How to use

createConceptName

method

in

net.sourceforge.ondex.core.ONDEXConcept

public ONDEXConcept lookupExperiment(String id) {
  Holder h = lookupConcept(experimentIndex, experiment, id);
  ONDEXConcept c = h.concept;
  if (h.isNew)
    c.createConceptName(id, true);
  return c;
}

public ONDEXConcept lookupHormone(String id) {
  Holder h = lookupConcept(hormoneIndex, hormone, id);
  ONDEXConcept c = h.concept;
  if (h.isNew)
    c.createConceptName(id, true);
  return c;
}

public ONDEXConcept lookupMutatant(String id) {
  Holder h = lookupConcept(mutatnIndex, mutant, id);
  ONDEXConcept c = h.concept;
  if (h.isNew)
    c.createConceptName(id, true);
  return c;
}

public ONDEXConcept lookupTreatment(String id, String hormone) {
  String trueId = treatmentCode.get(id);
  Holder h = lookupConcept(treatmentIndex, treatment, trueId + " - " + hormone);
  ONDEXConcept c = h.concept;
  if (h.isNew)
    c.createConceptName(trueId, true);
  return c;
}

public ONDEXConcept lookupProtein(String id, String name) {
  String id1 = id.toUpperCase();
  Holder h = lookupConcept(proteinIndex, protein, id1);
  ONDEXConcept c = h.concept;
  if (h.isNew) {
    if (c.getConceptNames().size() == 0 && name != null && name.length() != 0) {
      c.createConceptName(name, true);
    }
  }
  return c;
}

private ONDEXConcept createConcept(String nodelabel, String nodeId) {
  ONDEXConcept concept = graph.getFactory().createConcept(nodeId,
      dataSource, cc, et);
  concept.createConceptName(nodelabel, true);
  nodeID2Concept.put(nodeId, concept);
  return concept;
}

public static void createContextId(ONDEXGraph graph, String conceptClass, String prefix) throws Exception {
  ConceptClass cc = graph.getMetaData().getConceptClass(conceptClass);
  if (cc == null) {
    throw new Exception("Incorrect concept class specified: " + conceptClass);
  }
  Integer i = 0;
  for (ONDEXConcept c : graph.getConceptsOfConceptClass(cc)) {
    c.createConceptName(prefix + "_" + i.toString(), true);
    i++;
  }
}
/*

public ONDEXConcept lookupPhenotype(String... ids) {
  ArrayKey<String> key = new ArrayKey<String>(ids);
  Holder h = lookupConcept(phenotypeIndex, phenotype, key);
  ONDEXConcept c = h.concept;
  if (h.isNew)
    c.createConceptName(ids[0], true);
  return c;
}

private ONDEXConcept createGene(String geneid,
                String[] additionalIdsFrom,
                String conceptName) {
  ONDEXConcept gene = graph.getFactory()
      .createConcept(geneid, dataSource, cc_gene, eviType);
  createAccessions(additionalIdsFrom, gene);
  if (conceptName != null && !conceptName.equalsIgnoreCase("na")) {
    gene.createConceptName(conceptName.trim(), true);
  }
  gene.createAttribute(taxidAn, String.valueOf(3702), false);
  return gene;
}

private ONDEXConcept createProtein(
    String proteinid,
    String[] additionalIdsFrom,
    String conceptName
) {
  ONDEXConcept tf_prot = graph.getFactory()
      .createConcept(proteinid, dataSource, cc_protein, eviType);
  createAccessions(additionalIdsFrom, tf_prot);
  if (conceptName != null && !conceptName.equalsIgnoreCase("na")) {
    tf_prot.createConceptName(conceptName.trim(), true);
  }
  tf_prot.createAttribute(taxidAn, String.valueOf(3702), false);
  return tf_prot;
}

private ONDEXConcept createTranscriptionFactor(
    String tfid,
    String[] additionalIdsFrom,
    String conceptName
) {
  ONDEXConcept tf = graph.getFactory().createConcept(tfid, dataSource, cc_tf, eviType);
  createAccessions(additionalIdsFrom, tf);
  if (conceptName != null && !conceptName.equalsIgnoreCase("na")) {
    tf.createConceptName(conceptName.trim(), true);
  }
  tf.createAttribute(taxidAn, String.valueOf(3702), false);
  return tf;
}

