Example #1
0
  @Override
  public void itemStateChanged(ItemEvent event) {

    int state = event.getStateChange();
    String item = (String) event.getItem();
    if (ab.isVertex()) {
      ((BiologicalNodeAbstract) ab).setCompartment(item);
    }
  }
  private Paint withoutGraphTheory(BiologicalNodeAbstract v) {
    boolean medium_check = false;

    if (v instanceof Transition) {
      if (((Transition) v).isSimulationActive()) {
        return Color.red;
      }
    }

    if (psV.getPicked().isEmpty()) {
      if (psE.getPicked().isEmpty()) {

        if (v.isReference() || v.isHidden()) return Color.LIGHT_GRAY;
        else if (v.hasBrendaNode() || v.hasKEGGNode()) return Color.RED;
        else if (settings.isBackgroundColor()) return Color.WHITE;
        else
          // return Color.BLACK;
          return Color.DARK_GRAY;

      } else {
        Set<BiologicalEdgeAbstract> set = psE.getPicked();
        BiologicalEdgeAbstract e;
        for (Iterator<BiologicalEdgeAbstract> it = set.iterator(); it.hasNext(); ) {

          e = it.next();
          // Pair points = e.getEndpoints();
          if (v == e.getFrom() || v == e.getTo()) medium_check = true;
        }
        if (medium_check) {
          if (settings.isBackgroundColor()) {
            return Color.WHITE;
          } else {
            // return Color.BLACK;
            return Color.DARK_GRAY;
          }
        } else {
          return Color.LIGHT_GRAY;
        }
      }

    } else {
      if (psV.isPicked(v))
        if (settings.isBackgroundColor()) return Color.WHITE;
        else
          // return Color.BLACK;
          // return Color.DARK_GRAY;
          return Color.BLUE;
      else {
        BiologicalNodeAbstract w;
        Iterator<BiologicalNodeAbstract> iter =
            pw.getGraph().getJungGraph().getNeighbors(v).iterator();
        while (iter.hasNext()) {
          w = iter.next();
          if (psV.isPicked(w)) medium_check = true;
        }

        Set<BiologicalEdgeAbstract> set = psE.getPicked();
        BiologicalEdgeAbstract bea;
        for (Iterator<BiologicalEdgeAbstract> it = set.iterator(); it.hasNext(); ) {

          bea = it.next();

          if (v == bea.getFrom() || v == bea.getTo()) medium_check = true;
        }

        if (medium_check)
          if (settings.isBackgroundColor()) return Color.WHITE;
          else
            // return Color.BLACK;
            return Color.DARK_GRAY;
        else return Color.LIGHT_GRAY;
      }
    }
  }
Example #3
0
  private void updateWindow(GraphElementAbstract element) {
    p.removeAll();
    // this.element = element;
    // this.ab = (GraphElementAbstract) graphInstance
    // .getPathwayElement(element);
    original = element;
    PropertyWindowListener pwl = new PropertyWindowListener(element);

    JTextField label = new JTextField(20);
    JTextField name = new JTextField(20);

    if (ref != null) {
      this.ab = ref;
      label.setText(ref.getLabel());
      name.setText(ref.getName());
    } else {
      this.ab = original;
      label.setText(ab.getLabel());
      name.setText(ab.getName());
    }

    reference = new JCheckBox();
    knockedOut = new JCheckBox();
    colorButton = new JButton("Colour");
    hideNeighbours = new JButton("Hide all Neighbours");
    showNeighbours = new JButton("Show all Neighbours");
    parametersButton = new JButton("Parameters");
    showLabels = new JButton("Show Labels");

    colorButton.setBackground(ab.getColor());
    colorButton.setToolTipText("Colour");
    colorButton.setActionCommand("colour");
    colorButton.addActionListener(this);

    // System.out.println("label: "+ab.getLabel());
    // System.out.println("name: "+ab.getName());
    label.setName("label");
    name.setName("name");

    label.addFocusListener(pwl);
    name.addFocusListener(pwl);

    reference.setSelected(ab.isReference());
    reference.setToolTipText("Set this element to a reference");
    reference.setActionCommand("reference");
    reference.addActionListener(this);

