@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(); }
@Override public boolean canCheck(Object thing) { if ( thing instanceof ModificationFeature && ((ModificationFeature) thing).getModificationType() != null) { EntityReference er = ((ModificationFeature) thing).getEntityFeatureOf(); if (er instanceof NucleicAcidReference || er instanceof NucleicAcidRegionReference) return true; for (PhysicalEntity pe : ((ModificationFeature) thing).getFeatureOf()) { if (pe instanceof NucleicAcid) return true; } } return false; }
@Override public boolean canCheck(Object thing) { if (thing instanceof ModificationFeature && ((ModificationFeature) thing).getModificationType() != null && ((ModificationFeature) thing).getFeatureOf() != null) { for (PhysicalEntity pe : ((ModificationFeature) thing).getFeatureOf()) { if (pe instanceof Dna || pe instanceof Rna) { return true; } } } return false; }
private static String getPhosphoSiteLetter(ModificationFeature mf) { if (mf.getModificationType() != null) { for (String term : mf.getModificationType().getTerm()) { term = term.toLowerCase(); if (term.contains("phospho")) { if (term.contains("serine")) return "S"; if (term.contains("threonine")) return "T"; if (term.contains("tyrosine")) return "Y"; } } } return null; }
private static int getPhosphoSite(ModificationFeature mf) { SequenceLocation loc = mf.getFeatureLocation(); if (loc != null && loc instanceof SequenceSite) { return ((SequenceSite) loc).getSequencePosition(); } return -1; }
SequenceModificationVocabulary smv = findOrCreateControlledVocabulary( psiFeature.getFeatureType(), SequenceModificationVocabulary.class); //can be null ((ModificationFeature)entityFeature).setModificationType(smv);
@Override public boolean canCheck(Object thing) { if (thing instanceof ModificationFeature && ((ModificationFeature) thing).getModificationType() != null && ((ModificationFeature) thing).getFeatureOf() != null) { for (PhysicalEntity pe : ((ModificationFeature) thing).getFeatureOf()) { if (pe instanceof Protein) { return true; } } } return false; }
/** * Extracts terms of the modification features. * @param mfSet set of modification features * @return set of extracted terms */ protected Set<String> extractModifNames(Set mfSet) { Set<String> set = new HashSet<String>(); for (Object o : mfSet) { ModificationFeature mf = (ModificationFeature) o; if (mf.getModificationType() != null && !mf.getModificationType().getTerm().isEmpty()) { set.add(mf.getModificationType().getTerm().iterator().next()); } } return set; }
public String getKey() if (mf.getModificationType() != null && !mf.getModificationType().getTerm().isEmpty()) k = mf.getModificationType().getTerm().iterator().next(); 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 boolean canCheck(Object thing) { if (thing instanceof ModificationFeature && ((ModificationFeature) thing).getModificationType() != null) { EntityReference er = ((ModificationFeature) thing).getEntityFeatureOf(); if(er instanceof ProteinReference) return true; for (PhysicalEntity pe : ((ModificationFeature) thing).getFeatureOf()) { if (pe instanceof Protein) return true; } } return false; }
private void collectTerms(Set<ModificationFeature> mods, Set<String> terms) { for (ModificationFeature mf : mods) { SequenceModificationVocabulary type = mf.getModificationType(); if (type != null) { for (String term : type.getTerm()) { terms.add(term.toLowerCase()); } } } }
@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; }
SequenceModificationVocabulary modType = mf.getModificationType(); state.setValue(s); SequenceLocation loc = mf.getFeatureLocation(); if (locMapping.containsKey(term))