public CvContext getCvContext() { return IntactContext.getCurrentInstance().getCvContext(); }
private CvXrefQualifier getIdentity() throws IntactException { CvXrefQualifier identity = IntactContext.getCurrentInstance().getCvContext().getByMiRef( CvXrefQualifier.class, CvXrefQualifier.IDENTITY_MI_REF ); if ( identity == null ) { throw new IllegalStateException( "Could not find the qualifier(identity) in the Database. Please update your controlled vocabularies." ); } return identity; }
/** * Returns CvDatabase(newt) * * @return * * @throws IntactException */ private CvDatabase getNewt() throws IntactException { CvDatabase newt = IntactContext.getCurrentInstance().getCvContext().getByMiRef( CvDatabase.class, CvDatabase.NEWT_MI_REF ); if ( newt == null ) { throw new IllegalStateException( "Could not find newt in the Database. Please update your controlled vocabularies." ); } return newt; }
public static void check( final XrefTag xref ) { final String db = xref.getDb(); if ( !cache.keySet().contains( db ) ) { CvDatabase cvDatabase = null; try { cvDatabase = IntactContext.getCurrentInstance().getCvContext().getByLabel(CvDatabase.class, db ); if ( cvDatabase != null ) { System.out.println( "Found CvDatabase with shortlabel: " + db ); } else { MessageHolder.getInstance().addCheckerMessage( new Message( "Could not find CvDatabase " + "by shortlabel: " + db ) ); } } catch ( IntactException e ) { MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while searching " + "for CvDatabase " + "having the shortlabel: " + db ) ); e.printStackTrace(); } cache.put( db, cvDatabase ); } } }
public static void check( final XrefTag xref ) { final String db = xref.getDb(); if ( !cache.keySet().contains( db ) ) { CvDatabase cvDatabase = null; try { cvDatabase = IntactContext.getCurrentInstance().getCvContext().getByLabel(CvDatabase.class, db ); if ( cvDatabase != null ) { System.out.println( "Found CvDatabase with shortlabel: " + db ); } else { MessageHolder.getInstance().addCheckerMessage( new Message( "Could not find CvDatabase " + "by shortlabel: " + db ) ); } } catch ( IntactException e ) { MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while searching " + "for CvDatabase " + "having the shortlabel: " + db ) ); e.printStackTrace(); } cache.put( db, cvDatabase ); } } }
public static void checkCvInteractorType( ) { if ( false == interatorTypeChecked ) { // Load CvInteractorType( interaction / MI: ) cvProteinType = IntactContext.getCurrentInstance().getCvContext().getByMiRef(CvInteractorType.class, CvInteractorType.getInteractionMI()); if ( cvProteinType == null ) { MessageHolder.getInstance().addCheckerMessage( new Message( "Could not find CvInteractorType( interaction )." ) ); } interatorTypeChecked = true; } }
public static void checkCvInteractorType( ) { if ( false == interatorTypeChecked ) { // Load CvInteractorType( interaction / MI: ) cvProteinType = IntactContext.getCurrentInstance().getCvContext().getByMiRef(CvInteractorType.class, CvInteractorType.getInteractionMI()); if ( cvProteinType == null ) { MessageHolder.getInstance().addCheckerMessage( new Message( "Could not find CvInteractorType( interaction )." ) ); } interatorTypeChecked = true; } }
public static void checkCvInteractorType( ) { if ( false == interatorTypeChecked ) { // Load CvInteractorType( interaction / MI: ) cvInteractionType = IntactContext.getCurrentInstance().getCvContext().getByMiRef(CvInteractorType.class, CvInteractorType.getInteractionMI()); if ( cvInteractionType == null ) { MessageHolder.getInstance().addCheckerMessage( new Message( "Could not find CvInteractorType( interaction )." ) ); } interatorTypeChecked = true; } }
public static void checkCvInteractorType( ) { if ( false == interatorTypeChecked ) { // Load CvInteractorType( interaction / MI: ) cvInteractionType = IntactContext.getCurrentInstance().getCvContext().getByMiRef(CvInteractorType.class, CvInteractorType.getInteractionMI()); if ( cvInteractionType == null ) { MessageHolder.getInstance().addCheckerMessage( new Message( "Could not find CvInteractorType( interaction )." ) ); } interatorTypeChecked = true; } }
