private void synchronizeInstitution( Institution institution, boolean synchronyzeCommonAttributes ) { if (synchronyzeCommonAttributes){ synchronizeAnnotatedObjectCommons( institution ); } }
private void synchronizeInstitution( Institution institution, boolean synchronyzeCommonAttributes ) { if (synchronyzeCommonAttributes){ synchronizeAnnotatedObjectCommons( institution ); } }
private void synchronizeCvObject( CvObject cvObject, boolean synchronizeAnnotatedAttributes ) { if (cvObject instanceof CvDagObject) { CvDagObject cvDagObject = (CvDagObject)cvObject; if (IntactCore.isInitializedAndDirty(cvDagObject.getChildren())){ Collection<CvDagObject> children = synchronizeCollection(cvDagObject.getChildren()); cvDagObject.getChildren().clear(); cvDagObject.getChildren().addAll(children); } if (IntactCore.isInitializedAndDirty(cvDagObject.getParents())){ Collection<CvDagObject> parents = synchronizeCollection(cvDagObject.getParents()); cvDagObject.getParents().clear(); cvDagObject.getParents().addAll(parents); } } if (synchronizeAnnotatedAttributes){ synchronizeAnnotatedObjectCommons( cvObject ); } }
private void synchronizeBioSource( BioSource bioSource, boolean synchronizeAnnotatedAttributes ) { bioSource.setCvCellType( synchronize( bioSource.getCvCellType() ) ); bioSource.setCvTissue( synchronize( bioSource.getCvTissue() ) ); if (synchronizeAnnotatedAttributes){ synchronizeAnnotatedObjectCommons( bioSource ); } }
private void synchronizeCvObject( CvObject cvObject, boolean synchronizeAnnotatedAttributes ) { if (cvObject instanceof CvDagObject) { CvDagObject cvDagObject = (CvDagObject)cvObject; if (IntactCore.isInitializedAndDirty(cvDagObject.getChildren())){ Collection<CvDagObject> children = synchronizeCollection(cvDagObject.getChildren()); cvDagObject.getChildren().clear(); cvDagObject.getChildren().addAll(children); } if (IntactCore.isInitializedAndDirty(cvDagObject.getParents())){ Collection<CvDagObject> parents = synchronizeCollection(cvDagObject.getParents()); cvDagObject.getParents().clear(); cvDagObject.getParents().addAll(parents); } } if (synchronizeAnnotatedAttributes){ synchronizeAnnotatedObjectCommons( cvObject ); } }
private void synchronizeBioSource( BioSource bioSource, boolean synchronizeAnnotatedAttributes ) { bioSource.setCvCellType( synchronize( bioSource.getCvCellType() ) ); bioSource.setCvTissue( synchronize( bioSource.getCvTissue() ) ); if (synchronizeAnnotatedAttributes){ synchronizeAnnotatedObjectCommons( bioSource ); } }
private void synchronizeInteractor( Interactor interactor, boolean synchronizeAnnotatedAtributes ) { if (IntactCore.isInitializedAndDirty(interactor.getActiveInstances())){ Collection<Component> activeInstances = synchronizeCollection(interactor.getActiveInstances()); interactor.getActiveInstances().clear(); interactor.getActiveInstances().addAll(activeInstances); } interactor.setBioSource( synchronize( interactor.getBioSource() ) ); interactor.setCvInteractorType( synchronize( interactor.getCvInteractorType() ) ); if (synchronizeAnnotatedAtributes){ synchronizeAnnotatedObjectCommons( interactor ); } }
private void synchronizeInteractor( Interactor interactor, boolean synchronizeAnnotatedAtributes ) { if (IntactCore.isInitializedAndDirty(interactor.getActiveInstances())){ Collection<Component> activeInstances = synchronizeCollection(interactor.getActiveInstances()); interactor.getActiveInstances().clear(); interactor.getActiveInstances().addAll(activeInstances); } interactor.setBioSource( synchronize( interactor.getBioSource() ) ); interactor.setCvInteractorType( synchronize( interactor.getCvInteractorType() ) ); if (synchronizeAnnotatedAtributes){ synchronizeAnnotatedObjectCommons( interactor ); } }
