/** * 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); } } } }
Polymer p = (Polymer) clone; p.setSequence(((Polymer) interactor).getSequence()); p.setCrc64(((Polymer) interactor).getCrc64());
Polymer p = (Polymer) clone; p.setSequence(((Polymer) interactor).getSequence()); p.setCrc64(((Polymer) interactor).getCrc64());