/** * Adds an xref to the object. The xref will only be added * if an equivalent xref is not yet part of the object. */ public void addXref( T aXref ) { //if( !this.xrefs.contains( aXref ) ) { this.xrefs.add( aXref ); aXref.setParent( this ); //aXref.setParentAc(this.getAc()); //} }
/** * Adds an xref to the object. The xref will only be added * if an equivalent xref is not yet part of the object. */ public void addXref( T aXref ) { //if( !this.xrefs.contains( aXref ) ) { this.xrefs.add( aXref ); aXref.setParent( this ); //aXref.setParentAc(this.getAc()); //} }
/** * Adds an xref to the object. The xref will only be added * if an equivalent xref is not yet part of the object. */ public void addXref( T aXref ) { //if( !this.xrefs.contains( aXref ) ) { this.xrefs.add( aXref ); aXref.setParent( this ); //aXref.setParentAc(this.getAc()); //} }
public void removeXref( T xref ) { this.xrefs.remove( xref ); xref.setParent(null); }
public void removeXref( T xref ) { this.xrefs.remove( xref ); xref.setParent(null); }
public <X extends Xref> void populateWithPsiMi(AnnotatedObject annotatedObject, String psiMi) { this.institution = annotatedObject.getOwner(); Class<? extends Xref> xrefClass = AnnotatedObjectUtils.getXrefClassType(annotatedObject.getClass()); X xref = (X) createPsiMiXref(xrefClass, psiMi); xref.setParent(annotatedObject); if (xref instanceof CvObjectXref) { if (((CvObject)annotatedObject).getIdentifier() == null) { ((CvObjectXref)xref).prepareParentMi(); } } annotatedObject.getXrefs().add(xref); }
public <X extends Xref> X createXref(AnnotatedObject<X,?> parent, String primaryId, CvXrefQualifier cvXrefQualifer, CvDatabase cvDatabase) { X xref = (X) XrefUtils.newXrefInstanceFor(parent.getClass()); xref.setOwner(parent.getOwner()); xref.setParent(parent); xref.setPrimaryId(primaryId); xref.setCvXrefQualifier(cvXrefQualifer); xref.setCvDatabase(cvDatabase); return xref; }
public <X extends Xref> X createXref(AnnotatedObject<X,?> parent, String primaryId, CvXrefQualifier cvXrefQualifer, CvDatabase cvDatabase) { X xref = (X) XrefUtils.newXrefInstanceFor(parent.getClass()); xref.setOwner(parent.getOwner()); xref.setParent(parent); xref.setPrimaryId(primaryId); xref.setCvXrefQualifier(cvXrefQualifer); xref.setCvDatabase(cvDatabase); return xref; }
xrefClone.setParent( copy ); copiedXrefs.add( xrefClone );
public <X extends Xref> X createXref(AnnotatedObject<X,?> parent, String primaryId, CvXrefQualifier cvXrefQualifer, CvDatabase cvDatabase) { X xref = (X) XrefUtils.newXrefInstanceFor(parent.getClass()); xref.setOwner(parent.getOwner()); xref.setParent(parent); xref.setPrimaryId(primaryId); xref.setCvXrefQualifier(cvXrefQualifer); xref.setCvDatabase(cvDatabase); return xref; }
xrefClone.setParent( copy ); copiedXrefs.add( xrefClone );
xrefClone.setParent( copy ); copiedXrefs.add( xrefClone );
public static <X extends Xref> X createIdentityXref(AnnotatedObject<X,?> parent, String primaryId, CvXrefQualifier identityQual, CvDatabase cvDatabase) { X xref = (X) newXrefInstanceFor(parent.getClass()); Institution owner = parent.getOwner(); if (owner == null) { owner = IntactContext.getCurrentInstance().getInstitution(); } xref.setOwner(owner); xref.setCvDatabase(cvDatabase); xref.setCvXrefQualifier(identityQual); xref.setPrimaryId(primaryId); xref.setParent(parent); return xref; }
public static <X extends Xref> X createIdentityXref(AnnotatedObject<X, ?> parent, String primaryId, CvXrefQualifier identityQual, CvDatabase cvDatabase) { X xref = (X) newXrefInstanceFor(parent.getClass()); Institution owner = parent.getOwner(); if (owner == null) { owner = IntactContext.getCurrentInstance().getInstitution(); } xref.setOwner(owner); xref.setCvDatabase(cvDatabase); xref.setCvXrefQualifier(identityQual); xref.setPrimaryId(primaryId); xref.setParent(parent); return xref; }
