protected void copyBioSource( BioSource source, BioSource target ) { copyProperty(source, "taxId", target); copyProperty(source, "cvTissue", target); copyProperty(source, "cvCellType", target); }
protected void copyInstitution( Institution source, Institution target ) { copyProperty(source, "url", target); copyProperty(source, "postalAddress", target); }
protected void copyLifecycleEvent( LifecycleEvent source, LifecycleEvent target ) { copyProperty(source, "event", target); copyProperty(source, "who", target); copyProperty(source, "when", target); copyProperty(source, "publication", target); copyProperty(source, "note", target); }
protected void copyLifecycleEvent( LifecycleEvent source, LifecycleEvent target ) { copyProperty(source, "event", target); copyProperty(source, "who", target); copyProperty(source, "when", target); copyProperty(source, "publication", target); copyProperty(source, "note", target); }
protected void copyBioSource( BioSource source, BioSource target ) { copyProperty(source, "taxId", target); copyProperty(source, "cvTissue", target); copyProperty(source, "cvCellType", target); }
protected void copyInstitution( Institution source, Institution target ) { copyProperty(source, "url", target); copyProperty(source, "postalAddress", target); }
protected void copyExperiment( Experiment source, Experiment target ) { copyProperty(source, "bioSource", target); copyProperty(source, "publication", target); copyProperty(source, "cvIdentification", target); copyProperty(source, "cvInteraction", target); copyCollection( source.getInteractions(), target.getInteractions() ); }
protected void copyExperiment( Experiment source, Experiment target ) { copyProperty(source, "bioSource", target); copyProperty(source, "publication", target); copyProperty(source, "cvIdentification", target); copyProperty(source, "cvInteraction", target); copyCollection( source.getInteractions(), target.getInteractions() ); }
protected void copyPublication( Publication source, Publication target ) { copyCollection( source.getExperiments(), target.getExperiments() ); copyCollection( source.getLifecycleEvents(), target.getLifecycleEvents() ); copyProperty(source, "currentOwner", target); copyProperty(source, "currentReviewer", target); copyProperty(source, "publicationId", target); copyProperty(source, "status", target); }
protected void copyPublication( Publication source, Publication target ) { copyCollection( source.getExperiments(), target.getExperiments() ); copyCollection( source.getLifecycleEvents(), target.getLifecycleEvents() ); copyProperty(source, "currentOwner", target); copyProperty(source, "currentReviewer", target); copyProperty(source, "publicationId", target); copyProperty(source, "status", target); }
protected void copyFeature( Feature source, Feature target ) { //copyProperty(source, "component", target); copyProperty(source, "cvFeatureIdentification", target); copyProperty(source, "cvFeatureType", target); copyCollection( source.getRanges(), target.getRanges() ); }
protected void copyFeature( Feature source, Feature target ) { //copyProperty(source, "component", target); copyProperty(source, "cvFeatureIdentification", target); copyProperty(source, "cvFeatureType", target); copyCollection( source.getRanges(), target.getRanges() ); }
protected void copyInteractorCommons( Interactor source, Interactor target ) { if ( target.getBioSource() != null && source.getBioSource() == null ) { throw new PersisterException( "Operation not permitted: nullifying biosource of a " + target.getClass().getSimpleName() + " (" + target.getShortLabel() + ") - " + " current biosource is " + target.getBioSource().getShortLabel() ); } copyProperty(source, "bioSource", target); copyProperty(source, "cvInteractorType", target); }
protected void copyInteractorCommons( Interactor source, Interactor target ) { if ( target.getBioSource() != null && source.getBioSource() == null ) { throw new PersisterException( "Operation not permitted: nullifying biosource of a " + target.getClass().getSimpleName() + " (" + target.getShortLabel() + ") - " + " current biosource is " + target.getBioSource().getShortLabel() ); } copyProperty(source, "bioSource", target); copyProperty(source, "cvInteractorType", target); }
protected void copyComponent( Component source, Component target ) { copyProperty(source, "stoichiometry", target); copyProperty(source, "interaction", target); copyProperty(source, "interactor", target); copyProperty(source, "cvBiologicalRole", target); copyProperty(source, "cvExperimentalRole", target); copyProperty(source, "expressedIn", target); copyCollection( source.getBindingDomains(), target.getBindingDomains() ); for (Feature bindingDomain : target.getBindingDomains()) { bindingDomain.setComponent(target); } copyCollection( source.getExperimentalPreparations(), target.getExperimentalPreparations() ); copyCollection( source.getParticipantDetectionMethods(), target.getParticipantDetectionMethods() ); copyCollection( source.getParameters(), target.getParameters() ); }
protected void copyComponent( Component source, Component target ) { copyProperty(source, "stoichiometry", target); copyProperty(source, "interaction", target); copyProperty(source, "interactor", target); copyProperty(source, "cvBiologicalRole", target); copyProperty(source, "cvExperimentalRole", target); copyProperty(source, "expressedIn", target); copyCollection( source.getBindingDomains(), target.getBindingDomains() ); for (Feature bindingDomain : target.getBindingDomains()) { bindingDomain.setComponent(target); } copyCollection( source.getExperimentalPreparations(), target.getExperimentalPreparations() ); copyCollection( source.getParticipantDetectionMethods(), target.getParticipantDetectionMethods() ); copyCollection( source.getParameters(), target.getParameters() ); }
protected <X extends Xref, A extends Alias> void copyAnotatedObjectCommons( AnnotatedObject<X, A> source, AnnotatedObject<X, A> target ) { // if the source does not have an AC, we should not update the target shortLabel, fullName and owner // as it does not make much sense //if (source.getAc() != null) { copyProperty(source, "shortLabel", target); copyProperty(source, "fullName", target); copyProperty(source, "owner", target); //} copyXrefCollection( source.getXrefs(), target.getXrefs() ); copyAliasCollection( source.getAliases(), target.getAliases(), source, target ); copyAnnotationCollection( source.getAnnotations(), target.getAnnotations() ); }
protected <X extends Xref, A extends Alias> void copyAnotatedObjectCommons( AnnotatedObject<X, A> source, AnnotatedObject<X, A> target ) { // if the source does not have an AC, we should not update the target shortLabel, fullName and owner // as it does not make much sense //if (source.getAc() != null) { copyProperty(source, "shortLabel", target); copyProperty(source, "fullName", target); copyProperty(source, "owner", target); //} copyXrefCollection( source.getXrefs(), target.getXrefs() ); copyAliasCollection( source.getAliases(), target.getAliases(), source, target ); copyAnnotationCollection( source.getAnnotations(), target.getAnnotations() ); }
protected void copyInteraction( Interaction source, Interaction target ) { copyProperty(source, "KD", target); copyProperty(source, "crc", target); copyProperty(source, "cvInteractionType", target); copyCollection( source.getComponents(), target.getComponents() ); copyCollection( source.getExperiments(), target.getExperiments() ); copyCollection( source.getConfidences(), target.getConfidences() ); copyCollection( source.getParameters(), target.getParameters() ); copyInteractorCommons( source, target ); // we have ommited CRC on purpose }
protected void copyInteraction( Interaction source, Interaction target ) { copyProperty(source, "KD", target); copyProperty(source, "crc", target); copyProperty(source, "cvInteractionType", target); copyCollection( source.getComponents(), target.getComponents() ); copyCollection( source.getExperiments(), target.getExperiments() ); copyCollection( source.getConfidences(), target.getConfidences() ); copyCollection( source.getParameters(), target.getParameters() ); copyInteractorCommons( source, target ); // we have ommited CRC on purpose }