private static int getPhosphoSite(ModificationFeature mf) { SequenceLocation loc = mf.getFeatureLocation(); if (loc != null && loc instanceof SequenceSite) { return ((SequenceSite) loc).getSequencePosition(); } return -1; }
@Override public boolean equals(Object obj) { if (!(obj instanceof Modification)) return false; Modification m = (Modification) obj; if (mf == m.mf) return true; if (mf.getModificationType() == null || m.mf.getModificationType() == null) return false; if (!mf.getModificationType().getTerm().containsAll( m.mf.getModificationType().getTerm())) return false; if (mf.getFeatureLocation() == null && m.mf.getFeatureLocation() == null) return true; if (mf.getFeatureLocation() == null || m.mf.getFeatureLocation() == null) return false; return mf.getFeatureLocation().equivalenceCode() == m.mf.getFeatureLocation().equivalenceCode(); }
if (mf.getFeatureLocation() instanceof SequenceSite) SequenceSite ss = (SequenceSite) mf.getFeatureLocation(); int site = ss.getSequencePosition(); else if (mf.getFeatureLocation() instanceof SequenceInterval) SequenceInterval si = (SequenceInterval) mf.getFeatureLocation();
@Override public int hashCode() { int code = 0; SequenceModificationVocabulary type = mf.getModificationType(); if (type != null) { for (String term : type.getTerm()) { code += term.hashCode(); } } SequenceLocation loc = mf.getFeatureLocation(); if (loc != null) { if (loc instanceof SequenceInterval) { SequenceSite begin = ((SequenceInterval) loc).getSequenceIntervalBegin(); SequenceSite end = ((SequenceInterval) loc).getSequenceIntervalEnd(); if (begin != null) code += begin.getSequencePosition(); if (end != null) code += end.getSequencePosition(); } else if (loc instanceof SequenceSite) { code += ((SequenceSite) loc).getSequencePosition(); } } return code; }
state.setValue(s); SequenceLocation loc = mf.getFeatureLocation(); if (locMapping.containsKey(term))