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

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

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

edu.pitt.dbmi.nlp.noble.ontology.IProperty
This class describes propery construct @author tseytlin

   */
  public boolean evaluate(Object obj){
    if(obj instanceof IInstance){
      IInstance inst = (IInstance) obj;
      // see if this instance has a value that fits this restriction
      IProperty prop = getProperty();
      
      // is property satisfied
      boolean satisfied = isPropertySatisfied(prop, inst);
      
      // check if there is evidence to contradict inverse property
      // then the instance becomes inconsistent again
      if(satisfied && isPropertySatisfied(prop.getInverseProperty(), inst)){
        satisfied = false;
      }
      return satisfied;
    }else{
      return super.evaluate(obj);

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    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");

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   * @param ont
   * @param name
   * @return
   */
  private IProperty getProperty(IOntology ont, String name){
    IProperty code = ont.getProperty(name);
    if(code == null){
      code = ont.createProperty(name,IProperty.ANNOTATION_DATATYPE);
      code.setRange(new String [0]);
    }
    return code;
  }

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    for(IProperty sp : src.getProperties()){
      String name = sp.getName();
      // skip properties that are incorrectly named
      if(!name.matches("\\w+"))
        continue;
      IProperty tp = target.getProperty(name);
      if(tp == null && !target.hasResource(name)){
        tp = target.createProperty(name,sp.getPropertyType());
        
        // notify of progress
        String msg = "Copying property "+name+" ...";
        pcs.firePropertyChange(PROPERTY_PROGRESS_MSG, progressMessage, msg);
        progressMessage = msg;
        
        
        
        // copy stuff
        copyResourceInfo(sp,tp);
        
        // copy booleans
        tp.setFunctional(sp.isFunctional());
        tp.setTransitive(sp.isTransitive());
        tp.setSymmetric(sp.isSymmetric());
        
        // copy domain and ranges
        tp.setDomain((IResource []) convertResources(target,sp.getDomain(),IResource.class));
        tp.setRange(convertResources(target,sp.getRange()));
      }
    }
    
    // set rest of properties properties
    for(IProperty sp : src.getProperties()){
      String name = sp.getName();
      // skip properties that are incorrectly named
      if(!name.matches("\\w+"))
        continue;
      
      IProperty tp = target.getProperty(name);
      if(tp != null){
        tp.setInverseProperty((IProperty)convertResource(target,sp.getInverseProperty()));
        IProperty [] sub = sp.getSubProperties();
        if(sub != null && sub.length > 0){
          for(IProperty p: (IProperty []) convertResources(target,sub,IProperty.class)){
            tp.addSubProperty(p);
          }
        }
        IProperty [] sup = sp.getSuperProperties();
        if(sup != null && sup.length > 0){
          for(IProperty p: (IProperty []) convertResources(target,sup,IProperty.class)){
            tp.addSuperProperty(p);
          }
        }
        
      }
    }

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    IClass cls = ont.getClass(name);
    // if exists, then do the magic
    if(cls != null){
      // copy property values 
      for(IProperty sp: source.getProperties()){
        IProperty tp = (IProperty) convertResource(ont,sp);
        if(tp != null){
          // set property values
          if(tp.isFunctional())
            cls.setPropertyValue(tp,convertResource(ont,source.getPropertyValue(sp)));
          else
            cls.setPropertyValues(tp,convertResources(ont,source.getPropertyValues(sp)));
          
        }  
      }
      
      // copy disjoints
      for(IClass c: source.getDisjointClasses()){
        cls.addDisjointClass((IClass)convertResource(ont,c));
      }
      
      // copy necessary restrictions
      ILogicExpression exp = source.getNecessaryRestrictions();
      if(exp.getExpressionType() == ILogicExpression.OR){
        cls.addSuperClass(ont.createClass((ILogicExpression) convertResource(ont,exp)));
      }else{
        for(Object c: exp){
          if(c instanceof IRestriction)
            cls.addNecessaryRestriction((IRestriction)convertResource(ont,c));
          else if(c instanceof IClass)
            cls.addSuperClass((IClass) convertResource(ont,c));
          else if(c instanceof ILogicExpression)
            cls.addSuperClass(ont.createClass((ILogicExpression) convertResource(ont,exp)));    
        }
      }
      
      // copy equivalent restrictions
      exp = source.getEquivalentRestrictions();
      if(exp.getExpressionType() == ILogicExpression.OR){
        cls.addEquivalentClass(ont.createClass((ILogicExpression) convertResource(ont,exp)));
      }else{
        for(Object c: exp){
          if(c instanceof IRestriction)
            cls.addEquivalentRestriction((IRestriction)convertResource(ont,c));
          else if(c instanceof IClass)
            cls.addEquivalentClass((IClass) convertResource(ont,c));
          else if(c instanceof ILogicExpression)
            cls.addEquivalentClass(ont.createClass((ILogicExpression) convertResource(ont,exp)));
          
        }
      }
            
      // copy instances
      for(IInstance inst: source.getDirectInstances()){
        IInstance i = ont.getInstance(inst.getName());
        if(i == null){
          i = cls.createInstance(inst.getName());
          // copy property values
          for(IProperty sp : inst.getProperties()){
            IProperty tp = (IProperty) convertResource(ont,sp);
            if(tp != null){
              if(tp.isFunctional())
                i.setPropertyValue(tp,convertResource(ont,inst.getPropertyValue(sp)));
              else
                i.setPropertyValues(tp,convertResources(ont,inst.getPropertyValues(sp)));
            }
          }

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      if(e instanceof IClass){
        IClass cls = (IClass) e;
        buffer.append("<b>Equivalent: </b> "+Arrays.asList(cls.getEquivalentClasses())+"<br>");
        buffer.append("<b>Disjoint: </b> "+Arrays.asList(cls.getDisjointClasses())+"<br>");
      }else if(e instanceof IProperty){
        IProperty cls = (IProperty) e;
        buffer.append("<b>Domain: </b> "+Arrays.asList(cls.getDomain())+"<br>");
        buffer.append("<b>Range: </b> "+Arrays.asList(cls.getRange())+"<br>");
      }else if(e instanceof IInstance){
        IInstance cls = (IInstance) e;
        buffer.append("<b>Types: </b> "+Arrays.asList(cls.getTypes())+"<br>");
      }
      buffer.append("<b>Properties:</b>");
      IProperty[] p = e.getProperties();
      if(p.length > 0){
        buffer.append("<ul>");

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        }
        buffer.append("</td></tr>");
      }
      
    }else if(e instanceof IProperty){
      IProperty cls = (IProperty) e;
      buffer.append("<tr valign=top><td><b>Domain: </b></td><td>"+
          toHTML(cls.getDomain())+"</td></tr>");
      buffer.append("<tr valign=top><td><b>Range: </b></td><td>"+
          toHTML(cls.getRange())+"</td></tr>");
    }else if(e instanceof IInstance){
      IInstance cls = (IInstance) e;
      buffer.append("<tr valign=top><td><b>Types: </b></td><td>"+
          toHTML(cls.getDirectTypes())+"</td></tr>");
    }
    
    IProperty[] p = e.getProperties();
    if(p.length > 0){
      buffer.append("<tr valign=top><td><b>Properties:</b>");

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