public static void check( final OrganismTag organism, final BioSourceFactory bioSourceFactory ) { final String taxid = organism.getTaxId(); final CellTypeTag cellType = organism.getCellType(); final TissueTag tissue = organism.getTissue(); check( taxid, cellType, tissue, bioSourceFactory ); } }
public static BioSource getBioSource( final OrganismTag organism ) { if ( organism == null ) { return null; } final String taxid = organism.getTaxId(); final CellTypeTag cellType = organism.getCellType(); final TissueTag tissue = organism.getTissue(); return getBioSource( taxid, cellType, tissue ); }
public static BioSource getBioSource( final OrganismTag organism ) { if ( organism == null ) { return null; } final String taxid = organism.getTaxId(); final CellTypeTag cellType = organism.getCellType(); final TissueTag tissue = organism.getTissue(); return getBioSource( taxid, cellType, tissue ); }
public static void check( final OrganismTag organism, final BioSourceFactory bioSourceFactory ) { final String taxid = organism.getTaxId(); final CellTypeTag cellType = organism.getCellType(); final TissueTag tissue = organism.getTissue(); check( taxid, cellType, tissue, bioSourceFactory ); } }
public static BioSource getBioSource( final OrganismTag organism ) { if ( organism == null ) { return null; } final String taxid = organism.getTaxId(); final CellTypeTag cellType = organism.getCellType(); final TissueTag tissue = organism.getTissue(); return getBioSource( taxid, cellType, tissue ); }
public static void check( final OrganismTag organism, final BioSourceFactory bioSourceFactory ) { final String taxid = organism.getTaxId(); final CellTypeTag cellType = organism.getCellType(); final TissueTag tissue = organism.getTissue(); check( taxid, cellType, tissue, bioSourceFactory ); } }
/** * 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 ); } }
OrganismChecker.check( organism, bioSourceFactory );
/** * 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 ); } }
OrganismChecker.check( organism, bioSourceFactory );
/** * 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 ); } }
OrganismChecker.check( organism, bioSourceFactory );
BioSource bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() ); if ( bioSource == null ) { String message = "Could not find a BioSource using the definition: " + proteinInteractor.getOrganism();
BioSource bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() ); if ( bioSource == null ) { String message = "Could not find a BioSource using the definition: " + proteinInteractor.getOrganism();
BioSource bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() ); if ( bioSource == null ) { String message = "Could not find a BioSource using the definition: " + proteinInteractor.getOrganism();
final BioSource bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() ); final String proteinId = proteinInteractor.getPrimaryXref().getId(); final String db = proteinInteractor.getPrimaryXref().getDb();
final BioSource bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() ); final String proteinId = proteinInteractor.getPrimaryXref().getId(); final String db = proteinInteractor.getPrimaryXref().getDb();
final BioSource bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() ); final String proteinId = proteinInteractor.getPrimaryXref().getId(); final String db = proteinInteractor.getPrimaryXref().getDb();