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ONDEXConcept.createConceptName
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How to use
createConceptName
method
in
net.sourceforge.ondex.core.ONDEXConcept

Best Java code snippets using net.sourceforge.ondex.core.ONDEXConcept.createConceptName (Showing top 20 results out of 315)

origin: net.sourceforge.ondex.modules/arabidopsis

public ONDEXConcept lookupExperiment(String id) {
  Holder h = lookupConcept(experimentIndex, experiment, id);
  ONDEXConcept c = h.concept;
  if (h.isNew)
    c.createConceptName(id, true);
  return c;
}
origin: net.sourceforge.ondex.modules/arabidopsis

public ONDEXConcept lookupHormone(String id) {
  Holder h = lookupConcept(hormoneIndex, hormone, id);
  ONDEXConcept c = h.concept;
  if (h.isNew)
    c.createConceptName(id, true);
  return c;
}
origin: net.sourceforge.ondex.modules/arabidopsis

public ONDEXConcept lookupMutatant(String id) {
  Holder h = lookupConcept(mutatnIndex, mutant, id);
  ONDEXConcept c = h.concept;
  if (h.isNew)
    c.createConceptName(id, true);
  return c;
}
origin: net.sourceforge.ondex.modules/arabidopsis

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;
}
origin: net.sourceforge.ondex.modules/arabidopsis

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;
}
origin: net.sourceforge.ondex.modules/generic

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;
}
origin: net.sourceforge.ondex.apps/ovtk2

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++;
  }
}
/*
origin: net.sourceforge.ondex.modules/arabidopsis

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;
}
origin: net.sourceforge.ondex.modules/arabidopsis

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;
}
origin: net.sourceforge.ondex.modules/arabidopsis

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;
}
origin: net.sourceforge.ondex.modules/arabidopsis

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;
}
origin: net.sourceforge.ondex.modules/arabidopsis

@Override
public void parse(File file) throws IOException {
  pheno0 = graph.getFactory().createConcept("Phenotype", ahd, phenotype, evidence);
  pheno0.createConceptName("Phenotype", true);
  super.parse(file);
}
origin: net.sourceforge.ondex.apps/ovtk2

/**
 * 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());
  }
}
origin: net.sourceforge.ondex.core/tools

  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);
  }
}
origin: net.sourceforge.ondex.apps/ovtk2

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);
  }
}
origin: net.sourceforge.ondex.modules/poplar

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;
  }
}
origin: net.sourceforge.ondex.modules/cyc-pathwaydbs

@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);
}
origin: net.sourceforge.ondex.modules/cyc-pathwaydbs

@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);
}
origin: net.sourceforge.ondex.modules/legacy

@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);
}
origin: net.sourceforge.ondex.modules/generic

@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);
  }
}
net.sourceforge.ondex.coreONDEXConceptcreateConceptName

Javadoc

Creates a new ConceptName with the given name and the information if this name is preferred. Then adds the new ConceptName to the list of ConceptNames of this Concept.

Popular methods of ONDEXConcept

  • getId
  • createAttribute
  • createConceptAccession
    Creates a new ConceptAccession with the given accession, the information which DataSource it belongs
  • getOfType
  • getConceptAccessions
  • getElementOf
    Returns the DataSource, which this AbstractConcept belongs to.
  • getPID
    Returns the parser id of this instance of AbstractConcept.
  • getConceptNames
    Returns all ConceptNames contained in the list of ConceptNames.
  • getAttribute
  • getConceptName
    Returns a ConceptName or null if unsuccessful for a given name or null if unsuccessful.
  • getAnnotation
    Returns the annotation of this instance of AbstractConcept.
  • addTag
  • getAnnotation,
  • addTag,
  • getDescription,
  • getAttributes,
  • getTags,
  • getEvidence,
  • setAnnotation,
  • getConceptAccession,
  • setDescription

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