public static void check( final InteractionTypeTag interactionType ) { final XrefTag psiDef = interactionType.getPsiDefinition(); XrefChecker.check( psiDef ); final String id = psiDef.getId(); if ( !cache.keySet().contains( id ) ) { CvInteractionType cvInteractionType = null; try { cvInteractionType = IntactContext.getCurrentInstance().getCvContext().getByMiRef(CvInteractionType.class, id); if ( cvInteractionType == null ) { MessageHolder.getInstance().addCheckerMessage( new Message( "Could not find CvInteractionType " + "for the PSI definition: " + id ) ); } else { System.out.println( "Found InteractionType " + id + " as " + cvInteractionType.getShortLabel() ); } } catch ( IntactException e ) { MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while searching for CvInteractionType " + "having the PSI definition: " + id ) ); e.printStackTrace(); } cache.put( id, cvInteractionType ); } } }
public static void check( final ParticipantDetectionTag participantDetection ) { final XrefTag psiDef = participantDetection.getPsiDefinition(); XrefChecker.check( psiDef ); final String id = psiDef.getId(); if ( !cache.keySet().contains( id ) ) { CvIdentification cvIdentification = null; try { cvIdentification = IntactContext.getCurrentInstance().getCvContext().getByMiRef(CvIdentification.class,id); if ( cvIdentification == null ) { MessageHolder.getInstance().addCheckerMessage( new Message( "Could not find CvIdentification for the PSI definition: " + id ) ); } else { System.out.println( "Found ParticipantDetection " + id + " as " + cvIdentification.getShortLabel() ); } } catch ( IntactException e ) { MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while searching for CvInteraction " + "having the PSI definition: " + id ) ); e.printStackTrace(); } cache.put( id, cvIdentification ); } } }
public static void check( final InteractionDetectionTag interactionDetection ) { final XrefTag psiDef = interactionDetection.getPsiDefinition(); XrefChecker.check( psiDef ); final String id = psiDef.getId(); if ( !cache.keySet().contains( id ) ) { CvInteraction cvInteraction = null; try { cvInteraction = IntactContext.getCurrentInstance().getCvContext().getByMiRef(CvInteraction.class,id); if ( cvInteraction == null ) { MessageHolder.getInstance().addCheckerMessage( new Message( "Could not find CvInteraction by PSI definition: " + id ) ); } else { System.out.println( "Found CvInteraction " + id + " as " + cvInteraction.getShortLabel() ); } } catch ( IntactException e ) { MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while searching for CvInteraction " + "having the PSI definition: " + id ) ); e.printStackTrace(); } cache.put( id, cvInteraction ); } } }
public static void check( final InteractionTypeTag interactionType ) { final XrefTag psiDef = interactionType.getPsiDefinition(); XrefChecker.check( psiDef ); final String id = psiDef.getId(); if ( !cache.keySet().contains( id ) ) { CvInteractionType cvInteractionType = null; try { cvInteractionType = IntactContext.getCurrentInstance().getCvContext().getByMiRef(CvInteractionType.class, id); if ( cvInteractionType == null ) { MessageHolder.getInstance().addCheckerMessage( new Message( "Could not find CvInteractionType " + "for the PSI definition: " + id ) ); } else { System.out.println( "Found InteractionType " + id + " as " + cvInteractionType.getShortLabel() ); } } catch ( IntactException e ) { MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while searching for CvInteractionType " + "having the PSI definition: " + id ) ); e.printStackTrace(); } cache.put( id, cvInteractionType ); } } }
public static void check( final InteractionDetectionTag interactionDetection ) { final XrefTag psiDef = interactionDetection.getPsiDefinition(); XrefChecker.check( psiDef ); final String id = psiDef.getId(); if ( !cache.keySet().contains( id ) ) { CvInteraction cvInteraction = null; try { cvInteraction = IntactContext.getCurrentInstance().getCvContext().getByMiRef(CvInteraction.class,id); if ( cvInteraction == null ) { MessageHolder.getInstance().addCheckerMessage( new Message( "Could not find CvInteraction by PSI definition: " + id ) ); } else { System.out.println( "Found CvInteraction " + id + " as " + cvInteraction.getShortLabel() ); } } catch ( IntactException e ) { MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while searching for CvInteraction " + "having the PSI definition: " + id ) ); e.printStackTrace(); } cache.put( id, cvInteraction ); } } }
