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 ); } }
CvDatabase uniprot = XrefChecker.getCvDatabase( CvDatabase.UNIPROT ); CvXrefQualifier identity = ControlledVocabularyRepository.getIdentityQualifier();
XrefChecker.check( primary ); XrefChecker.check( secondaryRef ); if( XrefChecker.getCvDatabase( primary.getDb() ) != null ) { XrefChecker.check( uniprotDef );
XrefChecker.check( primary ); XrefChecker.check( secondaryRef ); if( XrefChecker.getCvDatabase( primary.getDb() ) != null ) { XrefChecker.check( uniprotDef );
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 ); } }
for ( Iterator iterator1 = xrefs.iterator(); iterator1.hasNext(); ) { final XrefTag xrefTag = (XrefTag) iterator1.next(); final CvDatabase cvDatabase = XrefChecker.getCvDatabase( xrefTag.getDb() ); if ( cvDatabase != null ) { CvXrefQualifier cvXrefQualifier = null;
XrefChecker.check( primary ); XrefChecker.check( secondaryRef ); if( XrefChecker.getCvDatabase( primary.getDb() ) != null ) { XrefChecker.check( uniprotDef );
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 ); } }
for ( Iterator iterator1 = xrefs.iterator(); iterator1.hasNext(); ) { final XrefTag xrefTag = (XrefTag) iterator1.next(); final CvDatabase cvDatabase = XrefChecker.getCvDatabase( xrefTag.getDb() ); if ( cvDatabase != null ) { CvXrefQualifier cvXrefQualifier = null;
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 );
for ( Iterator iterator1 = xrefs.iterator(); iterator1.hasNext(); ) { final XrefTag xrefTag = (XrefTag) iterator1.next(); final CvDatabase cvDatabase = XrefChecker.getCvDatabase( xrefTag.getDb() ); if ( cvDatabase != null ) { CvXrefQualifier cvXrefQualifier = null;
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 );
private static void createXref( Protein protein, XrefTag xrefTag, boolean identity ) throws IntactException { CvXrefQualifier qualifier = null; if ( identity ) { qualifier = ControlledVocabularyRepository.getIdentityQualifier(); } CvDatabase database = XrefChecker.getCvDatabase( xrefTag.getDb() ); if ( database == null ) { // failed to find the database, skip the Xref creation } else { InteractorXref xref = new InteractorXref( IntactContext.getCurrentInstance().getInstitution(), database, xrefTag.getId(), xrefTag.getSecondary(), xrefTag.getVersion(), qualifier ); protein.addXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( 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 );
private static void createXref( Protein protein, XrefTag xrefTag, boolean identity ) throws IntactException { CvXrefQualifier qualifier = null; if ( identity ) { qualifier = ControlledVocabularyRepository.getIdentityQualifier(); } CvDatabase database = XrefChecker.getCvDatabase( xrefTag.getDb() ); if ( database == null ) { // failed to find the database, skip the Xref creation } else { InteractorXref xref = new InteractorXref( IntactContext.getCurrentInstance().getInstitution(), database, xrefTag.getId(), xrefTag.getSecondary(), xrefTag.getVersion(), qualifier ); protein.addXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref ); } }
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 createXref( Protein protein, XrefTag xrefTag, boolean identity ) throws IntactException { CvXrefQualifier qualifier = null; if ( identity ) { qualifier = ControlledVocabularyRepository.getIdentityQualifier(); } CvDatabase database = XrefChecker.getCvDatabase( xrefTag.getDb() ); if ( database == null ) { // failed to find the database, skip the Xref creation } else { InteractorXref xref = new InteractorXref( IntactContext.getCurrentInstance().getInstitution(), database, xrefTag.getId(), xrefTag.getSecondary(), xrefTag.getVersion(), qualifier ); protein.addXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( 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 ); } } }
XrefChecker.getCvDatabase( bibRef.getDb() ), bibRef.getId(), bibRef.getSecondary(), XrefTag xrefTag = (XrefTag) iterator.next(); ExperimentXref seeAlsoXref = new ExperimentXref( institution, XrefChecker.getCvDatabase( xrefTag.getDb() ), xrefTag.getId(), xrefTag.getSecondary(), XrefChecker.getCvDatabase( xrefTag.getDb() ), xrefTag.getId(), xrefTag.getSecondary(),
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 ); } } }