    MigLayout headerlayout = new MigLayout("fillx", "[right]rel[grow,fill]", "");
    JPanel headerPanel = new JPanel(headerlayout);
    // headerPanel.setBackground(new Color(192, 215, 227));
    headerPanel.add(new JLabel(ab.getBiologicalElement()), "");
    headerPanel.add(new JSeparator(), "gap 10");

    MigLayout layout = new MigLayout("fillx", "[grow,fill]", "");
    p.setLayout(layout);
    p.add(new JLabel("Element"), "gap 5 ");
    p.add(new JLabel(ab.getBiologicalElement()), "wrap,span 3");
    p.add(new JLabel("Label"), "gap 5 ");
    p.add(label, "wrap,span 3");
    p.add(new JLabel("Name"), "gap 5 ");
    p.add(name, "wrap ,span 3");

    // JCheckBox transitionfire = new JCheckBox("Should transition fire:",
    // true);
    // JTextField transitionStatement = new JTextField("true");

    if (ab.isVertex()) {
      BiologicalNodeAbstract bna = (BiologicalNodeAbstract) original;
      String lbl = "";
      if (bna.hasRef()) {
        lbl = bna.getID() + "_" + bna.getRef().getLabel();
      }
      p.add(new JLabel("Reference:"), "gap 5 ");
      p.add(new JLabel(lbl), "wrap ,span 3");

      if (bna.hasRef()) {
        this.deleteRef = new JButton("Delete Reference");
        deleteRef.setToolTipText("Delete Reference");
        deleteRef.setActionCommand("deleteRef");
        deleteRef.addActionListener(this);
        p.add(deleteRef);
        this.pickOrigin = new JButton("Highlight Origin");
        pickOrigin.setToolTipText("Highlight Origin");
        pickOrigin.setActionCommand("pickOrigin");
        pickOrigin.addActionListener(this);
        p.add(pickOrigin);

      } else {
        this.chooseRef = new JButton("Choose Reference");
        chooseRef.setToolTipText("Choose Reference");
        chooseRef.setActionCommand("chooseRef");
        chooseRef.addActionListener(this);
        p.add(chooseRef);
        if (bna.getRefs().size() > 0) {
          this.pickRefs = new JButton("Highlight References");
          pickRefs.setToolTipText("Highlight References");
          pickRefs.setActionCommand("pickRefs");
          pickRefs.addActionListener(this);
          p.add(pickRefs);
        }
      }

      showLabels.setToolTipText("Show all Labels");
      showLabels.setActionCommand("showLabels");
      showLabels.addActionListener(this);
      p.add(showLabels, "wrap");

      JComboBox<String> compartment = new JComboBox<String>();
      addCompartmentItems(compartment);
      AutoCompleteDecorator.decorate(compartment);

      compartment.setSelectedItem(bna.getCompartment());
      compartment.addItemListener(this);

      p.add(new JLabel("Compartment"), "gap 5 ");
      p.add(compartment, "wrap ,span 3");

      // ADDing Attributes (for all nodes)

      // Show Database IDs
      JTextArea dbids = new JTextArea();
      String dbidstring = new String();
      dbids.setEditable(false);
      dbids.setFont(dbids.getFont().deriveFont(Font.BOLD));
      dbids.setBackground(Color.WHITE);

      p.add(new JLabel("IDs known:"), "gap 5");
      p.add(dbids, "wrap, span 3");

      // Show Experiment names and values
      JTextArea experiments = new JTextArea();
      String experimentstring = new String();
      experiments.setEditable(false);
      experiments.setBackground(Color.WHITE);

      p.add(new JLabel("Dataset:"), "gap 5");
      p.add(experiments, "wrap, span 3");

      // Show GO annotations
      JTextArea goannoations = new JTextArea();
      String annotationstring = new String();
      goannoations.setEditable(false);
      goannoations.setForeground(Color.BLUE);
      goannoations.setBackground(Color.WHITE);

      p.add(new JLabel("Gene Ontology:"), "gap 5");
      p.add(goannoations, "wrap, span 3");

      // Show graph properties (local property)
      JTextArea graphproperties = new JTextArea();
      String propertiesstring = new String();
      graphproperties.setEditable(false);
      graphproperties.setForeground(new Color(255, 55, 55));
      graphproperties.setBackground(Color.WHITE);

      p.add(new JLabel("Graph properties:"), "gap 5");
      p.add(graphproperties, "wrap, span 3");

