Package org.gvt.model.biopaxl2

Examples of org.gvt.model.biopaxl2.BioPAXGraph.recordLayout()

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      assert graph.getName().equals(tab.getText()) :
        "graph name: " + graph.getName() + " tab name: " + tab.getText();

      if (rememberLayout && graph.isMechanistic())
      {
        graph.recordLayout();
      }
    }
    boolean removed = openTabNames.remove(tab.getText());

    assert removed : "tab name: " + tab.getText();
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      assert graph.getName().equals(tab.getText()) :
        "graph name: " + graph.getName() + " tab name: " + tab.getText();

      if (rememberLayout && graph.isMechanistic())
      {
        graph.recordLayout();
      }
    }
    boolean removed = openTabNames.remove(tab.getText());

    assert removed : "tab name: " + tab.getText();
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          "Duplication is supported only in mechanistic views.");

        return;
      }

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

      String name = p.getNAME();
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    BioPAXGraph excised = graph.excise(cropto, true);
    excised.setName(graph.getName() + " cropped");

    main.createNewTab(excised);
    new CoSELayoutAction(main).run();
    excised.recordLayout();
  }
}
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    hLayer.highlighted.clear();

    viewer.deselectAll();

    // Record layout
    graph.recordLayout();

    // Create updated graph
    pathway p = graph.getPathway();
    BioPAXGraph newGraph = main.getRootGraph().excise(p);
    newGraph.setName(p.getNAME());
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      for (ScrollingGraphicalViewer viewer : main.getTabToViewerMap().values())
      {
        BioPAXGraph graph = (BioPAXGraph) viewer.getContents().getModel();
        if (graph.isMechanistic())
        {
          graph.recordLayout();
        }
      }

      JenaIOHandler jenaIOHandler = main.getJenaIOHandler();
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    hLayer.highlighted.clear();

    viewer.deselectAll();

    // Record layout
    graph.recordLayout();

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

    // Update pathway components if update needed
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