/** * * @param qualifier : the qualifier of the cross reference * @return true if the qualifier is 'identity' */ private boolean isIdentityCrossReference(CvXrefQualifier qualifier){ if (qualifier.getIdentifier() != null){ if (qualifier.getIdentifier().equals(CvXrefQualifier.IDENTITY_MI_REF)){ return true; } } else { if (qualifier.getShortLabel().equals(CvXrefQualifier.IDENTITY)){ return true; } } return false; }
/** * Collects all Xref having a CvXrefQualifier( target-species ) linked to the given experiement. * * @param experiment * * @return a Collection of Xref. never null. */ public List<ExperimentXref> getTargetSpeciesXrefs( Experiment experiment ) { List<ExperimentXref> targets = new ArrayList<ExperimentXref>(); for ( ExperimentXref xref : experiment.getXrefs() ) { if ( targetSpeciesQualifier.equals( xref.getCvXrefQualifier() ) ) { targets.add( xref ); } } return targets; }
public CvXrefQualifier createIdentityCvXrefQualifier(Institution institution) { if (cvXrefQualifier != null) { return cvXrefQualifier; } cvXrefQualifier = new CvXrefQualifier(institution, CvXrefQualifier.IDENTITY); cvXrefQualifier.setIdentifier(CvXrefQualifier.IDENTITY_MI_REF); CvObjectXref xref = createPsiMiXref(CvObjectXref.class, CvXrefQualifier.IDENTITY_MI_REF, institution); cvXrefQualifier.addXref(xref); return cvXrefQualifier; }
public CvXrefQualifier createIdentityCvXrefQualifier(Institution institution) { if (cvXrefQualifier != null) { return cvXrefQualifier; } cvXrefQualifier = new CvXrefQualifier(institution, CvXrefQualifier.IDENTITY); CvObjectXref xref = createPsiMiXref(CvObjectXref.class, CvXrefQualifier.IDENTITY_MI_REF, institution); cvXrefQualifier.addXref(xref); return cvXrefQualifier; }
@Override public String toString() { final StringBuffer sb = new StringBuffer(150); sb.append("Xref"); sb.append("{cvDatabase=").append(cvDatabase.getShortLabel()); sb.append(", cvXrefQualifier=").append((cvXrefQualifier == null ? "-" : cvXrefQualifier.getShortLabel())); sb.append(", primaryId='").append(primaryId).append('\''); sb.append(", secondaryId='").append((secondaryId == null ? "-" : secondaryId)).append('\''); sb.append(", dbRelease='").append((dbRelease == null ? "-" : dbRelease)).append('\''); sb.append('}'); return sb.toString(); }
private void prepareQuery(CvDatabase database, CvXrefQualifier qualifier, String primaryId, Query query) { query.setParameter("id", primaryId); query.setParameter("dbMi", (database.getIdentifier() != null ? database.getIdentifier() : CvObjectUtils.getIdentity(database))); query.setParameter("qualifierMi", (qualifier.getIdentifier() != null ? qualifier.getIdentifier() : CvObjectUtils.getIdentity(qualifier))); }
private boolean isAnIdentityOrSecondaryCrossReference(CvXrefQualifier qualifier){ if (qualifier == null){ return false; } if (qualifier.getIdentifier() != null){ if (qualifier.getIdentifier().equals(CvXrefQualifier.IDENTITY_MI_REF) || qualifier.getIdentifier().equals(CvXrefQualifier.SECONDARY_AC_MI_REF)){ return true; } } else { if (qualifier.getShortLabel() != null){ if (qualifier.getShortLabel().equals(CvXrefQualifier.IDENTITY) || qualifier.getShortLabel().equals(CvXrefQualifier.SECONDARY_AC)){ return true; } } else if (qualifier.getFullName() != null){ if (qualifier.getFullName().equals("identical object")){ return true; } } } return false; }
private boolean hasAnIdentityCrossReference(CvObject cvObject){ if (cvObject.getXrefs() != null){ if (!cvObject.getXrefs().isEmpty()){ for (Xref ref : cvObject.getXrefs()){ CvXrefQualifier qualifier = ref.getCvXrefQualifier(); if (qualifier.getAc() != null){ if (qualifier.getAc().equals("MI:0356")){ return true; } } else { if (qualifier.getShortLabel().equals("identity") || qualifier.getFullName().equals("identical object")){ return true; } } } } } return false; }
if ( CvDatabase.PUBMED.equalsIgnoreCase( database ) ) { qualifierCv = CvObjectUtils.createCvObject( owner, CvXrefQualifier.class, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF, qualifier ); qualifierCv.setFullName( "created by IntAct --- should have been removed !!!" ); databaseCv = CvObjectUtils.createCvObject( owner, CvDatabase.class, CvDatabase.PUBMED_MI_REF, CvDatabase.PUBMED ); } else if ( CvDatabase.GO.equalsIgnoreCase( database ) ) {
xrefQual = new CvXrefQualifier(getInstitution(), refType); xrefQual.setIdentifier(refTypeAc);
public static CvXrefQualifier createCvXrefQualifier(Institution institution, DbReference dbReference) { String xrefType = dbReference.getRefType(); CvXrefQualifier xrefQual = null; if (xrefType != null) { xrefQual = new CvXrefQualifier(institution, xrefType); } return xrefQual; }
