String psiMI = psiFeature.getFeatureType().getPsiDefinition().getId(); String intactMI = getPsiID( intactFeature.getCvFeatureType() );
String psiMI = psiFeature.getFeatureType().getPsiDefinition().getId(); String intactMI = getPsiID( intactFeature.getCvFeatureType() );
String psiMI = psiFeature.getFeatureType().getPsiDefinition().getId(); String intactMI = getPsiID( intactFeature.getCvFeatureType() );
sb.append( "type=" ).append( feature.getFeatureType().getPsiDefinition().getId() ); sb.append( ',' ); sb.append( "detection=" );
sb.append( "type=" ).append( feature.getFeatureType().getPsiDefinition().getId() ); sb.append( ',' ); sb.append( "detection=" );
sb.append( "type=" ).append( feature.getFeatureType().getPsiDefinition().getId() ); sb.append( ',' ); sb.append( "detection=" );
private static void checkCvTypeIdentification( FeatureTag feature ) { XrefTag psiDef = feature.getFeatureType().getPsiDefinition(); XrefChecker.check( psiDef ); final String id = psiDef.getId(); if ( !featureTypeCache.keySet().contains( id ) ) { CvFeatureType featureType = null; try { featureType = IntactContext.getCurrentInstance().getCvContext().getByMiRef(CvFeatureType.class,id); if ( featureType == null ) { MessageHolder.getInstance().addCheckerMessage( new Message( "Could not find CvFeatureType by PSI definition: " + id ) ); } else { System.out.println( "Found CvFeatureType " + id + " as " + featureType.getShortLabel() ); } } catch ( IntactException e ) { MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while searching for CvFeatureType " + "having the PSI definition: " + id ) ); e.printStackTrace(); } featureTypeCache.put( id, featureType ); } }
private static void checkCvTypeIdentification( FeatureTag feature ) { XrefTag psiDef = feature.getFeatureType().getPsiDefinition(); XrefChecker.check( psiDef ); final String id = psiDef.getId(); if ( !featureTypeCache.keySet().contains( id ) ) { CvFeatureType featureType = null; try { featureType = IntactContext.getCurrentInstance().getCvContext().getByMiRef(CvFeatureType.class,id); if ( featureType == null ) { MessageHolder.getInstance().addCheckerMessage( new Message( "Could not find CvFeatureType by PSI definition: " + id ) ); } else { System.out.println( "Found CvFeatureType " + id + " as " + featureType.getShortLabel() ); } } catch ( IntactException e ) { MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while searching for CvFeatureType " + "having the PSI definition: " + id ) ); e.printStackTrace(); } featureTypeCache.put( id, featureType ); } }
private static void checkCvTypeIdentification( FeatureTag feature ) { XrefTag psiDef = feature.getFeatureType().getPsiDefinition(); XrefChecker.check( psiDef ); final String id = psiDef.getId(); if ( !featureTypeCache.keySet().contains( id ) ) { CvFeatureType featureType = null; try { featureType = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getCvObjectDao(CvFeatureType.class).getByXref(id); if ( featureType == null ) { MessageHolder.getInstance().addCheckerMessage( new Message( "Could not find CvFeatureType by PSI definition: " + id ) ); } else { System.out.println( "Found CvFeatureType " + id + " as " + featureType.getShortLabel() ); } } catch ( IntactException e ) { MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while searching for CvFeatureType " + "having the PSI definition: " + id ) ); e.printStackTrace(); } featureTypeCache.put( id, featureType ); } }
final Protein protein ) throws IntactException { String typeId = featureTag.getFeatureType().getPsiDefinition().getId(); CvFeatureType featureType = FeatureChecker.getCvFeatureType( typeId );
final Protein protein ) throws IntactException { String typeId = featureTag.getFeatureType().getPsiDefinition().getId(); CvFeatureType featureType = FeatureChecker.getCvFeatureType( typeId );
final Protein protein ) throws IntactException { String typeId = featureTag.getFeatureType().getPsiDefinition().getId(); CvFeatureType featureType = FeatureChecker.getCvFeatureType( typeId );