public Xref( DbReference primaryRef ) { setPrimaryRef( primaryRef ); }
public Xref( DbReference primaryRef, Collection<DbReference> secondaryRef ) { setPrimaryRef( primaryRef ); this.secondaryRef = secondaryRef; }
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 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 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; }
private static <T extends CvType> T createUnspecifiedRole( Class<T> roleClass ) { T role; try { role = roleClass.newInstance(); } catch ( Exception e ) { throw new RuntimeException( e ); } Names names = new Names(); names.setShortLabel(CvExperimentalRole.UNSPECIFIED); names.setFullName(CvExperimentalRole.UNSPECIFIED); role.setNames( names ); Xref xref = new Xref(); String unspecifiedRoleMiRef = CvExperimentalRole.UNSPECIFIED_PSI_REF; DbReference dbRef = new DbReference( unspecifiedRoleMiRef, CvDatabase.PSI_MI ); dbRef.setRefType( CvXrefQualifier.IDENTITY ); dbRef.setRefTypeAc( CvXrefQualifier.IDENTITY_MI_REF ); dbRef.setDbAc( CvDatabase.PSI_MI_MI_REF ); xref.setPrimaryRef( dbRef ); role.setXref( xref ); return role; }
if (expRef.getPrimaryRef() == null){ Iterator<DbReference> iteratorDb = disjunction.iterator(); expRef.setPrimaryRef(iteratorDb.next());
xref.setPrimaryRef(new DbReference(CvDatabase.PSI_MI, CvDatabase.PSI_MI_MI_REF, IntactConverterUtils.AUTH_CONF_MI, CvXrefQualifier.IDENTITY, CvXrefQualifier.IDENTITY_MI_REF)); Unit unit = new Unit(); unit.setNames(names);
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 );
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.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.setPrimaryRef( primaryRef );
dbRef.setRefTypeAc(IDENTITY_REF); xref.setPrimaryRef(dbRef); found = true;
xref.setPrimaryRef(new DbReference(primaryRef.getCvDatabase().getShortLabel(), primaryRef.getCvDatabase().getIdentifier(), primaryRef.getPrimaryId(), primaryRef.getCvXrefQualifier().getShortLabel(), primaryRef.getCvXrefQualifier().getIdentifier())); bibref.setXref(xref);
dbRef.setRefTypeAc(IDENTITY_REF); xref.setPrimaryRef(dbRef); found = true;
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;
xref.setPrimaryRef(rangeRef);
dbRef.setRefTypeAc(IDENTITY_REF); xref.setPrimaryRef(dbRef); found = true;
validPubmedPrimaryRef = ref; if (bibref.getXref().getPrimaryRef() == null){ bibref.getXref().setPrimaryRef(ref); validDOIPrimaryRef = ref; if (bibref.getXref().getPrimaryRef() == null){ bibref.getXref().setPrimaryRef(ref); bibref.getXref().setPrimaryRef(ref); bibref.getXref().setPrimaryRef(ref);