Package org.gvt.model.biopaxl2

Examples of org.gvt.model.biopaxl2.BioPAXGraph

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    {
      man.associateExperimentData(rootGraph);

      for (ScrollingGraphicalViewer viewer : tabToViewerMap.values())
      {
        BioPAXGraph graph = (BioPAXGraph) viewer.getContents().getModel();
        man.associateExperimentData(graph);
      }
    }
  }
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    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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        int selection = queryTypeBox.getSelectionIndex();

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

  public void run()
  {
    ScrollingGraphicalViewer viewer = main.getViewer();
    BioPAXGraph pathway = main.getPathwayGraph();

    if (pathway == null)
    {
      MessageDialog.openError(main.getShell(), "Error!", "No BioPAX pathway.");
      return;
    }

    if (viewer != null)
    {
      BioPAXGraph original = (BioPAXGraph) viewer.getContents().getModel();

      if (!original.isMechanistic())
      {
        MessageDialog.openError(main.getShell(), "Not Supported!",
          "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();

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

      if (name.indexOf(" ") > 0)
      {
        String last = name.substring(name.lastIndexOf(" ") + 1);
        if (last.indexOf("(") == 0 && last.indexOf(")") == last.length() - 1)
        {
          boolean isdigit = true;
          for (int i = 1; isdigit && i < last.length() - 1; i++)
          {
            isdigit = Character.isDigit(last.charAt(i));
          }

          if (isdigit) name = name.substring(0, name.lastIndexOf(" "));
        }
      }

      graph.setName(name);
      main.createNewTab(graph);
      graph.fetchLayout(p.getRDFId());
    }
  }
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  private void openPathwayInTab(pathway 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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    item.setBackground(1, ChisioMain.higlightColor);
  }

  private void prepareForBioPAXGraph()
  {
    BioPAXGraph graph = (BioPAXGraph) model;

    for (String[] property : graph.getInspectable())
    {
      addRow(table, property[0]).setText(1, property[1]);
    }
    table.getColumn(1).pack();
    table.pack();
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      }
     
      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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    calculateAverageNodeDegree();
  }

  private void calculateAverageNodeDegree()
  {
    BioPAXGraph graph = main.getRootGraph();

    int totalDegree = 0;
    int nodeCounted = 0;

    for (Object o : graph.getNodes())
    {
      NodeModel node = (NodeModel) o;

      if (node instanceof ComplexMember ||
        node instanceof Compartment ||
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    this.main = main;
  }

  public void run()
  {
    BioPAXGraph graph = main.getPathwayGraph();

    if (graph == null)
    {
      MessageDialog.openError(main.getShell(), "Error!", "No BioPAX pathway.");
      return;
    }

    if (!graph.isMechanistic())
    {
      MessageDialog.openError(main.getShell(), "Not Supported!",
        "Cropping is supported only for mechanistic views.");

      return;
    }

    Set<GraphObject> cropto = new HashSet<GraphObject>();

    for (Object o : graph.getNodes())
    {
      NodeModel node = (NodeModel) o;
      if (node.isHighlight())
      {
        cropto.add((GraphObject) node);
      }
    }

    for (Object o : graph.getEdges())
    {
      EdgeModel edge = (EdgeModel) o;
      if (edge.isHighlight())
      {
        cropto.add((GraphObject) edge);
      }
    }

    if (cropto.isEmpty())
    {
      MessageDialog.openError(main.getShell(), "Error!",
        "Nothing is highlighted.");
      return;     
    }

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

    main.createNewTab(excised);
    new CoSELayoutAction(main).run();
    excised.recordLayout();
  }
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Related Classes of org.gvt.model.biopaxl2.BioPAXGraph

  • org.eclipse.draw2d.geometry.Dimension
  • org.eclipse.draw2d.geometry.Point
  • org.eclipse.swt.graphics.Color
  • org.eclipse.swt.graphics.Font
  • org.eclipse.swt.graphics.FontData
  • org.gvt.action.AbstractLocalQueryAction
  • org.gvt.action.CropToHighlightedAction
  • org.gvt.action.DebugButtonAction
  • org.gvt.action.DeletePathwayAction
  • org.gvt.action.DuplicatePathwayAction
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