net.sourceforge.ondex.core.ONDEXConcept java code examples

Common ways to obtain ONDEXConcept

private void myMethod () {
     ONDEXConcept o =ONDEXRelation r;r.getToConcept()
ONDEXRelation r;r.getFromConcept()
ONDEXGraph graph;graph.getConcept(id)
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}

/**
 * Tries to get the most worthwhile identifier for the concept
 * 
 * @param c
 *            - concept
 * @return - some id (in order of decreasing preference: name, pid,
 *         description, concepts class+is)
 */
private static String getSomething(ONDEXConcept c) {
  if (c.getConceptName() != null) {
    return c.getConceptName().getName();
  }
  if (c.getPID() != null && c.getPID().equals("")) {
    return c.getPID();
  }
  if (c.getDescription() != null && c.getDescription().equals("")) {
    return c.getDescription();
  }
  return "[" + c.getOfType().getId() + " " + c.getId() + "]";
}

for (EvidenceType et : copySourceConcept.getEvidence()) {
  copyTargetConcept.addEvidenceType(et);
for (ConceptAccession acc : copySourceConcept.getConceptAccessions()) {
  copyTargetConcept.createConceptAccession(acc.getAccession(),
      acc.getElementOf(), true);
for (ConceptName name : copySourceConcept.getConceptNames()) {
  copyTargetConcept.createConceptName(name.getName(),
      name.isPreferred());
for (Attribute attribute : copySourceConcept.getAttributes()) {
  copyTargetConcept.createAttribute(attribute.getOfType(),
      attribute.getValue(), attribute.isDoIndex());
if (copySourceConcept.getAnnotation() != null)
  copyTargetConcept.setAnnotation(copySourceConcept.getAnnotation());
if (copySourceConcept.getDescription() != null)
  copyTargetConcept
      .setDescription(copySourceConcept.getDescription());
for (ONDEXConcept c : copySourceConcept.getTags())
  copyTargetConcept.addTag(c);

/**
 * Clone concept with having a new PID.
 * 
 * @param oldC
 *            old ONDEXConcept
 * @param newPID
 *            new PID to use
 * @return new ONDEXConcept
 */
public ONDEXConcept clone(ONDEXConcept oldC, String newPID) {
  // first clone concept with new PID
  ONDEXConcept newC = graph.createConcept(newPID, oldC.getAnnotation(), oldC.getDescription(), oldC.getElementOf(), oldC.getOfType(), oldC.getEvidence());
  // copies everything else
  copyEverythingElse(oldC, newC);
  return newC;
}

@Override
protected void doAction() {
  // set flagged attribute to true on all concepts
  for (ONDEXConcept c : entities) {
    if (c.getAttribute(anFlag) == null) {
      c.createAttribute(anFlag, Boolean.TRUE, false);
    } else {
      c.getAttribute(anFlag).setValue(Boolean.TRUE);
    }
  }
}

/**
 * Clone concept with having a new DataSource.
 * 
 * @param oldC
 *            old ONDEXConcept
 * @param newDataSource
 *            new DataSource to use
 * @return new ONDEXConcept
 */
public ONDEXConcept clone(ONDEXConcept oldC, DataSource newDataSource) {
  // first clone concept with new DataSource
  ONDEXConcept newC = graph.createConcept(oldC.getPID(), oldC.getAnnotation(), oldC.getDescription(), newDataSource, oldC.getOfType(), oldC.getEvidence());
  // copies everything else
  copyEverythingElse(oldC, newC);
  return newC;
}

/**
 * Copies all of the attributes from one concept to another (only if they do
 * not already exist at target)
 * 
 * @param from
 *            - concept to copy from
 * @param to
 *            - concept to copy to
 * @throws AccessDeniedException
 * @throws NullValueException
 * @throws EmptyStringException
 */
public static void copyConceptAttributes(ONDEXConcept from, ONDEXConcept to)
    throws NullValueException, AccessDeniedException,
    EmptyStringException {
  for (EvidenceType et : from.getEvidence())
    addNewEvidence(to, et);
  for (ConceptAccession ca : from.getConceptAccessions())
    addNewAccession(to, ca);
  for (ConceptName cn : from.getConceptNames())
    addNewName(to, cn);
  for (Attribute attribute : from.getAttributes())
    addNewAttribute(to, attribute);
  if (from.getAnnotation() != null && to.getDescription() == null)
    to.setAnnotation(from.getAnnotation());
  if (from.getDescription() != null && to.getDescription() == null)
    to.setDescription(from.getDescription());
}

public String getName(ONDEXConcept ac) {
  String label = "";
  // get first preferred name as label
  for (ConceptName cn : ac.getConceptNames()) {
    if (cn.isPreferred()) {
      label = cn.getName();
      break;
    }
  }
  // next try annotation
  if (label == null || label.trim().length() == 0) {
    label = ac.getAnnotation();
  }
  // next try description
  if (label == null || label.trim().length() == 0) {
    label = ac.getDescription();
  }
  // next try pid
  if (label == null || label.trim().length() == 0) {
    label = ac.getPID();
  }
  // last resort to concept id
  if (label == null || label.trim().length() == 0) {
    label = String.valueOf(ac.getId());
  }
  return label;
}