@Override
public void parse(File file) throws IOException {
  pheno0 = graph.getFactory().createConcept("Phenotype", ahd, phenotype, evidence);
  pheno0.createConceptName("Phenotype", true);
  super.parse(file);
}

/**
 * Copies all names from old concept to new concept.
 * 
 * @param oldC
 *            old ONDEXConcept
 * @param newC
 *            new ONDEXConcept
 */
private void copyNames(ONDEXConcept oldC, ONDEXConcept newC) {
  // iterate over all old names
  for (ConceptName name : oldC.getConceptNames()) {
    // clone old name on new concept
    newC.createConceptName(name.getName(), name.isPreferred());
  }
}

  public void createTag(String conceptClass, String name) {
    ONDEXConcept c = graph.getFactory().createConcept(name, createDataSource(graph, "UC"), createCC(graph, conceptClass), createEvidence(graph, "M"));
    c.createConceptName(name, true);
    this.addTag(c);
  }
}

public static void createContext(OVTK2PropertiesAggregator viewer, String name) {
  ONDEXGraph graph = viewer.getONDEXJUNGGraph();
  ONDEXConcept context = graph.getFactory().createConcept(name, createDataSource(graph, "unknown"), createCC(graph, "Thing"), createEvidence(graph, "manual"));
  context.createConceptName(name, true);
  for (ONDEXConcept c : graph.getConcepts()) {
    c.addTag(context);
  }
}

public int getOrCreateGeneID(String geneId) {
  if (poplarReg.containsGene(geneId)) {
    return poplarReg.getGene(geneId);
  } else {
    ONDEXConcept gene = og.getFactory().createConcept(geneId, dataSourcePHYTOZOME, ccGene, etIMPD);
    gene.createConceptAccession(geneId, dataSourcePHYTOZOME, false);
    gene.createConceptName(geneId, false);
    Integer ondexGeneId = gene.getId();
    gene.createAttribute(anTaxID, Parser.POPLAR_TAX_ID, false);
    poplarReg.addGene(geneId, ondexGeneId);
    return ondexGeneId;
  }
}

@Override
public void nodeToConcept(AbstractNode node) {
  Reaction reaction = (Reaction) node;
  ONDEXConcept concept = graph.getFactory().createConcept(
      reaction.getUniqueId(), dataSourceAraC, ccReaction, etIMPD);
  if (reaction.getBalancedState() != null)
    concept.setAnnotation(reaction.getBalancedState());
  concept.createConceptName(constructFormula(reaction), false);
  if (reaction.getDeltaGo() != null) {
    concept.createAttribute(deltaGo, reaction.getDeltaGo(), false);
  }
  reaction.setConcept(concept);
}

@Override
public void nodeToConcept(AbstractNode node) {
  Reaction reaction = (Reaction) node;
  ONDEXConcept concept = graph.getFactory().createConcept(
      reaction.getUniqueId(), dataSourceMetaC, ccReaction, etIMPD);
  if (reaction.getBalancedState() != null)
    concept.setAnnotation(reaction.getBalancedState());
  concept.createConceptName(constructFormula(reaction), false);
  if (reaction.getDeltaGo() != null) {
    concept.createAttribute(deltaGo, reaction.getDeltaGo(), false);
  }
  reaction.setConcept(concept);
}

@Override
public void nodeToConcept(AbstractNode node) {
  Reaction reaction = (Reaction) node;
  ONDEXConcept concept = graph.getFactory().createConcept(
      reaction.getUniqueId(), dataSourceBioC, ccReaction, etIMPD);
  if (reaction.getBalancedState() != null)
    concept.setAnnotation(reaction.getBalancedState());
  concept.createConceptName(constructFormula(reaction), false);
  if (reaction.getDeltaGo() != null) {
    concept.createAttribute(deltaGo, reaction.getDeltaGo(), false);
  }
  reaction.setConcept(concept);
}

@Override
public void start() throws Exception {
  String conceptClass = (String) args.getUniqueValue(CC);
  String name = (String) args.getUniqueValue(NAME);
  Set<ONDEXConcept> cs = graph.getConcepts();
  Set<ONDEXRelation> rs = graph.getRelations();
  ONDEXConcept c = graph.getFactory().createConcept(name, createDataSource(graph, "UC"), createCC(graph, conceptClass), createEvidence(graph, "M"));
  c.createConceptName(name, true);
  for (ONDEXConcept co : cs) {
    co.addTag(c);
  }
  for (ONDEXRelation re : rs) {
    re.addTag(c);
  }
}