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 } }
String id = getFeatureId( feature, FeatureTag.FEATURE_CLUSTER_ID_XREF );
public static void persist( final ProteinParticipantTag proteinParticipant, final Interaction interaction ) throws IntactException { ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor(); final String db = proteinInteractor.getPrimaryXref().getDb(); final ProteinHolder proteinHolder = ProteinInteractorChecker.getProtein( proteinId, db, bioSource ); final CvComponentRole role = RoleChecker.getCvComponentRole( proteinParticipant.getRole() ); ExpressedInTag expressedIn = proteinParticipant.getExpressedIn(); if ( null != expressedIn ) { BioSource bs = ExpressedInChecker.getBioSource( expressedIn.getBioSourceShortlabel() ); Collection features = proteinParticipant.getFeatures(); for ( Iterator iterator = features.iterator(); iterator.hasNext(); ) { FeatureTag featureTag = (FeatureTag) iterator.next();
final CvComponentRole psiRole = RoleChecker.getCvComponentRole( psiComponent.getRole() ); ProteinParticipantTag psiComponent = (ProteinParticipantTag) iterator2.next(); sb.append( NEW_LINE ).append( '[' ); sb.append( psiComponent.getProteinInteractor().getPrimaryXref().getId() ); sb.append( ", " ); sb.append( psiComponent.getRole() ); if ( psiComponent.hasFeature() ) { sb.append( ", Feature[" ); for ( Iterator iterator3 = psiComponent.getFeatures().iterator(); iterator3.hasNext(); )
ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor(); String uniprotID = null; String taxid = null; ExpressedInTag expressedIn = proteinParticipant.getExpressedIn(); if ( null != expressedIn ) { ExpressedInChecker.check( expressedIn );
if ( psiComponent.hasFeature() && bindingDomains.isEmpty() == false ) { Map featureMap = psiComponent.getClusteredFeatures(); if ( false == psiComponent.hasFeature() && bindingDomains.size() == 0 ) {
Object o = (Object) iterator.next(); if ( o instanceof ProteinParticipantTag ) { uniprotID = ( (ProteinParticipantTag) o ).getProteinInteractor().getPrimaryXref().getId();
for ( Iterator iterator = proteins.iterator(); iterator.hasNext(); ) { ProteinParticipantTag proteinParticipant = (ProteinParticipantTag) iterator.next(); final String role = proteinParticipant.getRole(); final ProteinHolder proteinHolder = getProtein( proteinParticipant );
participants.add( new ProteinParticipantTag( interactor, role, expressedIn,
public static void persist( final ProteinParticipantTag proteinParticipant, final Interaction interaction ) throws IntactException { ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor(); final String db = proteinInteractor.getPrimaryXref().getDb(); final ProteinHolder proteinHolder = ProteinInteractorChecker.getProtein( proteinId, db, bioSource ); final CvComponentRole role = RoleChecker.getCvComponentRole( proteinParticipant.getRole() ); ExpressedInTag expressedIn = proteinParticipant.getExpressedIn(); if ( null != expressedIn ) { BioSource bs = ExpressedInChecker.getBioSource( expressedIn.getBioSourceShortlabel() ); Collection features = proteinParticipant.getFeatures(); for ( Iterator iterator = features.iterator(); iterator.hasNext(); ) { FeatureTag featureTag = (FeatureTag) iterator.next();
final CvComponentRole psiRole = RoleChecker.getCvComponentRole( psiComponent.getRole() ); ProteinParticipantTag psiComponent = (ProteinParticipantTag) iterator2.next(); sb.append( NEW_LINE ).append( '[' ); sb.append( psiComponent.getProteinInteractor().getPrimaryXref().getId() ); sb.append( ", " ); sb.append( psiComponent.getRole() ); if ( psiComponent.hasFeature() ) { sb.append( ", Feature[" ); for ( Iterator iterator3 = psiComponent.getFeatures().iterator(); iterator3.hasNext(); )
ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor(); String uniprotID = null; String taxid = null; ExpressedInTag expressedIn = proteinParticipant.getExpressedIn(); if ( null != expressedIn ) { ExpressedInChecker.check( expressedIn );
if ( psiComponent.hasFeature() && bindingDomains.isEmpty() == false ) { Map featureMap = psiComponent.getClusteredFeatures(); if ( false == psiComponent.hasFeature() && bindingDomains.size() == 0 ) {
Object o = (Object) iterator.next(); if ( o instanceof ProteinParticipantTag ) { uniprotID = ( (ProteinParticipantTag) o ).getProteinInteractor().getPrimaryXref().getId();
for ( Iterator iterator = proteins.iterator(); iterator.hasNext(); ) { ProteinParticipantTag proteinParticipant = (ProteinParticipantTag) iterator.next(); final String role = proteinParticipant.getRole(); final ProteinHolder proteinHolder = getProtein( proteinParticipant );
participants.add( new ProteinParticipantTag( interactor, role, expressedIn,
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 persist( final ProteinParticipantTag proteinParticipant, final Interaction interaction ) throws IntactException { ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor(); 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(); ExpressedInTag expressedIn = proteinParticipant.getExpressedIn(); if ( null != expressedIn ) { BioSource bs = ExpressedInChecker.getBioSource( expressedIn.getBioSourceShortlabel() ); Collection features = proteinParticipant.getFeatures(); for ( Iterator iterator = features.iterator(); iterator.hasNext(); ) { FeatureTag featureTag = (FeatureTag) iterator.next();
final CvExperimentalRole psiRole = RoleChecker.getCvExperimentalRole( psiComponent.getRole() ); ProteinParticipantTag psiComponent = (ProteinParticipantTag) iterator2.next(); sb.append( NEW_LINE ).append( '[' ); sb.append( psiComponent.getProteinInteractor().getPrimaryXref().getId() ); sb.append( ", " ); sb.append( psiComponent.getRole() ); if ( psiComponent.hasFeature() ) { sb.append( ", Feature[" ); for ( Iterator iterator3 = psiComponent.getFeatures().iterator(); iterator3.hasNext(); )
ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor(); String uniprotID = null; String taxid = null; ExpressedInTag expressedIn = proteinParticipant.getExpressedIn(); if ( null != expressedIn ) { ExpressedInChecker.check( expressedIn );