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 checkCvFeatureIdentification( FeatureTag feature ) { final XrefTag psiDef = feature.getFeatureDetection().getPsiDefinition(); XrefChecker.check( psiDef ); final String id = psiDef.getId(); if ( !featureIdentificationCache.keySet().contains( id ) ) { CvFeatureIdentification cvFeatureIdentification = null; try { cvFeatureIdentification = IntactContext.getCurrentInstance().getCvContext().getByMiRef(CvFeatureIdentification.class,id); if ( cvFeatureIdentification == null ) { MessageHolder.getInstance().addCheckerMessage( new Message( "Could not find CvFeatureIdentification by PSI definition: " + id ) ); } else { System.out.println( "Found CvFeatureIdentification " + id + " as " + cvFeatureIdentification.getShortLabel() ); } } catch ( IntactException e ) { MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while searching for CvFeatureIdentification " + "having the PSI definition: " + id ) ); e.printStackTrace(); } featureIdentificationCache.put( id, cvFeatureIdentification ); } } }
private static void checkCvFeatureIdentification( FeatureTag feature ) { final XrefTag psiDef = feature.getFeatureDetection().getPsiDefinition(); XrefChecker.check( psiDef ); final String id = psiDef.getId(); if ( !featureIdentificationCache.keySet().contains( id ) ) { CvFeatureIdentification cvFeatureIdentification = null; try { cvFeatureIdentification = IntactContext.getCurrentInstance().getCvContext().getByMiRef(CvFeatureIdentification.class,id); if ( cvFeatureIdentification == null ) { MessageHolder.getInstance().addCheckerMessage( new Message( "Could not find CvFeatureIdentification by PSI definition: " + id ) ); } else { System.out.println( "Found CvFeatureIdentification " + id + " as " + cvFeatureIdentification.getShortLabel() ); } } catch ( IntactException e ) { MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while searching for CvFeatureIdentification " + "having the PSI definition: " + id ) ); e.printStackTrace(); } featureIdentificationCache.put( id, cvFeatureIdentification ); } } }
private static void initialise( ) { if ( initialisationDone == false ) { CvContext cvContext = IntactContext.getCurrentInstance().getCvContext(); // load CVs by shortlabel authorConfidenceTopic = cvContext.getByMiRef(CvTopic.class, CvTopic.AUTHOR_CONFIDENCE_MI_REF); noUniprotUpdate = cvContext.getByLabel(CvTopic.class, CvTopic.NON_UNIPROT); // load CVs by MI reference primaryReferenceXrefQualifier = cvContext.getByMiRef( CvXrefQualifier.class, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF ); seeAlsoXrefQualifier = cvContext.getByMiRef( CvXrefQualifier.class, CvXrefQualifier.SEE_ALSO_MI_REF ); identityXrefQualifier = cvContext.getByMiRef( CvXrefQualifier.class, CvXrefQualifier.IDENTITY_MI_REF ); geneName = cvContext.getByMiRef(CvAliasType.class, CvAliasType.GENE_NAME_MI_REF ); initialisationDone = true; } } // init
private static void initialise( ) { if ( initialisationDone == false ) { CvContext cvContext = IntactContext.getCurrentInstance().getCvContext(); // load CVs by shortlabel authorConfidenceTopic = cvContext.getByMiRef(CvTopic.class, CvTopic.AUTHOR_CONFIDENCE_MI_REF); noUniprotUpdate = cvContext.getByLabel(CvTopic.class, CvTopic.NON_UNIPROT); // load CVs by MI reference primaryReferenceXrefQualifier = cvContext.getByMiRef( CvXrefQualifier.class, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF ); seeAlsoXrefQualifier = cvContext.getByMiRef( CvXrefQualifier.class, CvXrefQualifier.SEE_ALSO_MI_REF ); identityXrefQualifier = cvContext.getByMiRef( CvXrefQualifier.class, CvXrefQualifier.IDENTITY_MI_REF ); geneName = cvContext.getByMiRef(CvAliasType.class, CvAliasType.GENE_NAME_MI_REF ); initialisationDone = true; } } // init