      // JTextField aaSequence = new JTextField(20);
      // aaSequence.setText(protein.getAaSequence());
      // aaSequence.setName("protein");
      // aaSequence.addFocusListener(pwl);
      // p.add(new JLabel("AA-Sequence"), "gap 5 ");
      // p.add(aaSequence, "wrap, span 3");

      String atname, atsvalue;
      double atdvalue;

      ArrayList<String> experimententries = new ArrayList<>(),
          databaseidentries = new ArrayList<>(),
          annotationentries = new ArrayList<>(),
          graphpropertiesentries = new ArrayList<>();

      for (NodeAttribute att : bna.getNodeAttributes()) {
        atname = att.getName();
        atsvalue = att.getStringvalue();
        atdvalue = att.getDoublevalue();

        switch (att.getType()) {
          case NodeAttributeTypes.EXPERIMENT:
            experimententries.add(atname + ":\t" + atdvalue + "\n");
            break;

          case NodeAttributeTypes.DATABASE_ID:
            databaseidentries.add(atname + ":\t" + atsvalue + "\n");
            break;

          case NodeAttributeTypes.ANNOTATION:
            annotationentries.add(atname + ":\t" + atsvalue + "\n");
            break;

          case NodeAttributeTypes.GRAPH_PROPERTY:
            graphpropertiesentries.add(atname + ":\t" + atdvalue + "\n");
            break;

          default:
            break;
        }
      }

      // Sort for more convenient display
      Collections.sort(experimententries);
      for (String exp : experimententries) experimentstring += exp;

      Collections.sort(databaseidentries);
      for (String dbid : databaseidentries) dbidstring += dbid;

      Collections.sort(annotationentries);
      for (String ann : annotationentries) annotationstring += ann;

      Collections.sort(graphpropertiesentries);
      for (String gprop : graphpropertiesentries) propertiesstring += gprop;

      experiments.setText(experimentstring);
      dbids.setText(dbidstring);
      goannoations.setText(annotationstring);
      graphproperties.setText(propertiesstring);

      if (ab instanceof PathwayMap) {
        p.add(new JLabel("Linked to Pathway"), "gap 5 ");
        boolean b = ((PathwayMap) ab).getPathwayLink() == null;
        JCheckBox linked = new JCheckBox("", !b);
        linked.setToolTipText(
            "Shows whether there is a connected Pathway in Memory to this Map (uncheck the Box to delete that Pathway)");
        linked.setActionCommand("pathwayLink");
        linked.addActionListener(this);
        linked.setEnabled(!b);
        p.add(linked, "wrap ,span 3");
      } else if (ab instanceof Protein) {
        Protein protein = (Protein) ab;
        JTextField aaSequence = new JTextField(20);
        aaSequence.setText(protein.getAaSequence());
        aaSequence.setName("protein");
        aaSequence.addFocusListener(pwl);
        p.add(new JLabel("AA-Sequence"), "gap 5 ");
        p.add(aaSequence, "wrap, span 3");
      } else if (ab instanceof DNA) {
        DNA dna = (DNA) ab;
        JTextField ntSequence = new JTextField(20);
        ntSequence.setText(dna.getNtSequence());
        ntSequence.setName("dna");
        ntSequence.addFocusListener(pwl);
        p.add(new JLabel("NT-Sequence"), "gap 5 ");
        p.add(ntSequence, "wrap, span 3");
      } else if (ab instanceof Gene) {
        Gene dna = (Gene) ab;
        JTextField ntSequence = new JTextField(20);
        ntSequence.setText(dna.getNtSequence());
        ntSequence.setName("gene");
        ntSequence.addFocusListener(pwl);
        p.add(new JLabel("NT-Sequence"), "gap 5 ");
        p.add(ntSequence, "wrap, span 3");
      } else if (ab instanceof RNA) {
        RNA rna = (RNA) ab;
        JTextField ntSequence = new JTextField(20);
        ntSequence.setText(rna.getNtSequence());
        ntSequence.setName("rna");
        ntSequence.addFocusListener(pwl);
        p.add(new JLabel("NT-Sequence"), "gap 5 ");
        p.add(ntSequence, "wrap, span 3");
      } else if (ab instanceof Place) {
        p.add(new JLabel("ID"), "gap 5 ");
        JTextField id = new JTextField(20);
        id.setText("P" + Integer.toString(ab.getID()));
        id.setEditable(false);
        p.add(id, "wrap ,span 3");
        Place place = (Place) ab;

