private <T extends ControlledVocabulary> T findOrCreateControlledVocabulary(CvType cvType, Class<T> bpCvClass) { if (cvType == null) return null; // try full name first, else try short name String term = null; if (cvType.hasNames()) { term = getName(cvType.getNames()); } //xref and primaryRef must always exist, acc. to the schema UnificationXref bpXref = getPrimaryUnificationXref(cvType.getXref()); T toReturn = findOrCreateControlledVocabulary(term, bpXref, bpCvClass); return toReturn; }
@Override public boolean equals( Object o ) { if ( this == o ) return true; if ( o == null || getClass() != o.getClass() ) return false; if ( !super.equals( o ) ) return false; ExperimentalRole that = ( ExperimentalRole ) o; if ( experimentRefs != null ? !experimentRefs.equals( that.experimentRefs ) : that.experimentRefs != null ) return false; if ( experiments != null ? !experiments.equals( that.experiments ) : that.experiments != null ) return false; return true; }
/** * @param mCvType instance of the model implementation of OpenCvType. * @return */ public psidev.psi.mi.xml254.jaxb.CvType toJaxb( psidev.psi.mi.xml.model.CvType mCvType ) { if ( mCvType == null ) { throw new IllegalArgumentException( "You must give a non null JAXB OpenCvType." ); } psidev.psi.mi.xml254.jaxb.CvType jCvType = new psidev.psi.mi.xml254.jaxb.CvType(); // Initialise the model reading the Jaxb object // 1. set encapsulated objects // names jCvType.setNames( namesConverter.toJaxb( mCvType.getNames() ) ); // xref jCvType.setXref( xrefConverter.toJaxb( mCvType.getXref() ) ); return jCvType; }
private static <C extends CvType> C createCvType(Class<C> cvTypeClass, String name) { C cv; try { cv = cvTypeClass.newInstance(); cv.setNames(createNames(name, null)); } catch (Exception e) { throw new IllegalArgumentException("Is this a cvType?: "+cvTypeClass, e); } return cv; }
public static <C extends CvType> C createCvType(Class<C> cvTypeClass, String miRef, String label) { C cv = createCvType(cvTypeClass, label); cv.setXref(createXrefPsiMi(miRef)); return cv; }
@Override public int hashCode() { int result = super.hashCode(); result = 31 * result + ( experiments != null ? experiments.hashCode() : 0 ); result = 31 * result + ( experimentRefs != null ? experimentRefs.hashCode() : 0 ); return result; } }
/** * @param mCvType instance of the model implementation of OpenCvType. * @return */ public psidev.psi.mi.xml253.jaxb.CvType toJaxb( psidev.psi.mi.xml.model.CvType mCvType ) { if ( mCvType == null ) { throw new IllegalArgumentException( "You must give a non null JAXB OpenCvType." ); } psidev.psi.mi.xml253.jaxb.CvType jCvType = new psidev.psi.mi.xml253.jaxb.CvType(); // Initialise the model reading the Jaxb object // 1. set encapsulated objects // names jCvType.setNames( namesConverter.toJaxb( mCvType.getNames() ) ); // xref jCvType.setXref( xrefConverter.toJaxb( mCvType.getXref() ) ); return jCvType; }
@Override public int hashCode() { int result = super.hashCode(); result = 31 * result + ( experiments != null ? experiments.hashCode() : 0 ); result = 31 * result + ( experimentRefs != null ? experimentRefs.hashCode() : 0 ); return result; } }
@Override public boolean equals( Object o ) { if ( this == o ) return true; if ( o == null || getClass() != o.getClass() ) return false; if ( !super.equals( o ) ) return false; ExperimentalPreparation that = ( ExperimentalPreparation ) o; if ( experimentRefs != null ? !experimentRefs.equals( that.experimentRefs ) : that.experimentRefs != null ) return false; if ( experiments != null ? !experiments.equals( that.experiments ) : that.experiments != null ) return false; return true; }
public C psiToIntact(T psiObject) { psiStartConversion(psiObject); C cv = newCvInstance(intactCvClass); cv.setOwner(getInstitution()); IntactConverterUtils.populateNames(psiObject.getNames(), cv, aliasConverter); IntactConverterUtils.populateXref(psiObject.getXref(), cv, xrefConverter); psiEndConversion(psiObject); return cv; }
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; }