Package org.gvt.util

Examples of org.gvt.util.PathwayHolder

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      if (graph.isMechanistic())
      {
        graph.forgetLayout();
        Model model = graph.getBiopaxModel();
        PathwayHolder p = graph.getPathway();
        p.removeFromModel(model);

        main.getAllPathwayNames().remove(p.getName());
      }
    }
  }
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    // Record layout
    graph.recordLayout();

    // Create updated graph
    PathwayHolder p = graph.getPathway();

    // Update pathway components if update needed

    if (withContent != null)
    {
      p.updateContentWith(withContent);
    }

    // Excise pathway

    BioPAXGraph newGraph = main.getRootGraph().excise(p);
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    {
      BioPAXGraph graph = (BioPAXGraph) root;

      if (graph.isMechanistic() && graph.getPathway() == null)
      {
        PathwayHolder p = new PathwayHolder(getOwlModel());

        p.setName(adviceTabName(graph.getName()));

        graph.setName(p.getName());

        graph.setPathway(p);
        graph.registerContentsToPathway();
        allPathwayNames.add(p.getName());
      }
      else
      {
        graph.setName(graph.getPathway() != null ? graph.getPathway().getName() :
          adviceTabName(graph.getName()));
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        return;
      }

      original.recordLayout();

      PathwayHolder p = original.getPathway();
      BioPAXGraph graph = main.getRootGraph().excise(p);
      graph.setPathway(null);

      String name = p.getName();

      // If the name contains a copy number at the end (like "pathway name (2)"), remove it

      if (name.indexOf(" ") > 0)
      {
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  }

  public PathwayHolder getPathway()
  {
    if (pathway == null) return null;
    return new PathwayHolder(pathway);
  }
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    {
      Map<String, PathwayHolder> map = new HashMap<String, PathwayHolder>();

      for (Pathway p : biopaxModel.getObjects(Pathway.class))
      {
        PathwayHolder ph = new PathwayHolder(p);
        map.put(ph.getName(), ph);
      }
      return map;
    }
    return null;
  }
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  }

  public PathwayHolder getPathway()
  {
    if (pathway == null) return null;
    return new PathwayHolder(pathway);
  }
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    {
      Map<String, PathwayHolder> map = new HashMap<String, PathwayHolder>();

      for (pathway p : biopaxModel.getObjects(pathway.class))
      {
        PathwayHolder ph = new PathwayHolder(p);
        map.put(ph.getName(), ph);
      }
      return map;
    }
    return null;
  }
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Related Classes of org.gvt.util.PathwayHolder

  • org.biopax.paxtools.model.level2.conversion
  • org.gvt.action.DeletePathwayAction
  • org.gvt.action.DuplicatePathwayAction
  • org.gvt.action.UpdatePathwayAction
  • org.gvt.ChisioMain
  • org.gvt.model.biopaxl2.BioPAXL2Graph
  • org.gvt.model.biopaxl2.Conversion
  • org.gvt.model.biopaxl3.BioPAXL3Graph
  • org.gvt.model.biopaxl3.ChbConversion
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