public <X extends Xref> X createPrimaryReferenceXref(AnnotatedObject<X,?> parent, String primaryId) { CvXrefQualifier primaryReference = createCvObject(CvXrefQualifier.class, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF, CvXrefQualifier.PRIMARY_REFERENCE); CvDatabase pubmedDb = createCvObject(CvDatabase.class, CvDatabase.PUBMED_MI_REF, CvDatabase.PUBMED); return createXref(parent, primaryId, primaryReference, pubmedDb); }
public <X extends Xref> X createPrimaryReferenceXref(AnnotatedObject<X,?> parent, String primaryId) { CvXrefQualifier primaryReference = createCvObject(CvXrefQualifier.class, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF, CvXrefQualifier.PRIMARY_REFERENCE); CvDatabase pubmedDb = createCvObject(CvDatabase.class, CvDatabase.PUBMED_MI_REF, CvDatabase.PUBMED); return createXref(parent, primaryId, primaryReference, pubmedDb); }
public <X extends Xref> X createPrimaryReferenceXref(AnnotatedObject<X,?> parent, String primaryId) { CvXrefQualifier primaryReference = createCvObject(CvXrefQualifier.class, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF, CvXrefQualifier.PRIMARY_REFERENCE); CvDatabase pubmedDb = createCvObject(CvDatabase.class, CvDatabase.PUBMED_MI_REF, CvDatabase.PUBMED); return createXref(parent, primaryId, primaryReference, pubmedDb); }
public Protein createProteinChain(Protein masterProt, String uniprotId, String shortLabel) { Protein chain = createProtein(uniprotId, shortLabel); if (masterProt.getAc() == null) { throw new IllegalArgumentException("Cannot create a chain if the master protein does not have an AC: "+masterProt.getShortLabel()); } CvXrefQualifier chainParent = createCvObject(CvXrefQualifier.class, CvXrefQualifier.CHAIN_PARENT_MI_REF, CvXrefQualifier.CHAIN_PARENT); CvDatabase uniprotKb = createCvObject(CvDatabase.class, CvDatabase.INTACT_MI_REF, CvDatabase.INTACT); InteractorXref isoformXref = createXref(chain, masterProt.getAc(), chainParent, uniprotKb); chain.addXref(isoformXref); return chain; }
public Protein createProteinSpliceVariant(Protein masterProt, String uniprotId, String shortLabel) { Protein spliceVariant = createProtein(uniprotId, shortLabel); if (masterProt.getAc() == null) { throw new IllegalArgumentException("Cannot create an splice variant if the master protein does not have an AC: "+masterProt.getShortLabel()); } CvXrefQualifier isoformParent = createCvObject(CvXrefQualifier.class, CvXrefQualifier.ISOFORM_PARENT_MI_REF, CvXrefQualifier.ISOFORM_PARENT); CvDatabase uniprotKb = createCvObject(CvDatabase.class, CvDatabase.INTACT_MI_REF, CvDatabase.INTACT); InteractorXref isoformXref = createXref(spliceVariant, masterProt.getAc(), isoformParent, uniprotKb); spliceVariant.addXref(isoformXref); return spliceVariant; }
public Protein createProteinChain(Protein masterProt, String uniprotId, String shortLabel) { Protein chain = createProtein(uniprotId, shortLabel); if (masterProt.getAc() == null) { throw new IllegalArgumentException("Cannot create a chain if the master protein does not have an AC: "+masterProt.getShortLabel()); } CvXrefQualifier chainParent = createCvObject(CvXrefQualifier.class, CvXrefQualifier.CHAIN_PARENT_MI_REF, CvXrefQualifier.CHAIN_PARENT); CvDatabase uniprotKb = createCvObject(CvDatabase.class, CvDatabase.INTACT_MI_REF, CvDatabase.INTACT); InteractorXref isoformXref = createXref(chain, masterProt.getAc(), chainParent, uniprotKb); chain.addXref(isoformXref); return chain; }
public Protein createProteinSpliceVariant(Protein masterProt, String uniprotId, String shortLabel) { Protein spliceVariant = createProtein(uniprotId, shortLabel); if (masterProt.getAc() == null) { throw new IllegalArgumentException("Cannot create an splice variant if the master protein does not have an AC: "+masterProt.getShortLabel()); } CvXrefQualifier isoformParent = createCvObject(CvXrefQualifier.class, CvXrefQualifier.ISOFORM_PARENT_MI_REF, CvXrefQualifier.ISOFORM_PARENT); CvDatabase uniprotKb = createCvObject(CvDatabase.class, CvDatabase.INTACT_MI_REF, CvDatabase.INTACT); InteractorXref isoformXref = createXref(spliceVariant, masterProt.getAc(), isoformParent, uniprotKb); spliceVariant.addXref(isoformXref); return spliceVariant; }