Examples of Pathway

Examples of org.biopax.paxtools.model.level3.Pathway

    return !biopaxModel.getObjects(org.biopax.paxtools.model.level3.Pathway.class).isEmpty();
  }


  public String createGlobalPathway(String name)
  {
    Pathway p = biopaxModel.addNew(Pathway.class,
      "http://chisiobiopaxeditor/#" + System.currentTimeMillis());


    for (Interaction inter : biopaxModel.getObjects(Interaction.class))
    {
      p.addPathwayComponent(inter);
    }
    p.setDisplayName(makeUniquePathwayName(name));
    return p.getDisplayName();
  }

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Examples of org.biopax.paxtools.model.level3.Pathway

    return p.getDisplayName();
  }


  public String createPathway(String name, List<String> intids)
  {
    Pathway p = biopaxModel.addNew(Pathway.class,
      "http://chisiobiopaxeditor/#" + System.currentTimeMillis());


    for (Interaction inter : biopaxModel.getObjects(Interaction.class))
    {
      if (intids.contains(inter.getRDFId()))
      {
        p.addPathwayComponent(inter);
      }
    }
    p.setDisplayName(makeUniquePathwayName(name));
    return p.getDisplayName();
  }

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Examples of org.bnplusplus.model.bnpp.Pathway

   * @return ListHashMap with groups (according to pathways) that can be visualized
   * */
  private ListHashMap<Pathway, BasicNodeComponentUI> selectGroups(ListHashMap<Pathway, BasicNodeComponentUI> map) 
  {
    ListHashMap<Pathway, BasicNodeComponentUI> NewMap = new ListHashMap<Pathway, BasicNodeComponentUI>();
    Pathway pathwayA = new Pathway();    
    
    for(Entry<Pathway, LinkedList<BasicNodeComponentUI>> entry : map.entrySet())
    {            
      for (BasicNodeComponentUI node : entry.getValue())
      {  
        //node.setBorderColor(Color.WHITE);
        if(map.getKeys(node).size()==1)
        {
          Pathway pathway = map.getKeys(node).getFirst();
          NewMap.put(pathway, node);          
        }  
        else if(map.getKeys(node).size()>2)
        {        
          
          NewMap.put(pathwayA, node);  
          highlightNode(node, 3, null);
          
          Pathway pathway = entry.getKey();
          mapToDrawC.put(pathway, node);          
        }    
        else
        {
          highlightNode(node, 3, null);
          
          Pathway pathway = entry.getKey();
          mapToDrawC.put(pathway, node);          
        }
      }
    }  
    LinkedList<Pathway> listPath = new LinkedList<Pathway>();

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