Package org.biopax.paxtools.model.level3

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

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    for (Object o : getNodes())
    {
      Node node = (Node) o;

      Interaction inter = null;

      if (node instanceof ChbConversion)
      {
        inter = ((ChbConversion) node).getConversion();
      }
      else if (node instanceof ChbControl)
      {
        inter = ((ChbControl) node).getControl();
      }
      else if (node instanceof Hub)
      {
        inter = ((Hub) node).getInteraction();
      }

      if (inter != null)
      {
        if (!interactionMap.containsKey(inter))
        {
          interactionMap.put(inter, new ArrayList<GraphObject>());
        }
        interactionMap.get(inter).add(node);
      }
    }

    for (Object o : getEdges())
    {
      Interaction inter = null;

      if (o instanceof NonModulatedEffector)
      {
        inter = ((NonModulatedEffector) o).getControl();
      }
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    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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    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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Related Classes of org.biopax.paxtools.model.level3.Interaction

  • org.gvt.model.biopaxl3.BioPAXL3Graph
  • org.openbp.jaspira.action.JaspiraAction
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