Package org.biopax.paxtools.model

Examples of org.biopax.paxtools.model.Model

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          {
            continue;
          }

          System.out.println("Querying neighbors for " + ref);
          Model resultModel = ioHandler.getNeighbors(ref.getRef());

          main.unlock();
         
          if (resultModel != null && !resultModel.getObjects().isEmpty())
          {
            String pname = "Neighborhood for " + ref;

            if (main.getOwlModel() != null)
            {
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        LocalGoI();
    }

    public void LocalGoI()
    {
        Model owlModel = this.main.getOwlModel();

        if (owlModel == null)
        {
            MessageDialog.openError(main.getShell(), "Error!",
                "Load or query a BioPAX model first!");
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  }


  public void LocalNeighborhood()
  {
    Model owlModel = this.main.getOwlModel();

    if (owlModel == null)
    {
      MessageDialog.openError(main.getShell(), "Error!",
        "Load or query a BioPAX model first!");
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    CommonStreamQuery();
  }

  public void CommonStreamQuery()
  {
    Model owlModel = this.main.getOwlModel();

    if (owlModel == null)
    {
      MessageDialog.openError(main.getShell(), "Error!",
        "Load or query a BioPAX model first!");
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        LocalPoI();
    }

    public void LocalPoI()
    {
        Model owlModel = this.main.getOwlModel();

        if (owlModel == null)
        {
            MessageDialog.openError(main.getShell(), "Error!",
                "Load or query a BioPAX model first!");
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        LocalGoI();
    }

    public void LocalGoI()
    {
        Model owlModel = this.main.getOwlModel();

        if (owlModel == null)
        {
            MessageDialog.openError(main.getShell(), "Error!",
                "Load or query a BioPAX model first!");
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      {
        main.lockWithMessage("Querying Internal PC Database ...");
        PathwayCommonsIOHandler ioHandler = new PathwayCommonsIOHandler(new SimpleIOHandler());

        System.out.println("Querying neighbors for " + id);
        Model resultModel = ioHandler.getNeighbors(id); // TODO: implement to query internal PC hibernate DB

        main.unlock();

        if (resultModel != null && !resultModel.getObjects().isEmpty())
        {
          String pname = id;

          if (main.getOwlModel() != null)
          {
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        LocalPoI();
    }

    public void LocalPoI()
    {
        Model owlModel = this.main.getOwlModel();

        if (owlModel == null)
        {
            MessageDialog.openError(main.getShell(), "Error!",
                "Load or query a BioPAX model first!");
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    this.ruleTypes = new ArrayList<BinaryInteractionType>();
  }

  public void run()
  {
    Model model = main.getOwlModel();

    if (model == null)
    {
      return;
    }
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    main.setRootGraph(root);
  }

  public void run()
  {
    Model model = main.getOwlModel();

    if (model == null)
    {
      MessageDialog.openError(main.getShell(), "Error!",
        "Load or query a BioPAX model first!");
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Related Classes of org.biopax.paxtools.model.Model

  • gem.BioPAXWriter
  • org.gvt.action.DeletePathwayAction
  • org.gvt.action.ExportToSIFAction
  • org.gvt.action.LocalCommonStreamQueryAction
  • org.gvt.action.LocalCompartmentQueryAction
  • org.gvt.action.LocalGoIQueryAction
  • org.gvt.action.LocalNeighborhoodQueryAction
  • org.gvt.action.LocalPathIterationQueryAction
  • org.gvt.action.LocalPoIQueryAction
  • org.gvt.action.MergeAction
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