private void synchronizePublication( Publication publication, boolean synchronizeAnnotatedAttributes ) { if (IntactCore.isInitializedAndDirty(publication.getExperiments())){ Collection<Experiment> experiments = synchronizeCollection(publication.getExperiments()); publication.getExperiments().clear(); publication.getExperiments().addAll(experiments); } publication.setStatus( synchronize( publication.getStatus() ) ); publication.setCurrentOwner( synchronizeUser(publication.getCurrentOwner()) ); publication.setCurrentReviewer( synchronizeUser(publication.getCurrentReviewer()) ); final List<LifecycleEvent> events = publication.getLifecycleEvents(); if (IntactCore.isInitializedAndDirty( events )){ Collection<LifecycleEvent> synchedEvents = new ArrayList<LifecycleEvent>( events.size() ); for ( LifecycleEvent event : events ) { synchedEvents.add( synchronizeEvent(event) ); } events.clear(); events.addAll( synchedEvents ); } if (synchronizeAnnotatedAttributes){ synchronizeAnnotatedObjectCommons( publication ); } }
private void synchronizePublication( Publication publication, boolean synchronizeAnnotatedAttributes ) { if (IntactCore.isInitializedAndDirty(publication.getExperiments())){ Collection<Experiment> experiments = synchronizeCollection(publication.getExperiments()); publication.getExperiments().clear(); publication.getExperiments().addAll(experiments); } publication.setStatus( synchronize( publication.getStatus() ) ); publication.setCurrentOwner( synchronizeUser(publication.getCurrentOwner()) ); publication.setCurrentReviewer( synchronizeUser(publication.getCurrentReviewer()) ); final List<LifecycleEvent> events = publication.getLifecycleEvents(); if (IntactCore.isInitializedAndDirty( events )){ Collection<LifecycleEvent> synchedEvents = new ArrayList<LifecycleEvent>( events.size() ); for ( LifecycleEvent event : events ) { synchedEvents.add( synchronizeEvent(event) ); } events.clear(); events.addAll( synchedEvents ); } if (synchronizeAnnotatedAttributes){ synchronizeAnnotatedObjectCommons( publication ); } }
private void synchronizeFeature( Feature feature, boolean synchronizeAnnotatedAttributes ) { feature.setBoundDomain( synchronize( feature.getBoundDomain() ) ); feature.setComponent( synchronize( feature.getComponent() ) ); feature.setCvFeatureIdentification( synchronize( feature.getCvFeatureIdentification() ) ); feature.setCvFeatureType( synchronize( feature.getCvFeatureType() ) ); // cannot call setRanges in interaction because of orphan relationship limitation if (IntactCore.isInitializedAndDirty(feature.getRanges())){ Collection<Range> ranges = synchronizeRanges(feature.getRanges(), feature); feature.getRanges().clear(); feature.getRanges().addAll(ranges); } if (synchronizeAnnotatedAttributes){ synchronizeAnnotatedObjectCommons( feature ); } }
private void synchronizeExperiment( Experiment experiment, boolean synchronizeAnnotatedAttributes ) { experiment.setPublication( synchronize( experiment.getPublication() ) ); if (IntactCore.isInitializedAndDirty(experiment.getInteractions())){ Collection<Interaction> interactions = synchronizeCollection(experiment.getInteractions()); experiment.getInteractions().clear(); experiment.getInteractions().addAll(interactions); } experiment.setCvIdentification(synchronize(experiment.getCvIdentification())); experiment.setCvInteraction( synchronize( experiment.getCvInteraction() ) ); experiment.setBioSource( synchronize( experiment.getBioSource() ) ); if (synchronizeAnnotatedAttributes){ synchronizeAnnotatedObjectCommons( experiment ); } }
private void synchronizeExperiment( Experiment experiment, boolean synchronizeAnnotatedAttributes ) { experiment.setPublication( synchronize( experiment.getPublication() ) ); if (IntactCore.isInitializedAndDirty(experiment.getInteractions())){ Collection<Interaction> interactions = synchronizeCollection(experiment.getInteractions()); experiment.getInteractions().clear(); experiment.getInteractions().addAll(interactions); } experiment.setCvIdentification(synchronize(experiment.getCvIdentification())); experiment.setCvInteraction( synchronize( experiment.getCvInteraction() ) ); experiment.setBioSource( synchronize( experiment.getBioSource() ) ); if (synchronizeAnnotatedAttributes){ synchronizeAnnotatedObjectCommons( experiment ); } }
