Examples of BioPAXGraph

org.gvt.model.BioPAXGraph
@author Ozgun Babur
org.gvt.model.biopaxl2.BioPAXGraph
Top level compound node for biopax graph. @author Ozgun BaburCopyright: Bilkent Center for Bioinformatics, 2007 - present

Examples of org.gvt.model.BioPAXGraph


  private void openPathwayInTab(PathwayHolder p)
  {
    assert p != null;


    BioPAXGraph graph = main.getRootGraph().excise(p);
    boolean layedout = graph.fetchLayout();
    CTabItem tab = main.createNewTab(graph);


    if (refsToHighlight != null && !refsToHighlight.isEmpty())
    {
      ScrollingGraphicalViewer viewer = main.getTabToViewerMap().get(tab);

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Examples of org.gvt.model.BioPAXGraph

      }
      
      merger.merge(target, sources.toArray(new Model[sources.size()]));


      BioPAXReader reader = new BioPAXReader(target);
      BioPAXGraph graph = (BioPAXGraph) reader.readXMLFile(null);


      if (createNewPathway)
      {
        List<String> intids = getInteractionIDs(model);
        newPathwayName = graph.createPathway(
          newPathwayName == null ? "Neighborhood" : newPathwayName, intids);
        main.getAllPathwayNames().add(newPathwayName);
      }


      main.setRootGraph(graph);

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Examples of org.gvt.model.BioPAXGraph

                 "No path can be found with specified parameters");
         }
    // Result of PoI will be displayed in new niew
    else
    {
      BioPAXGraph pathwayGraph = main.getRootGraph().excise(resultSet);
      pathwayGraph.setName("Path Iteration");
      main.createNewTab(pathwayGraph);
      new CoSELayoutAction(main).run();


      resultSet = pathwayGraph.getCorrespMember(resultSet);


      for (GraphObject go : resultSet)
      {
        go.setHighlight(true);
      }

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Examples of org.gvt.model.BioPAXGraph

  }


  // Replace graph
  private void updateViewerContent(ScrollingGraphicalViewer viewer)
  {
    BioPAXGraph graph = (BioPAXGraph) viewer.getContents().getModel();


    // Updating is supported only for mechanistic views
    if (!graph.isMechanistic()) return;


    // Remember highlighted object's original nodes (members of chisio root graph)


    Map<String, Color> highlightMap = new HashMap<String, Color>();


    for (Object o : graph.getNodes())
    {
      IBioPAXNode node = (IBioPAXNode) o;
      if (node.isHighlighted())
      {
        highlightMap.put(node.getIDHash(), node.getHighlightColor());
      }
    }


    for (Object o : graph.getEdges())
    {
      IBioPAXEdge edge = (IBioPAXEdge) o;
      if (edge.isHighlighted())
      {
        highlightMap.put(edge.getIDHash(), edge.getHighlightColor());
      }
    }


    // Reset highlight


    HighlightLayer hLayer = (HighlightLayer)
      ((ChsScalableRootEditPart) viewer.getRootEditPart()).getLayer(
        HighlightLayer.HIGHLIGHT_LAYER);


    hLayer.removeAll();
    hLayer.highlighted.clear();


    viewer.deselectAll();


    // 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);
    newGraph.setAsRoot();


    // Replace the graph
    viewer.setContents(newGraph);


    // Use same layout
    boolean layedout = newGraph.fetchLayout();


    if (!layedout)
    {
      new CoSELayoutAction(main).run();
    }


    viewer.deselectAll();
    GraphAnimation.run(viewer);


    // Recover highlights


    for (Object o : newGraph.getNodes())
    {
      IBioPAXNode node = (IBioPAXNode) o;
      if (highlightMap.containsKey(node.getIDHash()))
      {
        node.setHighlightColor(highlightMap.get(node.getIDHash()));
        node.setHighlight(true);
      }
    }


    for (Object o : newGraph.getEdges())
    {
      IBioPAXEdge edge = (IBioPAXEdge) o;
      if (highlightMap.containsKey(edge.getIDHash()))
      {
        edge.setHighlightColor(highlightMap.get(edge.getIDHash()));

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Examples of org.gvt.model.BioPAXGraph

    }
  }


  private void updateRoot()
  {
    BioPAXGraph root = (BioPAXGraph) new BioPAXReader(main.getOwlModel()).readXMLFile(null);
    main.setRootGraph(root);
  }

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Examples of org.gvt.model.BioPAXGraph


    String name;


    if (root instanceof BioPAXGraph)
    {
      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()));
      }


      name = graph.getName();
    }
    else
    {
      name = adviceTabName(null);
    }

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Examples of org.gvt.model.BioPAXGraph

    ScrollingGraphicalViewer viewer = tabToViewerMap.get(tab);
    CompoundModel root = (CompoundModel) viewer.getContents().getModel();


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


      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());

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Examples of org.gvt.model.BioPAXGraph




    Object compmod = tabToViewerMap.get(tab).getContents().getModel();
    if (compmod instanceof BioPAXGraph)
    {
      BioPAXGraph graph = (BioPAXGraph) compmod;
      graph.setName(newName);
    }
    tab.setText(newName);


    assert nameToTabMap.size() == openTabNames.size();
  }

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Examples of org.gvt.model.BioPAXGraph

      man.clearExperimentData(rootGraph);
      man.associateExperimentData(rootGraph);


      for (ScrollingGraphicalViewer viewer : tabToViewerMap.values())
      {
        BioPAXGraph graph = (BioPAXGraph) viewer.getContents().getModel();
        man.clearExperimentData(graph);
        man.associateExperimentData(graph);
      }
    }
  }

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Examples of org.gvt.model.BioPAXGraph


    int limit = 10;
    int k = 0;
    int t = 0;


    BioPAXGraph graph = globalSearch ? main.getRootGraph() : main.getPathwayGraph();


    if (targets.isEmpty()) targets = null;


    Map<Node, Map<Integer, List<CausativePath>>> allMap =
      AlgoRunner.searchCausativePaths(graph, targets, limit, t, k);


    // Search the paths map for each target and
    // prepare the result paths to visualize


    List<String> pathIDs = new ArrayList<String>();
    idMap = new HashMap<String, CausativePath>();


    // Collect all paths in a list to be used in excising the original graph and displaying the
    // merge graph


    List<Path> paths = new ArrayList<Path>();


    for (Map<Integer, List<CausativePath>> integerListMap : allMap.values())
    {
      for (List<CausativePath> list : integerListMap.values())
      {
        paths.addAll(list);
      }
    }


    // Open merge graph of result pathways in a new view


    if (!paths.isEmpty() && globalSearch)
    {
      pathwayGraph = graph.excise(paths, false, true);
      pathwayGraph.setName("Causative Paths");
      main.createNewTab(pathwayGraph);
      new CoSELayoutAction(main).run();
      
      new ColorWithExperimentAction(main, pathwayGraph, ExperimentData.EXPRESSION_DATA).run();

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