@Override public String toString() { final StringBuffer sb = new StringBuffer(150); sb.append("Xref"); sb.append("{cvDatabase=").append(cvDatabase.getShortLabel()); sb.append(", cvXrefQualifier=").append((cvXrefQualifier == null ? "-" : cvXrefQualifier.getShortLabel())); sb.append(", primaryId='").append(primaryId).append('\''); sb.append(", secondaryId='").append((secondaryId == null ? "-" : secondaryId)).append('\''); sb.append(", dbRelease='").append((dbRelease == null ? "-" : dbRelease)).append('\''); sb.append('}'); return sb.toString(); }
private void prepareQuery(CvDatabase database, CvXrefQualifier qualifier, String primaryId, Query query) { query.setParameter("id", primaryId); query.setParameter("dbMi", (database.getIdentifier() != null ? database.getIdentifier() : CvObjectUtils.getIdentity(database))); query.setParameter("qualifierMi", (qualifier.getIdentifier() != null ? qualifier.getIdentifier() : CvObjectUtils.getIdentity(qualifier))); }
private boolean isAnIdentityOrSecondaryCrossReference(CvXrefQualifier qualifier){ if (qualifier == null){ return false; } if (qualifier.getIdentifier() != null){ if (qualifier.getIdentifier().equals(CvXrefQualifier.IDENTITY_MI_REF) || qualifier.getIdentifier().equals(CvXrefQualifier.SECONDARY_AC_MI_REF)){ return true; } } else { if (qualifier.getShortLabel() != null){ if (qualifier.getShortLabel().equals(CvXrefQualifier.IDENTITY) || qualifier.getShortLabel().equals(CvXrefQualifier.SECONDARY_AC)){ return true; } } else if (qualifier.getFullName() != null){ if (qualifier.getFullName().equals("identical object")){ return true; } } } return false; }
private boolean hasAnIdentityCrossReference(CvObject cvObject){ if (cvObject.getXrefs() != null){ if (!cvObject.getXrefs().isEmpty()){ for (Xref ref : cvObject.getXrefs()){ CvXrefQualifier qualifier = ref.getCvXrefQualifier(); if (qualifier.getAc() != null){ if (qualifier.getAc().equals("MI:0356")){ return true; } } else { if (qualifier.getShortLabel().equals("identity") || qualifier.getFullName().equals("identical object")){ return true; } } } } } return false; }
identity.setFullName("identical object"); intactContext.getDataContext().getDaoFactory().getCvObjectDao(CvXrefQualifier.class).persist(identity);
@Override public void visitXref( Xref xref ) { final CvDatabase db = xref.getCvDatabase(); String mi = db.getIdentifier(); if ( mi != null ) { String key = createCvKey( db.getClass(), mi ); final CvDatabase oboTerm = ( CvDatabase ) mi2cv.get( key ); if ( oboTerm == null ) { log.warn( "Could not find xref " + db.getClass().getSimpleName() + "( " + db.getShortLabel() + " ) by MI: " + mi ); } else { xref.setCvDatabase( oboTerm ); } } final CvXrefQualifier qualifier = xref.getCvXrefQualifier(); if( qualifier != null ) { mi = qualifier.getIdentifier(); if ( mi != null ) { final String key = createCvKey( qualifier.getClass(), mi ); final CvXrefQualifier oboQualifier = ( CvXrefQualifier ) mi2cv.get( key ); if ( oboQualifier == null ) { log.warn( "Could not find qualifier " + qualifier.getClass().getSimpleName() + "( " + qualifier.getShortLabel() + " ) by MI: " + mi ); } else { xref.setCvXrefQualifier( oboQualifier ); } } } }
@Override public String toString() { final StringBuffer sb = new StringBuffer( 150 ); sb.append( "Xref" ); sb.append( "{cvDatabase=" ).append( cvDatabase.getShortLabel() ); sb.append( ", cvXrefQualifier=" ).append( ( cvXrefQualifier == null ? "-" : cvXrefQualifier.getShortLabel() ) ); sb.append( ", primaryId='" ).append( primaryId ).append( '\'' ); sb.append( ", secondaryId='" ).append( ( secondaryId == null ? "-" : secondaryId ) ).append( '\'' ); sb.append( ", dbRelease='" ).append( ( dbRelease == null ? "-" : dbRelease ) ).append( '\'' ); sb.append( '}' ); return sb.toString(); }
private static Collection<InteractorXref> extractCrossReferencesFrom(Protein protein, String databaseMiRef, String qualifierMiRef) { Collection<InteractorXref> parents = new ArrayList<InteractorXref>(); for (InteractorXref ref : protein.getXrefs()) { if (ref.getCvDatabase().getIdentifier().equals(databaseMiRef)) { if (ref.getCvXrefQualifier().getIdentifier().equals(qualifierMiRef)) { parents.add(ref); } } } return parents; }
/** * Search for all Xrefs having Xref with the given CvXrefQualifier. * * @param ao the non null AnnotatedObject to search on. * @param qu the non null CvXrefQualifier filter. * * @return a non null Collection of Xref, may be empty. */ public static Collection<Xref> searchXrefs( AnnotatedObject ao, CvXrefQualifier qu ) { if ( ao == null ) { throw new NullPointerException( "AnnotatedObject must not be null." ); } if ( qu == null ) { throw new NullPointerException( "CvXrefQualifier must not be null." ); } Collection<Xref> xrefs = new ArrayList<Xref>( ao.getXrefs().size() ); for ( Iterator<Xref> iterator = ao.getXrefs().iterator(); iterator.hasNext(); ) { Xref xref = iterator.next(); if ( qu.equals( xref.getCvXrefQualifier() ) ) { xrefs.add( xref ); } } return xrefs; }