@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(); }
/** * Add all the cross references with qualifier 'identity' to the list of identifiers of the protein (intact cross references are ignored) * @param refs : the refs of the protein * @param context : the context of the protein */ private void addIdentityCrossreferencesToContext(Collection<InteractorXref> refs, UpdateContext context){ for (InteractorXref ref : refs){ if (ref.getPrimaryId() != null){ if (ref.getCvXrefQualifier() != null){ CvXrefQualifier qualifier = ref.getCvXrefQualifier(); if (isIdentityCrossReference(qualifier)){ CvDatabase database = ref.getCvDatabase(); if (database != null){ if (database.getIdentifier() != null && !CvDatabase.INTACT_MI_REF.equals(database.getIdentifier())){ context.addIdentifier(database.getIdentifier(), ref.getPrimaryId()); } else if (database.getShortLabel() != null && !CvDatabase.INTACT.equals(database.getShortLabel())) { context.addIdentifier(database.getShortLabel(), ref.getPrimaryId()); } } } } } } }
/** * Search for all Xrefs having Xref with the given CvDatabase. * * @param ao the non null AnnotatedObject to search on. * @param db the non null CvDatabase filter. * * @return a non null Collection of Xref, may be empty. */ public static Collection<Xref> searchXrefs( AnnotatedObject ao, CvDatabase db ) { if ( ao == null ) { throw new NullPointerException( "AnnotatedObject must not be null." ); } if ( db == null ) { throw new NullPointerException( "CvDatabase 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 ( db.equals( xref.getCvDatabase() ) ) { xrefs.add( xref ); } } return xrefs; }
public CvDatabase createPsiMiCvDatabase(Institution institution) { if (cvDatabase != null) { return cvDatabase; } cvDatabase = new CvDatabase(institution, CvDatabase.PSI_MI); cvDatabase.setIdentifier(CvDatabase.PSI_MI_MI_REF); CvObjectXref xref = createPsiMiXref(CvObjectXref.class, CvDatabase.PSI_MI_MI_REF, institution); cvDatabase.addXref(xref); return cvDatabase; }
public CvDatabase createPsiMiCvDatabase(Institution institution) { if (cvDatabase != null) { return cvDatabase; } cvDatabase = new CvDatabase(institution, CvDatabase.PSI_MI); CvObjectXref xref = createPsiMiXref(CvObjectXref.class, CvDatabase.PSI_MI_MI_REF, institution); cvDatabase.addXref(xref); return cvDatabase; }
public static <X extends Xref> X getIdentityXref(AnnotatedObject<X, ?> annotatedObject, CvDatabase cvDatabase) { String dbMi = cvDatabase.getIdentifier(); return getIdentityXref(annotatedObject, dbMi); }
String dbname = xref.getCvDatabase().getShortLabel(); Collection<Annotation> annots = xref.getCvDatabase().getAnnotations(); for (Annotation annot : annots)
protected InteractorXref createImexXref(Interaction interaction, String imexId) { CvDatabase cvImex = CvObjectUtils.createCvObject(interaction.getOwner(), CvDatabase.class, CvDatabase.IMEX_MI_REF, CvDatabase.IMEX); cvImex.setFullName(CvDatabase.IMEX); CvXrefQualifier imexPrimary = CvObjectUtils.createCvObject(interaction.getOwner(), CvXrefQualifier.class, CvXrefQualifier.IMEX_PRIMARY_MI_REF, CvXrefQualifier.IMEX_PRIMARY); return XrefUtils.createIdentityXref(interaction, imexId, imexPrimary, cvImex); }
String dbAc = psiObject.getDbAc(); CvDatabase cvDb = new CvDatabase(getInstitution(), db); cvDb.setIdentifier(dbAc);
for (Iterator iterator = cvDatabase.getAnnotations().iterator(); iterator.hasNext() && false == stop; ) { Annotation annotation = (Annotation) iterator.next();
public static <X extends Xref> X getIdentityXref(AnnotatedObject<X, ?> annotatedObject, CvDatabase cvDatabase) { String dbMi = cvDatabase.getIdentifier(); return getIdentityXref(annotatedObject, dbMi); }
public CvDatabase createPsiMiCvDatabase(Institution institution) { if (cvDatabase != null) { return cvDatabase; } cvDatabase = new CvDatabase(institution, CvDatabase.PSI_MI); cvDatabase.setIdentifier(CvDatabase.PSI_MI_MI_REF); CvObjectXref xref = createPsiMiXref(CvObjectXref.class, CvDatabase.PSI_MI_MI_REF, institution); cvDatabase.addXref(xref); return cvDatabase; }
psi.setFullName("psi-mi"); intactContext.getDataContext().getDaoFactory().getCvObjectDao(CvDatabase.class).persist(psi);
for ( Iterator iterator = cvDatabase.getAnnotations().iterator(); iterator.hasNext() && false == stop; ) { Annotation annotation = ( Annotation ) iterator.next();
@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(); }
@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 ); } } } }
public List<T> getByXref(CvDatabase database, String primaryId) { Query query = getEntityManager().createQuery("select distinct(o) from " + getEntityClass().getName() + " o inner join o.xrefs as xref " + "where xref.primaryId = :id " + " and xref.cvDatabase.identifier = :dbMi"); query.setParameter("id", primaryId); query.setParameter("dbMi", (database.getIdentifier() != null ? database.getIdentifier() : CvObjectUtils.getIdentity(database))); return query.getResultList(); }
/** * Search for all Xrefs having Xref with both the given CvDatabase and CvXrefQualifier. * * @param ao the non null AnnotatedObject to search on. * @param db the non null CvDatabase filter. * @param qu the non null CvXrefQualifier filter. * * @return a non null Collection of Xref, may be empty. */ public static Collection<Xref> searchXrefs( AnnotatedObject ao, CvDatabase db, CvXrefQualifier qu ) { if ( ao == null ) { throw new NullPointerException( "AnnotatedObject must not be null." ); } if ( db == null ) { throw new NullPointerException( "CvDatabase 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 ( db.equals( xref.getCvDatabase() ) && qu.equals( xref.getCvXrefQualifier() ) ) { xrefs.add( xref ); } } return xrefs; }
psi.setFullName("psi-mi"); intactContext.getDataContext().getDaoFactory().getCvObjectDao(CvDatabase.class).persist(psi);
for (Iterator iterator = cvDatabase.getAnnotations().iterator(); iterator.hasNext() && false == stop; ) { Annotation annotation = (Annotation) iterator.next();