public String getUniprotkb() { return this.uniprotkb != null ? this.uniprotkb.getId() : null; }
public String getRefseq() { return this.refseq != null ? this.refseq.getId() : null; }
public String getMIIdentifier() { return this.miIdentifier != null ? this.miIdentifier.getId() : null; }
public String getRefseq() { return this.refseq != null ? this.refseq.getId() : null; }
public String getImexId() { return this.imexId != null ? this.imexId.getId() : null; }
public String getChebi() { return chebi != null ? chebi.getId() : null; }
public String getEnsembl() { return this.ensembl != null ? this.ensembl.getId() : null; }
public String getDoi() { return this.doi != null ? this.doi.getId() : null; }
public String getPARIdentifier() { return this.parIdentifier != null ? this.parIdentifier.getId() : null; }
public String getEntrezGeneId() { return this.entrezGeneId != null ? this.entrezGeneId.getId() : null; }
public String getPubmedId() { return this.pubmedId != null ? this.pubmedId.getId() : null; }
public String getInterpro() { return this.interpro != null ? this.interpro.getId() : null; }
public String getMODIdentifier() { return this.modIdentifier != null ? this.modIdentifier.getId() : null; }
public String getEnsemblGenome() { return this.ensemblGenome != null ? this.ensemblGenome.getId() : null; }
@Override public String toString() { return imexId != null ? imexId.getId() : super.toString(); }
@Override public void onImexIdAssigned(Publication intactPublication, String imex) { String pubId = intactPublication.getPubmedId() != null ? intactPublication.getPubmedId() : intactPublication.getDoi(); if (pubId == null && !intactPublication.getIdentifiers().isEmpty()){ Xref id = intactPublication.getXrefs().iterator().next(); pubId = id.getId(); } NewAssignedImexEvent evt = new NewAssignedImexEvent(this, pubId, imex, null, null); getImexCentralManager().fireOnNewImexAssigned(evt); }
@Override public void onMissingImexId(Publication intactPublication) { String pubId = intactPublication.getPubmedId() != null ? intactPublication.getPubmedId() : intactPublication.getDoi(); if (pubId == null && !intactPublication.getIdentifiers().isEmpty()){ Xref id = intactPublication.getXrefs().iterator().next(); pubId = id.getId(); } ImexErrorEvent errorEvt = new ImexErrorEvent(this, ImexErrorType.no_IMEX_id, pubId, null, null, null, "Publication " + ((IntactPublication)intactPublication).getAc() + " does not have a valid IMEx id and is ignored."); imexCentralManager.fireOnImexError(errorEvt); // do not update experiments and interactions getImexCentralManager().setEnableExperimentsAndInteractionsUpdate(false); }
@Override public void onImexIdConflicts(Publication intactPublication, Collection<Xref> conflictingXrefs) { String pubId = intactPublication.getPubmedId() != null ? intactPublication.getPubmedId() : intactPublication.getDoi(); if (pubId == null && !intactPublication.getIdentifiers().isEmpty()){ Xref id = intactPublication.getXrefs().iterator().next(); pubId = id.getId(); } ImexErrorEvent errorEvt = new ImexErrorEvent(this, ImexErrorType.publication_imex_conflict, pubId, null, null, null, "Publication " + pubId + " cannot be updated because of IMEx identifier conflicts."); getImexCentralManager().fireOnImexError(errorEvt); // do not update experiments and interactions getImexCentralManager().setEnableExperimentsAndInteractionsUpdate(false); }
@Override public void onImexIdNotRecognized(Publication intactPublication, String imex) { String pubId = intactPublication.getPubmedId() != null ? intactPublication.getPubmedId() : intactPublication.getDoi(); if (pubId == null && !intactPublication.getIdentifiers().isEmpty()){ Xref id = intactPublication.getXrefs().iterator().next(); pubId = id.getId(); } ImexErrorEvent errorEvt = new ImexErrorEvent(this, ImexErrorType.imex_not_recognized, pubId, imex, null, null, "Publication " + ((IntactPublication)intactPublication).getAc() + " is not matching any record in IMEx central with id " + imex); getImexCentralManager().fireOnImexError(errorEvt); // do not update experiments and interactions getImexCentralManager().setEnableExperimentsAndInteractionsUpdate(false); }
public void write(Xref object) throws IOException { MIJsonUtils.writeStartObject(writer); MIJsonUtils.writeProperty("db", JSONValue.escape(object.getDatabase().getShortName()), writer); MIJsonUtils.writeSeparator(writer); MIJsonUtils.writeProperty("id", JSONValue.escape(object.getId()), writer); MIJsonUtils.writeEndObject(writer); } }