How to use

getId

method

in

psidev.psi.mi.jami.model.Xref

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);
  }
}