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;
  }
}

/**
 * Clone concept with having a new ConceptClass.
 * 
 * @param oldC
 *            old ONDEXConcept
 * @param newCC
 *            new ConceptClass to use
 * @return new ONDEXConcept
 */
public ONDEXConcept clone(ONDEXConcept oldC, ConceptClass newCC) {
  // first clone concept with new ConceptClass
  ONDEXConcept newC = graph.createConcept(oldC.getPID(), oldC.getAnnotation(), oldC.getDescription(), oldC.getElementOf(), newCC, oldC.getEvidence());
  // copies everything else
  copyEverythingElse(oldC, newC);
  return newC;
}

/**
 * Generate metadata for Context.
 * @param context
 *            A Context tag (from the Ondex API).
 * @return JSONObject
 *            JSONObject containing information about the Context tag.
 */
private JSONObject buildContext(ONDEXConcept context) {
 JSONObject contextJson= new JSONObject();
  contextJson.put(JSONAttributeNames.ID, context.getId());
 return contextJson;
}

  @Override
  public String getUri ( ONDEXConcept c, Map<String, Object> params )
  {
    String ns = Java2RdfUtils.getParam ( params, "instanceNamespace", NamespaceUtils.ns ( "bkr" ) );
    
    String ccPart = Optional
      .ofNullable ( c.getOfType () )
      .flatMap ( cc -> Optional.ofNullable ( cc.getId () ) )
      .orElse ( null );
    
    return OndexRDFUtils.iri ( ns, ccPart, c.getPID (), c.getId () );
  }                
}

/**
 * helper method to extract a usable concept name.
 * 
 * @param c
 *            a concept.
 * @return a usable name.
 */
private String extractName(ONDEXConcept c) {
  String str = "";
  if (c.getConceptName() != null)
    str = c.getConceptName().getName();
  if (str.trim().length() == 0)
    str = c.getPID();
  if (str.trim().length() == 0)
    str = c.getId() + "";
  return str;
}

@Override
public void nodeToConcept(AbstractNode node) {
  Publication pub = (Publication) node;
  if(StandardFunctions.nullChecker(pub.getUniqueId(), dataSourceBioC, ccPublication, etIMPD))
    return;
  ONDEXConcept concept = this.graph.getFactory().createConcept(pub.getUniqueId(), dataSourceBioC, ccPublication, etIMPD);
  
  if (pub.getPubMedId() != 0){
    concept.createConceptAccession(new String(pub.getPubMedId() + ""), dataSourceNLM, false);
  }
  if (pub.getTitle() != null &&  !pub.getTitle().equals("")){
    concept.createAttribute(attTitle, pub.getTitle(), false);
  }
  pub.setConcept(concept);
}

@Override
public ConceptClass getOfType() {
  return parent.getOfType();
}

  @Override
  public Font transform(ONDEXConcept n) {
    ONDEXConcept c = graph.getConcept(n.getId());
    Attribute attribute = c.getAttribute(an);
    if (attribute != null) {
      Float size = (float) (((Double) attribute.getValue() / (Double) gdsMax) * (maxSize - minSize) + minSize);
      return newFont.deriveFont(size);
    }
    return newFont;
  }
});

private void updateSelectedNodes() {
  selected.clear();
  OVTK2PropertiesAggregator viewer = OVTK2Desktop.getDesktopResources()
      .getSelectedViewer();
  if (viewer != null) {
    PickedState<ONDEXConcept> state = viewer.getVisualizationViewer()
        .getPickedVertexState();
    Set<ONDEXConcept> set = state.getPicked();
    for (ONDEXConcept node : set) {
      ONDEXConcept ac = node;
      selected.put(ac.getId() + ":" + ac.getPID(), ac.getId());
    }
  }
}

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;
}

@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);
}

/**
 * Copies all accessions from old concept to new concept.
 * 
 * @param oldC
 *            old ONDEXConcept
 * @param newC
 *            new ONDEXConcept
 */
private void copyAccessions(ONDEXConcept oldC, ONDEXConcept newC) {
  // iterate over all old accessions
  for (ConceptAccession acc : oldC.getConceptAccessions()) {
    // clone old accession on new concept
    newC.createConceptAccession(acc.getAccession(), acc.getElementOf(), acc.isAmbiguous());
  }
}

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

Javadoc

This class represents a ONDEX Concept. It can have 0..* ConceptNames, 0.. ConceptAccessions and 0..* ConceptAttribute. ConceptNames, ConceptAccessions and ConceptAttribute can be added with the create*-methods.

Most used methods

getId
createAttribute
createConceptAccession
Creates a new ConceptAccession with the given accession, the information which DataSource it belongs
createConceptName
Creates a new ConceptName with the given name and the information if this name is preferred. Then ad
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.

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