public static <X extends Xref> X createIdentityXref(AnnotatedObject<X, ?> parent, String primaryId, CvXrefQualifier identityQual, CvDatabase cvDatabase) { X xref = (X) newXrefInstanceFor(parent.getClass()); Institution owner = parent.getOwner(); if (owner == null) { owner = IntactContext.getCurrentInstance().getInstitution(); } xref.setOwner(owner); xref.setCvDatabase(cvDatabase); xref.setCvXrefQualifier(identityQual); xref.setPrimaryId(primaryId); xref.setParent(parent); return xref; }
/** * Note: this does not clone the parent. * * @param xref * @return * @throws uk.ac.ebi.intact.model.clone.IntactClonerException * */ protected Xref cloneXref(Xref xref) throws IntactClonerException { if (xref == null) return null; Class clazz = CgLibUtil.removeCglibEnhanced(xref.getClass()); Xref clone = null; try { final Constructor constructor = clazz.getConstructor(); clone = (Xref) constructor.newInstance(); clonerManager.addClone(xref, clone); clone.setPrimaryId(xref.getPrimaryId()); clone.setSecondaryId(xref.getSecondaryId()); clone.setDbRelease(xref.getDbRelease()); clone.setCvDatabase(clone(xref.getCvDatabase())); clone.setCvXrefQualifier(clone(xref.getCvXrefQualifier())); } catch (Exception e) { throw new IntactClonerException("An error occured upon building a " + clazz.getSimpleName(), e); } clone.setParent(clone(xref.getParent())); return clone; }
/** * Note: this does not clone the parent. * * @param xref * @return * @throws uk.ac.ebi.intact.model.clone.IntactClonerException * */ protected Xref cloneXref(Xref xref) throws IntactClonerException { if (xref == null) return null; Class clazz = CgLibUtil.removeCglibEnhanced(xref.getClass()); Xref clone = null; try { final Constructor constructor = clazz.getConstructor(); clone = (Xref) constructor.newInstance(); clonerManager.addClone(xref, clone); clone.setPrimaryId(xref.getPrimaryId()); clone.setSecondaryId(xref.getSecondaryId()); clone.setDbRelease(xref.getDbRelease()); clone.setCvDatabase(clone(xref.getCvDatabase())); clone.setCvXrefQualifier(clone(xref.getCvXrefQualifier())); } catch (Exception e) { throw new IntactClonerException("An error occured upon building a " + clazz.getSimpleName(), e); } clone.setParent(clone(xref.getParent())); return clone; }
private Xref synchronizeXref( Xref xref, AnnotatedObject parent ) { if (xref.getAc() != null) { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory() .getXrefDao().getByAc(xref.getAc()); } xref.setCvDatabase( synchronize( xref.getCvDatabase() ) ); xref.setCvXrefQualifier( synchronize( xref.getCvXrefQualifier() ) ); xref.setParent(parent); if (xref.getAc() == null && xref.getAc() != null) { annotatedObjectsToPersist.put(keyBuilder.keyForXref(xref), xref); } return xref; }
private Xref synchronizeXref( Xref xref, AnnotatedObject parent ) { if (xref.getAc() != null) { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory() .getXrefDao().getByAc(xref.getAc()); } xref.setCvDatabase( synchronize( xref.getCvDatabase() ) ); xref.setCvXrefQualifier( synchronize( xref.getCvXrefQualifier() ) ); xref.setParent(parent); if (xref.getAc() == null && xref.getAc() != null) { annotatedObjectsToPersist.put(keyBuilder.keyForXref(xref), xref); } return xref; }
xref.setCvXrefQualifier(cvXrefQual); xref.setParent(intactObject); xref.setOwner(institutionPersister.syncIfTransient(xref.getOwner()));