public static void ckeck( FeatureTag feature ) { if ( feature.hasFeatureDetection() ) { checkCvFeatureIdentification( feature ); } checkCvTypeIdentification( feature ); for ( Iterator iterator = feature.getXrefs().iterator(); iterator.hasNext(); ) { XrefTag xref = (XrefTag) iterator.next(); XrefChecker.check( xref ); } }
CvFeatureType featureType = FeatureChecker.getCvFeatureType( typeId ); if ( featureTag.hasFeatureDetection() ) { detectionId = featureTag.getFeatureDetection().getPsiDefinition().getId(); CvFeatureIdentification featureDetection = FeatureChecker.getCvFeatureIdentification( detectionId ); feature.setCvFeatureIdentification( featureDetection );
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 } }
CvFeatureType featureType = FeatureChecker.getCvFeatureType( typeId ); if ( featureTag.hasFeatureDetection() ) { detectionId = featureTag.getFeatureDetection().getPsiDefinition().getId(); CvFeatureIdentification featureDetection = FeatureChecker.getCvFeatureIdentification( detectionId ); feature.setCvFeatureIdentification( featureDetection );
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 ckeck( FeatureTag feature ) { if ( feature.hasFeatureDetection() ) { checkCvFeatureIdentification( feature ); } checkCvTypeIdentification( feature ); for ( Iterator iterator = feature.getXrefs().iterator(); iterator.hasNext(); ) { XrefTag xref = (XrefTag) iterator.next(); XrefChecker.check( xref ); } }
CvFeatureType featureType = FeatureChecker.getCvFeatureType( typeId ); if ( featureTag.hasFeatureDetection() ) { detectionId = featureTag.getFeatureDetection().getPsiDefinition().getId(); CvFeatureIdentification featureDetection = FeatureChecker.getCvFeatureIdentification( detectionId ); feature.setCvFeatureIdentification( featureDetection );
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 ckeck( FeatureTag feature ) { if ( feature.hasFeatureDetection() ) { checkCvFeatureIdentification( feature ); } checkCvTypeIdentification( feature ); for ( Iterator iterator = feature.getXrefs().iterator(); iterator.hasNext(); ) { XrefTag xref = (XrefTag) iterator.next(); XrefChecker.check( xref ); } }