/** * 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 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); } }
private Set<Xref> getXrefs(psidev.psi.mi.xml.model.Xref psiXREF) { // set to return Set<Xref> toReturn = new HashSet<Xref>(); // check args if (psiXREF == null) return toReturn; // create the list of all other psimi xrefs List<DbReference> psiDBRefList = new ArrayList<DbReference>(); DbReference primaryRef = psiXREF.getPrimaryRef(); if(primaryRef != null) { //looks, it should never be null in a valid PSI-MI model if ("identity".equals(primaryRef.getRefType()) || "identical object".equals(primaryRef.getRefType())) { UnificationXref bpXref = unificationXref(primaryRef.getDb(), primaryRef.getId()); toReturn.add(bpXref); } else { psiDBRefList.add(psiXREF.getPrimaryRef()); } } if (psiXREF.hasSecondaryRef()) { psiDBRefList.addAll(psiXREF.getSecondaryRef()); } for (DbReference psiref : psiDBRefList) { if(psiref==null) continue; xref(psiref, toReturn); } return toReturn; }
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 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.xml253.jaxb.XrefType 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.xml253.jaxb.XrefType jXref = new psidev.psi.mi.xml253.jaxb.XrefType(); // Initialise the JAXB object reading the model // 1. set attributes jXref.setPrimaryRef( dbReferenceConverter.toJaxb( mXref.getPrimaryRef() ) ); // 2. set encapsulated objects if ( mXref.hasSecondaryRef() ) { for ( DbReference mRef : mXref.getSecondaryRef() ) { jXref.getSecondaryReves().add( dbReferenceConverter.toJaxb( mRef ) ); } } return jXref; } }
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; } }
expRef.getSecondaryRef().add(iteratorDb.next()); expRef.getSecondaryRef().add(iteratorDb.next()); expRef.getSecondaryRef().addAll(disjunction);
private boolean extractPrimaryRefFromExperiment(Experiment intactObject, Bibref bibref) { if (!intactObject.getXrefs().isEmpty()){ Collection<uk.ac.ebi.intact.model.Xref> primaryRefs = searchXrefs(intactObject, CvDatabase.PUBMED_MI_REF, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF, isCheckInitializedCollections()); if (primaryRefs.isEmpty()){ primaryRefs = searchXrefs(intactObject, CvDatabase.DOI_MI_REF, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF, isCheckInitializedCollections()); } if (!primaryRefs.isEmpty()){ Iterator<uk.ac.ebi.intact.model.Xref> iterator = primaryRefs.iterator(); uk.ac.ebi.intact.model.Xref primaryRef = iterator.next(); Xref xref = new Xref(); xref.setPrimaryRef(new DbReference(primaryRef.getCvDatabase().getShortLabel(), primaryRef.getCvDatabase().getIdentifier(), primaryRef.getPrimaryId(), primaryRef.getCvXrefQualifier().getShortLabel(), primaryRef.getCvXrefQualifier().getIdentifier())); bibref.setXref(xref); while (iterator.hasNext()){ primaryRef = iterator.next(); xref.getSecondaryRef().add(new DbReference(primaryRef.getCvDatabase().getShortLabel(), primaryRef.getCvDatabase().getIdentifier(), primaryRef.getPrimaryId(), primaryRef.getCvXrefQualifier().getShortLabel(), primaryRef.getCvXrefQualifier().getIdentifier())); } return true; } } return false; }
xref.getSecondaryRef().addAll(CollectionUtils.subtract(dbRefs, Arrays.asList(primaryRef))); if ( !xref.getSecondaryRef().contains( secDbRef ) ) { xref.getSecondaryRef().add( secDbRef );
if ( !xref.getSecondaryRef().contains( secDbRef ) ) { xref.getSecondaryRef().add( secDbRef );
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);
} else { DbReference secondaryRef = new DbReference(xref.getIdentifier(), xref.getDatabase()); ref.getSecondaryRef().add(secondaryRef); experimentDescription.setXref(ref); } else { experimentDescription.getXref().getSecondaryRef().addAll(ref.getAllDbReferences());
xref.getSecondaryRef().add(dbRef);
xref.getSecondaryRef().add(new DbReference(primaryRef.getCvDatabase().getShortLabel(), primaryRef.getCvDatabase().getIdentifier(), primaryRef.getPrimaryId(), primaryRef.getCvXrefQualifier().getShortLabel(), primaryRef.getCvXrefQualifier().getIdentifier()));
xref.getSecondaryRef().add(dbRef);
xref.getSecondaryRef().add(dbRef);
bibref.getXref().getSecondaryRef().add(ref); bibref.getXref().getSecondaryRef().add(ref); bibref.getXref().getSecondaryRef().add(ref); bibref.getXref().getSecondaryRef().add(ref); bibref.getXref().getSecondaryRef().add(ref);