/** * 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 ); } }
uniprotID = proteinInteractor.getPrimaryXref().getId(); if ( proteinInteractor != null && proteinInteractor.getOrganism() != null ) { taxid = proteinInteractor.getOrganism().getTaxId();
uniprotID = proteinInteractor.getPrimaryXref().getId(); if ( proteinInteractor != null && proteinInteractor.getOrganism() != null ) { taxid = proteinInteractor.getOrganism().getTaxId();
uniprotID = proteinInteractor.getPrimaryXref().getId(); if ( proteinInteractor != null && proteinInteractor.getOrganism() != null ) { taxid = proteinInteractor.getOrganism().getTaxId();
if ( proteinInteractor != null && proteinInteractor.getOrganism() != null ) { taxid = proteinInteractor.getOrganism().getTaxId(); } else { taxid = "taxid not specified";
if ( proteinInteractor != null && proteinInteractor.getOrganism() != null ) { taxid = proteinInteractor.getOrganism().getTaxId(); } else { taxid = "taxid not specified";
if ( proteinInteractor != null && proteinInteractor.getOrganism() != null ) { taxid = proteinInteractor.getOrganism().getTaxId(); } else { taxid = "taxid not specified";
final BioSourceFactory bioSourceFactory ) { final OrganismTag organism = proteinInteractor.getOrganism(); String taxId = null; if ( organism != null ) {
final BioSourceFactory bioSourceFactory ) { final OrganismTag organism = proteinInteractor.getOrganism(); String taxId = null; if ( organism != null ) {
final BioSourceFactory bioSourceFactory ) { final OrganismTag organism = proteinInteractor.getOrganism(); String taxId = null; if ( organism != null ) {
if ( protein1.getBioSource().getTaxId().equals( proteinInteractor.getOrganism().getTaxId() ) ) { proteinInteractor.getOrganism().getTaxId() + ") and Xref: " + db + "(" + proteinId + "):"; BioSource bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() ); if ( bioSource == null ) { String message = "Could not find a BioSource using the definition: " + proteinInteractor.getOrganism(); proteinInteractor.getOrganism().getTaxId() + ") and Xref: " + db + "(" + proteinId + "). Reason: " + ie.getMessage(); ie.printStackTrace();
if ( protein1.getBioSource().getTaxId().equals( proteinInteractor.getOrganism().getTaxId() ) ) { proteinInteractor.getOrganism().getTaxId() + ") and Xref: " + db + "(" + proteinId + "):"; BioSource bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() ); if ( bioSource == null ) { String message = "Could not find a BioSource using the definition: " + proteinInteractor.getOrganism(); proteinInteractor.getOrganism().getTaxId() + ") and Xref: " + db + "(" + proteinId + "). Reason: " + ie.getMessage(); ie.printStackTrace();
if ( protein1.getBioSource().getTaxId().equals( proteinInteractor.getOrganism().getTaxId() ) ) { proteinInteractor.getOrganism().getTaxId() + ") and Xref: " + db + "(" + proteinId + "):"; BioSource bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() ); if ( bioSource == null ) { String message = "Could not find a BioSource using the definition: " + proteinInteractor.getOrganism(); proteinInteractor.getOrganism().getTaxId() + ") and Xref: " + db + "(" + proteinId + "). Reason: " + ie.getMessage(); ie.printStackTrace();
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();