/** * Collect all DbReference under an xref. * * @param xref * @return a non null collection. */ public static List<DbReference> getAllDbReferences( Xref xref ) { ArrayList<DbReference> xrefs = new ArrayList<DbReference>(); xrefs.add( xref.getPrimaryRef() ); if ( xref.hasSecondaryRef() ) { for ( DbReference sec : xref.getSecondaryRef() ) { xrefs.add( sec ); } } return xrefs; }
public psidev.psi.mi.xml.model.Xref fromJaxb( psidev.psi.mi.xml253.jaxb.XrefType jXref ) { if ( jXref == null ) { throw new IllegalArgumentException( "You must give a non null JAXB Xref." ); } psidev.psi.mi.xml.model.Xref mXref = new psidev.psi.mi.xml.model.Xref(); // Initialise the model reading the Jaxb object // 1. set attributes mXref.setPrimaryRef( dbReferenceConverter.fromJaxb( jXref.getPrimaryRef() ) ); // 2. set encapsulated objects for ( DbReferenceType jRef : jXref.getSecondaryReves() ) { mXref.getSecondaryRef().add( dbReferenceConverter.fromJaxb( jRef ) ); } return mXref; }
public static Xref createXrefIdentity(String primaryId, String dbMi, String dbName) { Xref xref = new Xref(); xref.setPrimaryRef(createDbReference(primaryId, dbMi, dbName, "MI:0356", "identity")); return xref; }
public static <X extends Xref> void populateXref(psidev.psi.mi.xml.model.Xref psiXref, AnnotatedObject<X, ?> annotatedObject, XrefConverter<X> xrefConverter) { if (psiXref == null) { return; } if (psiXref.getPrimaryRef() != null) { addXref(psiXref.getPrimaryRef(), annotatedObject, xrefConverter); } for (DbReference secondaryRef : psiXref.getSecondaryRef()) { addXref(secondaryRef, annotatedObject, xrefConverter); } }
existingDbRefs.addAll(expDesc.getBibref().getXref().getAllDbReferences()); Iterator<DbReference> iteratorDb = disjunction.iterator(); Xref expRef = new Xref(iteratorDb.next()); expRef.getSecondaryRef().add(iteratorDb.next()); Xref expRef = expDesc.getXref(); Set<DbReference> existingDbRefs = new HashSet(expRef.getAllDbReferences()); existingDbRefs.addAll(expDesc.getBibref().getXref().getAllDbReferences()); if (expRef.getPrimaryRef() == null){ Iterator<DbReference> iteratorDb = disjunction.iterator(); expRef.setPrimaryRef(iteratorDb.next()); expRef.getSecondaryRef().add(iteratorDb.next()); expRef.getSecondaryRef().addAll(disjunction);
private UnificationXref getPrimaryUnificationXref(psidev.psi.mi.xml.model.Xref psiXref) { if (psiXref==null || psiXref.getPrimaryRef() == null) return null; UnificationXref toReturn = null; DbReference psiDBRef = psiXref.getPrimaryRef(); String refType = (psiDBRef.hasRefType()) ? psiDBRef.getRefType() : null; // If multiple ids given with comma separated values, then split them. if (refType==null || "identity".equals(refType) || "identical object".equals(refType)) { toReturn = unificationXref(psiDBRef.getDb(), psiDBRef.getId()); } return toReturn; }
expDesc.setBibref(bibref); PsiConverterUtils.populateXref(intactObject, bibref, xrefConverter); if (bibref.getXref() != null && bibref.getXref().getPrimaryRef() != null){ isBibRefSet = true; Xref xref = new Xref(); xref.setPrimaryRef(new DbReference(CvDatabase.PUBMED, CvDatabase.PUBMED_MI_REF, publication.getShortLabel(), CvXrefQualifier.PRIMARY_REFERENCE, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF)); bibref.setXref(xref); isBibRefSet = true; if (bibref.getXref() != null && bibref.getXref().getPrimaryRef() != null){ expDesc.setBibref(bibref);
if (ref == null) { DbReference primaryRef = new DbReference(xref.getIdentifier(), xref.getDatabase()); ref = new Xref(primaryRef); } else { DbReference secondaryRef = new DbReference(xref.getIdentifier(), xref.getDatabase()); ref.getSecondaryRef().add(secondaryRef); experimentDescription.setXref(ref); } else { experimentDescription.getXref().getSecondaryRef().addAll(ref.getAllDbReferences());
Xref interactorXref = new Xref(primaryReferece, secondaryRefs); xmlInteractor.setXref(interactorXref); } else { Xref interactorXref = new Xref(primaryReferece); xmlInteractor.setXref(interactorXref); if (!interactorType.hasNames() && interactorType.getXref() != null && interactorType.getXref().getPrimaryRef() != null) { String id = interactorType.getXref().getPrimaryRef().getId(); Names interactorTypeName = new Names(); String xrefPrimaryDB = xmlInteractor.getXref().getPrimaryRef().getDb(); if (xrefPrimaryDB.equals(UNIPROT)) { dbRef.setRefType(IDENTITY); dbRef.setRefTypeAc(IDENTITY_REF); interactorTypeXref = new Xref(dbRef); } else if (xrefPrimaryDB.equals(CHEBI)) { dbRef.setRefType(IDENTITY); dbRef.setRefTypeAc(IDENTITY_REF); interactorTypeXref = new Xref(dbRef); } else { dbRef.setRefType(IDENTITY); dbRef.setRefTypeAc(IDENTITY_REF); interactorTypeXref = new Xref(dbRef); log.debug("Interactor type is unknown"); dbRef.setRefType(IDENTITY);
