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 ); } }
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 ); } }
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 ); } }
XrefChecker.check( experimentDescription.getBibRef() ); Collection additionalBibRef = experimentDescription.getAdditionalBibRef(); for ( Iterator iterator = additionalBibRef.iterator(); iterator.hasNext(); ) { XrefTag bibRef = (XrefTag) iterator.next(); XrefChecker.check( bibRef ); for ( Iterator iterator = xrefs.iterator(); iterator.hasNext(); ) { XrefTag xref = (XrefTag) iterator.next(); XrefChecker.check( xref );
XrefChecker.check( experimentDescription.getBibRef() ); Collection additionalBibRef = experimentDescription.getAdditionalBibRef(); for ( Iterator iterator = additionalBibRef.iterator(); iterator.hasNext(); ) { XrefTag bibRef = (XrefTag) iterator.next(); XrefChecker.check( bibRef ); for ( Iterator iterator = xrefs.iterator(); iterator.hasNext(); ) { XrefTag xref = (XrefTag) iterator.next(); XrefChecker.check( xref );
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 ); } } }
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 ); } } }
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 ); } } }
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 ); } } }
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 ); } } }
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().getDataContext().getDaoFactory().getCvObjectDao(CvIdentification.class).getByXref(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 ); } } }
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().getDataContext().getDaoFactory().getCvObjectDao(CvFeatureIdentification.class).getByXref(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 ); } } }
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().getDataContext().getDaoFactory().getCvObjectDao(CvInteraction.class).getByXref(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().getDataContext().getDaoFactory().getCvObjectDao(CvInteractionType.class).getByXref(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 ); } } }
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 ); } }