Object o = (Object) iterator.next(); if ( o instanceof ProteinParticipantTag ) { uniprotID = ( (ProteinParticipantTag) o ).getProteinInteractor().getPrimaryXref().getId();
Object o = (Object) iterator.next(); if ( o instanceof ProteinParticipantTag ) { uniprotID = ( (ProteinParticipantTag) o ).getProteinInteractor().getPrimaryXref().getId();
Object o = (Object) iterator.next(); if ( o instanceof ProteinParticipantTag ) { uniprotID = ( (ProteinParticipantTag) o ).getProteinInteractor().getPrimaryXref().getId();
public static void check( final ProteinParticipantTag proteinParticipant, final UpdateProteinsI proteinFactory, final BioSourceFactory bioSourceFactory ) { final String role = proteinParticipant.getRole(); RoleChecker.check( role ); final ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor(); ProteinInteractorChecker.check( proteinInteractor, proteinFactory, bioSourceFactory ); final Collection features = proteinParticipant.getFeatures(); for ( Iterator iterator = features.iterator(); iterator.hasNext(); ) { FeatureTag feature = (FeatureTag) iterator.next(); FeatureChecker.ckeck( feature ); } // check feature clustering (specific to PSI version 1) try { proteinParticipant.getClusteredFeatures(); } catch ( IllegalArgumentException iae ) { MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while checking if the feature were clusterizable: " + iae.getMessage() ) ); } // TODO check isOverExpressed // TODO check isTaggedProtein: as we have to create a Feature having CvFeatureType(tagged-protein) with undetermined range } }
public static void check( final ProteinParticipantTag proteinParticipant, final UpdateProteinsI proteinFactory, final BioSourceFactory bioSourceFactory ) { final String role = proteinParticipant.getRole(); RoleChecker.check( role ); final ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor(); ProteinInteractorChecker.check( proteinInteractor, proteinFactory, bioSourceFactory ); final Collection features = proteinParticipant.getFeatures(); for ( Iterator iterator = features.iterator(); iterator.hasNext(); ) { FeatureTag feature = (FeatureTag) iterator.next(); FeatureChecker.ckeck( feature ); } // check feature clustering (specific to PSI version 1) try { proteinParticipant.getClusteredFeatures(); } catch ( IllegalArgumentException iae ) { MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while checking if the feature were clusterizable: " + iae.getMessage() ) ); } // TODO check isOverExpressed // TODO check isTaggedProtein: as we have to create a Feature having CvFeatureType(tagged-protein) with undetermined range } }
public static void check( final ProteinParticipantTag proteinParticipant, final UpdateProteinsI proteinFactory, final BioSourceFactory bioSourceFactory ) { final String role = proteinParticipant.getRole(); RoleChecker.check( role ); final ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor(); ProteinInteractorChecker.check( proteinInteractor, proteinFactory, bioSourceFactory ); final Collection features = proteinParticipant.getFeatures(); for ( Iterator iterator = features.iterator(); iterator.hasNext(); ) { FeatureTag feature = (FeatureTag) iterator.next(); FeatureChecker.ckeck( feature ); } // check feature clustering (specific to PSI version 1) try { proteinParticipant.getClusteredFeatures(); } catch ( IllegalArgumentException iae ) { MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while checking if the feature were clusterizable: " + iae.getMessage() ) ); } // TODO check isOverExpressed // TODO check isTaggedProtein: as we have to create a Feature having CvFeatureType(tagged-protein) with undetermined range } }
ProteinParticipantTag psiComponent = (ProteinParticipantTag) iterator2.next(); sb.append( NEW_LINE ).append( '[' ); sb.append( psiComponent.getProteinInteractor().getPrimaryXref().getId() ); sb.append( ", " ); sb.append( psiComponent.getRole() );
ProteinParticipantTag psiComponent = (ProteinParticipantTag) iterator2.next(); sb.append( NEW_LINE ).append( '[' ); sb.append( psiComponent.getProteinInteractor().getPrimaryXref().getId() ); sb.append( ", " ); sb.append( psiComponent.getRole() );
ProteinParticipantTag psiComponent = (ProteinParticipantTag) iterator2.next(); sb.append( NEW_LINE ).append( '[' ); sb.append( psiComponent.getProteinInteractor().getPrimaryXref().getId() ); sb.append( ", " ); sb.append( psiComponent.getRole() );
ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor(); String uniprotID = null; String taxid = null;
ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor(); String uniprotID = null; String taxid = null;
ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor(); String uniprotID = null; String taxid = null;
/** * 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 ); } }
public static void persist( final ProteinParticipantTag proteinParticipant, final Interaction interaction ) throws IntactException { ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor();
public static void persist( final ProteinParticipantTag proteinParticipant, final Interaction interaction ) throws IntactException { ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor();
public static void persist( final ProteinParticipantTag proteinParticipant, final Interaction interaction ) throws IntactException { ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor();