/** * 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; }
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.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; } }