public Interaction createInteractionRandomBinary(String imexId) { CvInteractionType cvInteractionType = createCvObject(CvInteractionType.class, CvInteractionType.DIRECT_INTERACTION_MI_REF, CvInteractionType.DIRECT_INTERACTION); CvInteractorType intType = createCvObject(CvInteractorType.class, CvInteractorType.INTERACTION_MI_REF, CvInteractorType.INTERACTION ); Experiment experimentEmpty = createExperimentEmpty(); Interaction interaction = new InteractionImpl(new ArrayList<Experiment>(Arrays.asList(experimentEmpty)), cvInteractionType, intType, nextString("label"), getInstitution()); experimentEmpty.getInteractions().add(interaction); createComponentBait(interaction, createProteinRandom()); createComponentPrey(interaction, createProteinRandom()); String shortLabel = InteractionUtils.calculateShortLabel(interaction); interaction.setShortLabel(shortLabel); if (imexId != null) { CvObjectBuilder cvBuilder = new CvObjectBuilder(); CvXrefQualifier idQual = cvBuilder.createIdentityCvXrefQualifier(getInstitution()); CvDatabase imexDb = createCvObject(CvDatabase.class, CvDatabase.IMEX_MI_REF, CvDatabase.IMEX); interaction.addXref(new InteractorXref(getInstitution(), imexDb, imexId, idQual)); } return interaction; }
/** * Create a new InteractorXref for the protein * @param uniprotAc : the uniprot accession * @return the InteractorXref with the uniprot ac and qualifier identity */ private InteractorXref createIdentityInteractorXrefForUniprotAc(String uniprotAc){ IntactContext intactContext = IntactContext.getCurrentInstance(); if (uniprotAc == null){ return null; } final CvDatabase uniprot = intactContext.getDaoFactory().getCvObjectDao(CvDatabase.class).getByPsiMiRef( CvDatabase.UNIPROT_MI_REF ); final CvXrefQualifier identity = intactContext.getDaoFactory().getCvObjectDao(CvXrefQualifier.class).getByPsiMiRef(CvXrefQualifier.IDENTITY_MI_REF); InteractorXref xRef = new InteractorXref(intactContext.getInstitution(), uniprot, uniprotAc, identity); return xRef; }
public Interaction createInteractionRandomBinary(String imexId) { CvInteractionType cvInteractionType = createCvObject(CvInteractionType.class, CvInteractionType.DIRECT_INTERACTION_MI_REF, CvInteractionType.DIRECT_INTERACTION); CvInteractorType intType = createCvObject(CvInteractorType.class, CvInteractorType.INTERACTION_MI_REF, CvInteractorType.INTERACTION ); Experiment experimentEmpty = createExperimentEmpty(); Interaction interaction = new InteractionImpl(new ArrayList<Experiment>(Arrays.asList(experimentEmpty)), cvInteractionType, intType, nextString("label"), getInstitution()); experimentEmpty.getInteractions().add(interaction); createComponentBait(interaction, createProteinRandom()); createComponentPrey(interaction, createProteinRandom()); String shortLabel = InteractionUtils.calculateShortLabel(interaction); interaction.setShortLabel(shortLabel); if (imexId != null) { CvObjectBuilder cvBuilder = new CvObjectBuilder(); CvXrefQualifier idQual = cvBuilder.createIdentityCvXrefQualifier(getInstitution()); CvDatabase imexDb = createCvObject(CvDatabase.class, CvDatabase.IMEX_MI_REF, CvDatabase.IMEX); interaction.addXref(new InteractorXref(getInstitution(), imexDb, imexId, idQual)); } return interaction; }
xref = new InteractorXref( object.getOwner(), session.getSourceDatabase(), object.getAc(),
xref = new InteractorXref( object.getOwner(), session.getSourceDatabase(), object.getAc(),
InteractorXref xref = new InteractorXref( institution, cvDatabase, xrefTag.getId(), secondaryId, null, cvXrefQualifier ); interaction.addXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref );
InteractorXref xref = new InteractorXref( institution, cvDatabase, xrefTag.getId(), secondaryId, null, cvXrefQualifier ); interaction.addXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref );
InteractorXref xref = new InteractorXref( institution, cvDatabase, xrefTag.getId(), secondaryId, "", cvXrefQualifier ); interaction.addXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref );
xref = new InteractorXref( object.getOwner(), session.getSourceDatabase(), object.getAc(),
xref = new InteractorXref(object.getOwner(), session.getSourceDatabase(), object.getAc(),
xref = new InteractorXref(object.getOwner(), session.getSourceDatabase(), object.getAc(),
xref = new InteractorXref(object.getOwner(), session.getSourceDatabase(), object.getAc(),
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 ); } }