getDaoFactory().getXrefDao().persist(xref); log.debug("Added required PSI Xref to " + shortlabel + ": " + mi);
value ); Collection<Xref> xrefs = getDaoFactory().getXrefDao().getByPrimaryIdLike( value );
if (experimentXref.getPrimaryId().equals(bioSourceToRemove.getTaxId())) { iterator.remove(); getDataContext().getDaoFactory().getXrefDao(ExperimentXref.class).delete(experimentXref); break;
private Collection<ProteinImpl> getProteinByXref(String primaryId, CvDatabase database, CvXrefQualifier qualifier) { XrefDao<InteractorXref> xrefDao = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao(InteractorXref.class); Collection<InteractorXref> xrefs = xrefDao.getByPrimaryId(primaryId, false); Collection<ProteinImpl> proteins = new ArrayList<ProteinImpl>(); for (InteractorXref xref : xrefs) { if ((null != database && database.equals(xref.getCvDatabase())) || (null == database && null == xref.getCvDatabase())) { if ((null != qualifier && qualifier.equals(xref.getCvXrefQualifier())) || (null == qualifier && null == xref.getCvXrefQualifier())) { proteins.add((ProteinImpl) xref.getParent()); } } } return proteins; }
IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref );
value); Collection<Xref> xrefs = getDaoFactory().getXrefDao().getByPrimaryIdLike(value);
IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref );
IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref );
private static void createXref( Protein protein, XrefTag xrefTag, boolean identity ) throws IntactException { CvXrefQualifier qualifier = null; if ( identity ) { qualifier = ControlledVocabularyRepository.getIdentityQualifier(); } CvDatabase database = XrefChecker.getCvDatabase( xrefTag.getDb() ); if ( database == null ) { // failed to find the database, skip the Xref creation } else { InteractorXref xref = new InteractorXref( IntactContext.getCurrentInstance().getInstitution(), database, xrefTag.getId(), xrefTag.getSecondary(), xrefTag.getVersion(), qualifier ); protein.addXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref ); } }
private static void createXref( Protein protein, XrefTag xrefTag, boolean identity ) throws IntactException { CvXrefQualifier qualifier = null; if ( identity ) { qualifier = ControlledVocabularyRepository.getIdentityQualifier(); } CvDatabase database = XrefChecker.getCvDatabase( xrefTag.getDb() ); if ( database == null ) { // failed to find the database, skip the Xref creation } else { InteractorXref xref = new InteractorXref( IntactContext.getCurrentInstance().getInstitution(), database, xrefTag.getId(), xrefTag.getSecondary(), xrefTag.getVersion(), qualifier ); protein.addXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref ); } }
private static void createXref( Protein protein, XrefTag xrefTag, boolean identity ) throws IntactException { CvXrefQualifier qualifier = null; if ( identity ) { qualifier = ControlledVocabularyRepository.getIdentityQualifier(); } CvDatabase database = XrefChecker.getCvDatabase( xrefTag.getDb() ); if ( database == null ) { // failed to find the database, skip the Xref creation } else { InteractorXref xref = new InteractorXref( IntactContext.getCurrentInstance().getInstitution(), database, xrefTag.getId(), xrefTag.getSecondary(), xrefTag.getVersion(), qualifier ); protein.addXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref ); } }
IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( primaryXref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( seeAlsoXref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref );
IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( primaryXref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( seeAlsoXref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref );
IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( primaryXref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( seeAlsoXref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref );
qualifier ); feature.addXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref );
qualifier ); feature.addXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref );
qualifier ); feature.addXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref );