/** * TODO: base this methods on the interactor equals (except AC check) */ @Override protected BehaviourType syncedAndCandidateAreEqual(T synced, T candidate) { if (synced == null) return BehaviourType.NEW; if (synced.getXrefs().size() != candidate.getXrefs().size()) { return BehaviourType.UPDATE; } if (synced.getAliases().size() != candidate.getAliases().size()) { return BehaviourType.UPDATE; } return BehaviourType.IGNORE; }
@Override protected boolean update(T candidateObject, T objectToUpdate) throws PersisterException { Collection<InteractorXref> objToUpdateXrefs = objectToUpdate.getXrefs(); for (InteractorXref xref : candidateObject.getXrefs()) { if (!objToUpdateXrefs.contains(xref)) { objectToUpdate.addXref(xref); } } for (InteractorAlias alias : candidateObject.getAliases()) { objectToUpdate.addAlias(alias); } super.updateCommonAttributes(candidateObject, objectToUpdate); return true; } }
for (Alias alias : protein.getAliases()) { CvAliasType aliasType = alias.getCvAliasType(); if (aliasType != null) {
for (Alias alias : protein.getAliases()) { CvAliasType aliasType = alias.getCvAliasType(); if (aliasType != null) {
for ( Alias alias : protein.getAliases()) { CvAliasType aliasType = alias.getCvAliasType(); CvObjectXref aliasTypeIdentityXref = CvObjectUtils.getPsiMiIdentityXref(aliasType);
/** * Enrich the mitab interactor following data best practices for nucleic acids * @param interactor * @param mitabInteractor * @return the standard InchiKey for the small molecule. Can be null if no standard inchi key available */ public void enrichInteractorFromIntact(uk.ac.ebi.intact.model.Interactor interactor, Interactor mitabInteractor){ if (interactor != null && mitabInteractor != null){ Collection<InteractorXref> interactorXrefs = interactor.getXrefs(); Collection<InteractorAlias> aliases = interactor.getAliases(); // xrefs boolean hasFoundIdentity = processXrefs(mitabInteractor, interactorXrefs); // ac and display long processAccessionAndDisplay(interactor, mitabInteractor, hasFoundIdentity); // convert aliases if (!aliases.isEmpty()){ processAliases(mitabInteractor, aliases); } // uses crc64 for checksum if (interactor instanceof Polymer){ Polymer polymer = (Polymer) interactor; if (polymer.getCrc64() != null){ Checksum checksum = new ChecksumImpl(InteractorConverter.CRC64, polymer.getCrc64()); mitabInteractor.getChecksums().add(checksum); } } } }
/** * Enrich the mitab interactor following data best practices for nucleic acids * @param gene * @param mitabInteractor * @return the standard InchiKey for the small molecule. Can be null if no standard inchi key available */ public void enrichGeneFromIntact(uk.ac.ebi.intact.model.Interactor gene, Interactor mitabInteractor){ hasFoundDisplayShort = false; if (gene != null && mitabInteractor != null){ Collection<InteractorXref> interactorXrefs = gene.getXrefs(); Collection<InteractorAlias> aliases = gene.getAliases(); // xrefs boolean hasFoundENSEMBLIdentity = processXrefs(mitabInteractor, interactorXrefs); // convert aliases if (!aliases.isEmpty()){ processAliases(mitabInteractor, aliases); } // ac and display long processAccessionAndDisplay(gene, mitabInteractor, hasFoundENSEMBLIdentity); // uses crc64 for checksum if (gene instanceof Polymer){ Polymer polymer = (Polymer) gene; if (polymer.getCrc64() != null){ Checksum checksum = new ChecksumImpl(InteractorConverter.CRC64, polymer.getCrc64()); mitabInteractor.getChecksums().add(checksum); } } } }
for ( Alias alias : interactor.getAliases() ) { String aliasName = escapeXml( alias.getName() ); writeField( out, alias.getCvAliasType().getShortLabel(), aliasName, iii );
protected void indexInteractorNames(Interactor interactor, SolrInputDocument solrDocument){ // shortname solrDocument.addField ( ComplexFieldNames.INTERACTOR_ALIAS, interactor.getShortLabel ( ) ) ; // fullname if (interactor.getFullName() != null){ solrDocument.addField ( ComplexFieldNames.INTERACTOR_ALIAS, interactor.getFullName ( ) ) ; } // aliases for ( Alias alias : interactor.getAliases ( ) ) { if (alias.getName() != null){ if (alias.getCvAliasType() != null){ CvAliasType type = alias.getCvAliasType(); solrDocument.addField ( ComplexFieldNames.INTERACTOR_ALIAS, type.getShortLabel() ) ; solrDocument.addField ( ComplexFieldNames.INTERACTOR_ALIAS, alias.getName() ) ; solrDocument.addField ( ComplexFieldNames.INTERACTOR_ALIAS, type.getShortLabel()+":"+alias.getName()) ; } else{ solrDocument.addField ( ComplexFieldNames.INTERACTOR_ALIAS, alias.getName()); } } } }