Package edu.pitt.dbmi.nlp.noble.ontology

Examples of edu.pitt.dbmi.nlp.noble.ontology.IClass


          Element n = getElementByTagName(e,"conceptIdShort");
          if(n != null){
            String name = n.getTextContent().trim();
            //IClass cls = getClass(name);
            //if(cls == null)
            IClass cls = new BClass(this,name);
            cls.getConcept().setSearchString(text);
            cls.getConcept().setTerminology(this);
            list.add(cls.getConcept());
          }
        }
      }
      return list.toArray(new Concept [0]);
    }
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      //TODO:
     
      // get template contents
      List<IClass> templateContent = new ArrayList<IClass>();
      for(IRestriction r: template.getRestrictions(ont.getProperty("hasPrognostic"))){
        IClass c = (IClass) r.getParameter().getOperand();
        templateContent.add(c);
      }
     
      // sort them in order
      Collections.sort(templateContent,new Comparator<IClass>() {
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      item.setValueDomain(TemplateItem.DOMAIN_SELF);
    }
   
    // if feature process attributes
    if(isFeature(c)){
      IClass feature = getFeature(c)
     
      if(!feature.equals(c)){
        item.setFeature(convertSlideTutorClass(feature,template));
       
        // if feature is a child of value then, it is a fully specified feature attr/value, and
        // we just need a feature
        if(isOfParent(c,VALUES))
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   */
  public static boolean isOfParent(IClass cls,String parent){
    if(cls == null)
      return false;
    IOntology o = cls.getOntology();
    IClass p = o.getClass(parent);
    return cls.equals(p) || cls.hasSuperClass(p);
  }
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   * Lookup concept information if unique identifier is available
   * @param CUI
   * @return Concept object
   */
  public Concept lookupConcept(String cui) throws TerminologyException {
    IClass c = getClass(cui);
    return (c != null)?c.getConcept():null;
  }
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   * @return Map where relation is a key and list of related concepts is a value
   */
  public Map getRelatedConcepts(Concept c) throws TerminologyException{
    Map<Relation,Concept[]> map = new HashMap<Relation,Concept[]>();
    Relation [] r = getRelations();
    IClass cls = getClass(c.getCode());
    if(cls != null){
      map.put(r[0],getConcepts(cls.getDirectSuperClasses()));
      map.put(r[1],getConcepts(cls.getDirectSubClasses()));
      map.put(r[2],getConcepts(cls.getDisjointClasses()));
    }
    return map;
  }
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    if(isFilteredOut(c, semanticTypeFilter)){
      return;
    }
    IOntology ont = parent.getOntology();
    String clsName = getClassName(c.getName());
    IClass cls = ont.getClass(clsName);
    // if class exists, then we have a cycle, just add a parent and quit
    if(cls != null){
      if(!(cls.equals(parent) || cls.hasSuperClass(parent) || cls.hasSubClass(parent)))
        cls.addSuperClass(parent);
      return;
    }
   
    // create class
    cls = parent.createSubClass(clsName);
   
    Set<String> labels = new LinkedHashSet<String>();
    labels.add(c.getName());
    Collections.addAll(labels,c.getSynonyms());
   
    // add synonyms
    for(String s: labels){
      cls.addLabel(s);
    }
    // add definitions
    for(Definition d: c.getDefinitions()){
      cls.addComment(d.getDefinition());
    }
   
    // get concept code
    IProperty code = getProperty(ont,"code");
    cls.setPropertyValue(code,c.getCode());
   
    // get semantic types
    IProperty stype = getProperty(ont,"SemanticType");
    for(SemanticType st: c.getSemanticTypes())
      cls.addPropertyValue(stype,st.getName());
   
    // output
    console.append(prefix+c.getName()+"\n");
    SwingUtilities.invokeLater(new Runnable(){
      public void run(){
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  /**
   * get related concepts map
   */
  public Map getRelatedConcepts(Concept c) throws TerminologyException {
    // if we have a class, build the map from it, forget concept
    IClass cls = c.getConceptClass();
    if(cls != null){
      Map<Relation,Concept []> map = new HashMap<Relation,Concept []>();
      map.put(Relation.BROADER,getRelatedConcepts(c,Relation.BROADER));
      map.put(Relation.NARROWER,getRelatedConcepts(c,Relation.NARROWER));
      return map;
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    return Collections.EMPTY_MAP;
  }
 
  public Concept[] getRelatedConcepts(Concept c, Relation r) throws TerminologyException {
    // if we have a class already, use the ontology
    IClass cls = c.getConceptClass();
    if(cls != null){
      if(r == Relation.BROADER){
        return convertConcepts(cls.getDirectSuperClasses());
      }else if(r == Relation.NARROWER){
        return convertConcepts(cls.getDirectSubClasses());
      }else if(r == Relation.SIMILAR){
        List<IClass> clses = new ArrayList<IClass>();
        for(IClass eq: cls.getEquivalentClasses()){
          if(!eq.isAnonymous()){
            clses.add(eq);
          }
        }
        return convertConcepts(clses);
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  public Source[] getFilterSources() {
    return getSources();
  }

  public Concept[] getRelatedConcepts(Concept c, Relation r) throws TerminologyException {
    IClass cls = c.getConceptClass();
    if(r == Relation.BROADER){
      //IClass cls = ontology.getClass(c.getCode());
      if(cls != null){
        return convertConcepts(cls.getDirectSuperClasses());
      }
    }else if(r == Relation.NARROWER){
      //IClass cls = ontology.getClass(c.getCode());
      if(cls != null){
        return convertConcepts(cls.getDirectSubClasses());
      }
    }else if(r == Relation.SIMILAR){
      //IClass cls = ontology.getClass(c.getCode());
      if(cls != null){
        List<IClass> clses = new ArrayList<IClass>();
        for(IClass eq: cls.getEquivalentClasses()){
          if(!eq.isAnonymous()){
            clses.add(eq);
          }
        }
        return convertConcepts(clses);
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