private void synchronizeInteraction( Interaction interaction, boolean synchronizeAnnotatedAttributes ) { interaction.setCvInteractionType( synchronize( interaction.getCvInteractionType() ) ); interaction.setCvInteractorType( synchronize( interaction.getCvInteractorType() ) ); if (IntactCore.isInitializedAndDirty(interaction.getComponents())){ Collection<Component> components = synchronizeCollection(interaction.getComponents()); interaction.getComponents().clear(); interaction.getComponents().addAll(components); } interaction.setBioSource( synchronize( interaction.getBioSource() ) ); if (IntactCore.isInitializedAndDirty(interaction.getExperiments())){ Collection<Experiment> experiment = synchronizeCollection(interaction.getExperiments()); interaction.getExperiments().clear(); interaction.getExperiments().addAll(experiment); } // cannot call setConfidences in interaction because of orphan relationship limitation if (IntactCore.isInitializedAndDirty(interaction.getConfidences())){ Collection<Confidence> confidences = synchronizeConfidences(interaction.getConfidences(), interaction); interaction.getConfidences().clear(); interaction.getConfidences().addAll(confidences); } // cannot call setParameters in interaction because of orphan relationship limitation if (IntactCore.isInitializedAndDirty(interaction.getParameters())){ Collection<InteractionParameter> interactionParameters = synchronizeInteractionParameters(interaction.getParameters(), interaction); interaction.getParameters().clear(); interaction.getParameters().addAll(interactionParameters); } if (synchronizeAnnotatedAttributes){ synchronizeAnnotatedObjectCommons( interaction ); } }
private void synchronizeFeature( Feature feature, boolean synchronizeAnnotatedAttributes ) { feature.setBoundDomain( synchronize( feature.getBoundDomain() ) ); feature.setComponent( synchronize( feature.getComponent() ) ); feature.setCvFeatureIdentification( synchronize( feature.getCvFeatureIdentification() ) ); feature.setCvFeatureType( synchronize( feature.getCvFeatureType() ) ); // cannot call setRanges in interaction because of orphan relationship limitation if (IntactCore.isInitializedAndDirty(feature.getRanges())){ Collection<Range> ranges = synchronizeRanges(feature.getRanges(), feature); feature.getRanges().clear(); feature.getRanges().addAll(ranges); } if (synchronizeAnnotatedAttributes){ synchronizeAnnotatedObjectCommons( feature ); } }
private void synchronizeInteraction( Interaction interaction, boolean synchronizeAnnotatedAttributes ) { interaction.setCvInteractionType( synchronize( interaction.getCvInteractionType() ) ); interaction.setCvInteractorType( synchronize( interaction.getCvInteractorType() ) ); if (IntactCore.isInitializedAndDirty(interaction.getComponents())){ Collection<Component> components = synchronizeCollection(interaction.getComponents()); interaction.getComponents().clear(); interaction.getComponents().addAll(components); } interaction.setBioSource( synchronize( interaction.getBioSource() ) ); if (IntactCore.isInitializedAndDirty(interaction.getExperiments())){ Collection<Experiment> experiment = synchronizeCollection(interaction.getExperiments()); interaction.getExperiments().clear(); interaction.getExperiments().addAll(experiment); } // cannot call setConfidences in interaction because of orphan relationship limitation if (IntactCore.isInitializedAndDirty(interaction.getConfidences())){ Collection<Confidence> confidences = synchronizeConfidences(interaction.getConfidences(), interaction); interaction.getConfidences().clear(); interaction.getConfidences().addAll(confidences); } // cannot call setParameters in interaction because of orphan relationship limitation if (IntactCore.isInitializedAndDirty(interaction.getParameters())){ Collection<InteractionParameter> interactionParameters = synchronizeInteractionParameters(interaction.getParameters(), interaction); interaction.getParameters().clear(); interaction.getParameters().addAll(interactionParameters); } if (synchronizeAnnotatedAttributes){ synchronizeAnnotatedObjectCommons( interaction ); } }