && endTo == 0 ) { return createRangeUndetermined(); } Range range = new Range(institution, beginFrom, endFrom, beginTo, endTo, null); final CvFuzzyType fuzzyType = createCvObject(CvFuzzyType.class, CvFuzzyType.RANGE_MI_REF, CvFuzzyType.RANGE); range.setFromCvFuzzyType(fuzzyType); range.setToCvFuzzyType(fuzzyType); return range; }
public Range createRange(int beginFrom, int endFrom, int beginTo, int endTo) { if( beginFrom == 0 && endFrom == 0 && beginTo == 0 && endTo == 0 ) { return createRangeUndetermined(); } Range range = new Range(institution, beginFrom, endFrom, beginTo, endTo, null); final CvFuzzyType fuzzyType = createCvObject(CvFuzzyType.class, CvFuzzyType.RANGE_MI_REF, CvFuzzyType.RANGE); range.setFromCvFuzzyType(fuzzyType); range.setToCvFuzzyType(fuzzyType); return range; }
setToCvFuzzyType(range); setToCvFuzzyType(certain);
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; }
private Collection<Range> synchronizeRanges( Collection<Range> rangesToSychronize, Feature parentFeature ) { List<Range> ranges = new ArrayList<Range>(rangesToSychronize.size()); for ( Range range : rangesToSychronize ) { if (range.getAc() != null && IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getRangeDao().isTransient(range)) { range = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getRangeDao().getByAc(range.getAc()); } range.setFromCvFuzzyType( synchronize( range.getFromCvFuzzyType() ) ); range.setToCvFuzzyType( synchronize( range.getToCvFuzzyType() ) ); range.setFeature(parentFeature); ranges.add(range); } return ranges; }
private Collection<Range> synchronizeRanges( Collection<Range> rangesToSychronize, Feature parentFeature ) { List<Range> ranges = new ArrayList<Range>(rangesToSychronize.size()); for ( Range range : rangesToSychronize ) { if (range.getAc() != null && IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getRangeDao().isTransient(range)) { range = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getRangeDao().getByAc(range.getAc()); } range.setFromCvFuzzyType( synchronize( range.getFromCvFuzzyType() ) ); range.setToCvFuzzyType( synchronize( range.getToCvFuzzyType() ) ); range.setFeature(parentFeature); ranges.add(range); } return ranges; }
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; }
range.setToCvFuzzyType(syncedToCvFuzzyType);