Package org.gvt.util

Examples of org.gvt.util.EntityHolder

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    // Encountered rules. For avoiding duplicate edges.
    Set<String> encountered = new HashSet<String>();

    for (SimpleInteraction simpleInt : simpleInts)
    {
      EntityHolder source = new EntityHolder(simpleInt.getSource());
      EntityHolder target = new EntityHolder(simpleInt.getTarget());

      if (!map.containsKey(source))
      {
        map.put(source, new SIFNode(this, source));
      }
      if (!map.containsKey(target))
      {
        map.put(target, new SIFNode(this, target));
      }
      SIFNode sourceNode = map.get(source);
      SIFNode targetNode = map.get(target);

      String id = source.getID() + " - " + target.getID();

      if (encountered.contains(id))
      {
        continue;
      }

      new SIFEdge(sourceNode, targetNode, simpleInt.getType());

      encountered.add(id);

      if (!simpleInt.getType().isDirected())
      {
        encountered.add(target.getID() + " - " + source.getID());
      }
    }
  }
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    return cmp;
  }

  public EntityHolder getEntity()
  {
    return new EntityHolder(cmp);
  }
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        for (String selected : selectionResult)
        {
          //search among all addedEntities
          for (int j = 0 ; j < addedEntities.size() ; j++)
          {
            EntityHolder entity = addedEntities.get(j);
           
            //if corresponding entity is found
            if (selected != null && selected.equals(entity.getName()))
            {
              //remove entity from addedEntities ArrayList
              addedEntities.remove(j);
             
              //remove entity keyName from from List
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          {
            Node corresponding = (Node) actor.getLabel(BioPAXGraph.EXCISED_FROM);

            if (corresponding instanceof EntityAssociated)
            {
              EntityHolder entity = ((EntityAssociated) corresponding).getEntity();
              List<Node> nodeList = entityToNodeMap.get(entity);

              for (Node node : nodeList)
              {
                targets.add(node);
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    if (isLevel2())
    {
      for (physicalEntity pe : getOwlModel().getObjects(physicalEntity.class))
      {
        entities.add(new EntityHolder(pe));
      }
    }
    else if (isLevel3())
    {
      for (EntityReference er : getOwlModel().getObjects(EntityReference.class))
      {
        entities.add(new EntityHolder(er));
      }
      if (entities.isEmpty())
      {
        for (PhysicalEntity pe : getOwlModel().getObjects(PhysicalEntity.class))
        {
          entities.add(new EntityHolder(pe));
        }
      }
    }

    return entities;
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//    }
  }

  public EntityHolder getEntity()
  {
    return new EntityHolder(entity);
  }
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    return cmp;
  }

  public EntityHolder getEntity()
  {
    return new EntityHolder(cmp);
  }
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        for (String selected : selectionResult)
        {
          //search among all addedEntities
          for (int j = 0 ; j < addedEntities.size() ; j++)
          {
            EntityHolder entity = addedEntities.get(j);
           
            //if corresponding entity is found
            if (selected != null &&
              selected.equals(entity.getName()))
            {
              //remove entity from addedEntities ArrayList
              addedEntities.remove(j);
             
              //remove entity keyName from from List
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                for (String selected : selectionResult)
                {
                    //search among all addedEntities
                    for (int j = 0 ; j < addedEntities.size() ; j++)
                    {
                        EntityHolder entity = addedEntities.get(j);

                        //if corresponding entity is found
                        if (selected != null &&
                            selected.equals(entity.getName()))
                        {
                            //remove entity from addedEntities ArrayList
                            addedEntities.remove(j);

                            //remove entity keyName from from List
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         * Could, and perhaps should, be done in a better way...
         * */
        boolean isProt = false;
        if (node instanceof Actor){
          Actor a = (Actor) node;
          EntityHolder holder = a.getEntity();
          isProt = holder.l3pe.getClass().toString().contains("tein");
         
        }

        if (data == null)
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Related Classes of org.gvt.util.EntityHolder

  • org.gvt.action.SearchCausativePathsAction
  • org.gvt.ChisioMain
  • org.gvt.gui.CommonStreamQueryParamWithEntitiesDialog
  • org.gvt.gui.GoIQueryParamWithEntitiesDialog
  • org.gvt.gui.NeighborhoodQueryParamWithEntitiesDialog
  • org.gvt.gui.PoIQueryParamWithEntitiesDialog
  • org.gvt.model.biopaxl2.Actor
  • org.gvt.model.biopaxl2.BioPAXL2Graph
  • org.gvt.model.biopaxl2.Complex
  • org.gvt.model.biopaxl3.Actor
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