Package org.gvt.model

Examples of org.gvt.model.BioPAXGraph

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    CompoundModel root = (CompoundModel) viewer.getContents().getModel();

    if (root instanceof BioPAXGraph)
    {
      BioPAXGraph graph = (BioPAXGraph) root;

      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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            graph.setLastAppliedColoring(null);
            new ColorWithExperimentAction(main, graph, dataManager.getType()).run();
          }
        }

        BioPAXGraph currentGraph = main.getPathwayGraph();
        if (currentGraph != null && currentGraph.getLastAppliedColoring() == null)
        {
          new ColorWithExperimentAction(main, currentGraph, dataManager.getType()).run();
        }

        shell.dispose();
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        int selection = queryTypeBox.getSelectionIndex();

        switch (selection)
        {
          case 0: // Neighbors in loaded file
            BioPAXGraph root = main.getRootGraph();
            if (root != null)
            {
              Collection<EntityHolder> entities = root.getRelatedEntities(refs);

              if (entities.isEmpty())
              {
                MessageDialog.openInformation(main.getShell(), "Not found",
                  "Selected entities are not found in the current model.");
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Related Classes of org.gvt.model.BioPAXGraph

  • org.gvt.action.AbstractLocalQueryAction
  • org.gvt.action.CropToHighlightedAction
  • org.gvt.action.DeletePathwayAction
  • org.gvt.action.DuplicatePathwayAction
  • org.gvt.action.GetNeighborhoodOfSelectedEntityAction
  • org.gvt.action.HighlightPathsBetweenSelectedAction
  • org.gvt.action.LoadBioPaxModelAction
  • org.gvt.action.LocalPathIterationQueryAction
  • org.gvt.action.MergeAction
  • org.gvt.action.OpenPathwaysAction
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