public void prepareSequence( String sequence ) { prepareSequence( sequence, true ); }
public void prepareSequence( String sequence ) { prepareSequence( sequence, true ); }
this.toIntervalEnd = toEnd; this.sequence = 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(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); } } }
range.prepareSequence(proteinSequence, enforceConsistency);
range.prepareSequence(proteinSequence, enforceConsistency);
/** * 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); } } }
for (Range r : feature.getRanges()){ r.prepareSequence(polymer.getSequence());
for (Range r : feature.getRanges()){ r.prepareSequence(polymer.getSequence());