/** * Get an Intact Protein out of a ProteinInteractorTag. * * @param proteinParticipant * * @return the IntAct Protein correcponding to the given ProteinParticipantTag. */ private static ProteinHolder getProtein( final ProteinParticipantTag proteinParticipant ) { final ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor(); OrganismTag organism = proteinInteractor.getOrganism(); BioSource bioSource = null; if ( organism != null ) { bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() ); } String proteinId = proteinInteractor.getPrimaryXref().getId(); String db = proteinInteractor.getPrimaryXref().getDb(); // System.out.println( "Search interactor (" + proteinInteractor.getShortlabel() + ") from cache(" + // proteinId + ", " + db + ", " + bioSource.getShortLabel() + ")" ); return ProteinInteractorChecker.getProtein( proteinId, db, bioSource ); } }
/** * Get an Intact Protein out of a ProteinInteractorTag. * * @param proteinParticipant * * @return the IntAct Protein correcponding to the given ProteinParticipantTag. */ private static ProteinHolder getProtein( final ProteinParticipantTag proteinParticipant ) { final ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor(); OrganismTag organism = proteinInteractor.getOrganism(); BioSource bioSource = null; if ( organism != null ) { bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() ); } String proteinId = proteinInteractor.getPrimaryXref().getId(); String db = proteinInteractor.getPrimaryXref().getDb(); // System.out.println( "Search interactor (" + proteinInteractor.getShortlabel() + ") from cache(" + // proteinId + ", " + db + ", " + bioSource.getShortLabel() + ")" ); return ProteinInteractorChecker.getProtein( proteinId, db, bioSource ); } }
/** * Get an Intact Protein out of a ProteinInteractorTag. * * @param proteinParticipant * * @return the IntAct Protein correcponding to the given ProteinParticipantTag. */ private static ProteinHolder getProtein( final ProteinParticipantTag proteinParticipant ) { final ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor(); OrganismTag organism = proteinInteractor.getOrganism(); BioSource bioSource = null; if ( organism != null ) { bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() ); } String proteinId = proteinInteractor.getPrimaryXref().getId(); String db = proteinInteractor.getPrimaryXref().getDb(); // System.out.println( "Search interactor (" + proteinInteractor.getShortlabel() + ") from cache(" + // proteinId + ", " + db + ", " + bioSource.getShortLabel() + ")" ); return ProteinInteractorChecker.getProtein( proteinId, db, bioSource ); } }
final String proteinId = proteinInteractor.getPrimaryXref().getId(); final String db = proteinInteractor.getPrimaryXref().getDb(); final ProteinHolder proteinHolder = ProteinInteractorChecker.getProtein( proteinId, db, bioSource ); final CvComponentRole role = RoleChecker.getCvComponentRole( proteinParticipant.getRole() );
final String proteinId = proteinInteractor.getPrimaryXref().getId(); final String db = proteinInteractor.getPrimaryXref().getDb(); final ProteinHolder proteinHolder = ProteinInteractorChecker.getProtein( proteinId, db, bioSource ); final CvComponentRole role = RoleChecker.getCvComponentRole( proteinParticipant.getRole() );
final String proteinId = proteinInteractor.getPrimaryXref().getId(); final String db = proteinInteractor.getPrimaryXref().getDb(); final ProteinHolder proteinHolder = ProteinInteractorChecker.getProtein( proteinId, db, bioSource ); final CvExperimentalRole expRole = RoleChecker.getCvExperimentalRole( proteinParticipant.getRole() ); CvBiologicalRole bioRole = RoleChecker.getDefaultCvBiologicalRole();