xref = new Xref(secondaryRef); } else { xref.getSecondaryRef().add(secondaryRef); xref = new Xref(secondaryRef); } else { xref.getSecondaryRef().add(secondaryRef); interaction.setXref(new Xref(sourceReference)); } else { interaction.getXref().getSecondaryRef().add(sourceReference); interaction.setXref(new Xref()); interaction.getXref().getSecondaryRef().addAll(secondaryRefs);
public static Bibref createBibref(String publicationId, String dbAc, String dbName) { DbReference dbReference = createDbReference(publicationId, dbAc, dbName, "MI:0358", "primary-reference"); Xref xref = new Xref(dbReference); return new Bibref(xref); }
public Xref( DbReference primaryRef, Collection<DbReference> secondaryRef ) { setPrimaryRef( primaryRef ); this.secondaryRef = secondaryRef; }
xref = new Xref(); xref.setPrimaryRef( primaryPubmedRef ); } else { final DbReference primaryDoiRef = getPrimaryReference( dbRefs , CvDatabase.DOI_MI_REF ); xref.setPrimaryRef(primaryDoiRef); xref.setPrimaryRef(primaryRef); } else { if (log.isWarnEnabled()) log.warn("No primary-reference (refTypeAc="+ CvXrefQualifier.PRIMARY_REFERENCE_MI_REF+") " + xref.setPrimaryRef( primaryRef ); if ( !xref.getSecondaryRef().contains( secDbRef ) ) { xref.getSecondaryRef().add( secDbRef ); if (xref.getPrimaryRef() != null) { xrefContainer.setXref( xref );
protected boolean containsRole(Collection<ExperimentalRole> experimentalRoles, String[] rolesToFind) { if (experimentalRoles != null) { for (ExperimentalRole expRole : experimentalRoles) { if (expRole.getXref() != null && expRole.getXref().getPrimaryRef()!=null) { String ac = expRole.getXref().getPrimaryRef().getRefTypeAc(); for (String roleToFind : rolesToFind) { if (roleToFind.equals(ac)) { return true; } } } } } return false; } }
public static Xref createXref(String primaryId, String dbMi, String dbName, String qualifierMi, String qualifierName) { Xref xref = new Xref(); xref.setPrimaryRef(createDbReference(primaryId, dbMi, dbName, qualifierMi, qualifierName)); return xref; }
public Xref imexPrimaryFromMitab( CrossReference ref ) { Xref imex = null; if (ref != null && ref.getIdentifier() != null && ref.getDatabase() != null){ String db = ref.getDatabase(); String id = ref.getIdentifier(); DbReference primaryRef = new DbReference(id, db); primaryRef.setRefType("imex-primary"); primaryRef.setRefTypeAc("MI:0662"); if (db.equals("imex")) primaryRef.setDbAc("MI:0670"); imex = new Xref(primaryRef); } return imex; } }
public Xref( DbReference primaryRef ) { setPrimaryRef( primaryRef ); }
xref = new Xref(); xref.setPrimaryRef( primaryRef ); } else { primaryRef = getPrimaryReference( dbRefs , CvDatabase.DOI_MI_REF ); xref.setPrimaryRef(primaryRef); xref.setPrimaryRef(primaryRef); } else { if (log.isWarnEnabled()) log.warn("No primary-reference (refTypeAc="+ CvXrefQualifier.PRIMARY_REFERENCE_MI_REF+") " + xref.getSecondaryRef().addAll(CollectionUtils.subtract(dbRefs, Arrays.asList(primaryRef))); xref.setPrimaryRef( primaryRef ); if ( !xref.getSecondaryRef().contains( secDbRef ) ) { xref.getSecondaryRef().add( secDbRef ); if (xref.getPrimaryRef() != null) { xrefContainer.setXref( xref );
public psidev.psi.mi.xml.model.Xref fromJaxb( psidev.psi.mi.xml254.jaxb.Xref jXref ) { if ( jXref == null ) { throw new IllegalArgumentException( "You must give a non null JAXB Xref." ); } psidev.psi.mi.xml.model.Xref mXref = new psidev.psi.mi.xml.model.Xref(); // Initialise the model reading the Jaxb object // 1. set attributes mXref.setPrimaryRef( dbReferenceConverter.fromJaxb( jXref.getPrimaryRef() ) ); // 2. set encapsulated objects for ( DbReference jRef : jXref.getSecondaryReves() ) { mXref.getSecondaryRef().add( dbReferenceConverter.fromJaxb( jRef ) ); } return mXref; }
public psidev.psi.mi.xml254.jaxb.Xref toJaxb( psidev.psi.mi.xml.model.Xref mXref ) { if ( mXref == null ) { throw new IllegalArgumentException( "You must give a non null model Xref." ); } psidev.psi.mi.xml254.jaxb.Xref jXref = new psidev.psi.mi.xml254.jaxb.Xref(); // Initialise the JAXB object reading the model // 1. set attributes jXref.setPrimaryRef( dbReferenceConverter.toJaxb( mXref.getPrimaryRef() ) ); // 2. set encapsulated objects if ( mXref.hasSecondaryRef() ) { for ( psidev.psi.mi.xml.model.DbReference mRef : mXref.getSecondaryRef() ) { jXref.getSecondaryReves().add( dbReferenceConverter.toJaxb( mRef ) ); } } return jXref; } }