        JLabel lswitchPlace = new JLabel("Place Type");
        JComboBox<String> placeList =
            new JComboBox<String>(new String[] {"discrete", "continuous"});
        if (place.isDiscrete()) placeList.setSelectedItem("discrete");
        else placeList.setSelectedItem("continuous");
        placeList.setName("placeList");
        placeList.addFocusListener(pwl);
        p.add(lswitchPlace, "gap 5 ");
        p.add(placeList, "wrap");

        MyJFormattedTextField token;
        MyJFormattedTextField tokenStart;

        JLabel lblTokenStart = new JLabel("Token Start");
        if (place.isDiscrete()) {
          token = new MyJFormattedTextField(MyNumberFormat.getIntegerFormat());
          tokenStart = new MyJFormattedTextField(MyNumberFormat.getIntegerFormat());
          tokenMin = new MyJFormattedTextField(MyNumberFormat.getIntegerFormat());
          tokenMax = new MyJFormattedTextField(MyNumberFormat.getIntegerFormat());
          token.setText((int) place.getToken() + "");
          tokenStart.setText((int) place.getTokenStart() + "");
          tokenMin.setText((int) place.getTokenMin() + "");
          tokenMax.setText((int) place.getTokenMax() + "");
        } else {
          token = new MyJFormattedTextField(MyNumberFormat.getDecimalFormat());
          tokenStart = new MyJFormattedTextField(MyNumberFormat.getDecimalFormat());
          tokenMin = new MyJFormattedTextField(MyNumberFormat.getDecimalFormat());
          tokenMax = new MyJFormattedTextField(MyNumberFormat.getDecimalFormat());
          token.setText(place.getToken() + "");
          tokenStart.setText(place.getTokenStart() + "");
          tokenMin.setText(place.getTokenMin() + "");
          tokenMax.setText(place.getTokenMax() + "");
        }
        JLabel lblToken = new JLabel("Token");

        token.setName("token");
        // token.addFocusListener(pwl);
        token.setEditable(false);
        token.setFocusLostBehavior(JFormattedTextField.COMMIT_OR_REVERT);

        tokenStart.setName("tokenStart");
        tokenStart.setFocusLostBehavior(JFormattedTextField.COMMIT);
        tokenStart.addFocusListener(pwl);

        tokenMin.setName("tokenMin");
        tokenMin.setFocusLostBehavior(JFormattedTextField.COMMIT_OR_REVERT);
        tokenMin.addFocusListener(pwl);
        JLabel lblTokenMin = new JLabel("min Tokens");

        tokenMax.setName("tokenMax");
        tokenMax.setFocusLostBehavior(JFormattedTextField.COMMIT_OR_REVERT);
        tokenMax.addFocusListener(pwl);
        JLabel lblTokenMax = new JLabel("max Tokens");
        p.add(lblToken, "gap 5 ");
        p.add(token, "wrap");

        p.add(lblTokenStart, "gap 5 ");
        p.add(tokenStart, "");

        constCheck = new JCheckBox("constant");
        constCheck.setActionCommand("constCheck");
        constCheck.addActionListener(this);
        constCheck.setSelected(place.isConstant());
        p.add(constCheck, "wrap");

        if (constCheck.isSelected()) {
          tokenMin.setEnabled(false);
          tokenMax.setEnabled(false);
        }
        p.add(lblTokenMin, "gap 5 ");
        p.add(tokenMin, "wrap");
        p.add(lblTokenMax, "gap 5");
        p.add(tokenMax, "wrap");
      } else if (ab instanceof Transition) {
        JLabel lswitchTrans = new JLabel("Transition Type");
        JComboBox<String> transList =
            new JComboBox<String>(
                new String[] {
                  DiscreteTransition.class.getName(),
                  ContinuousTransition.class.getName(),
                  StochasticTransition.class.getName()
                });
        transList.setSelectedItem(ab.getClass().getCanonicalName());
        transList.setName("transList");
        transList.addFocusListener(pwl);
        p.add(lswitchTrans, "gap 5");
        p.add(transList, "wrap");

        JTextField firingCondition = new JTextField(4);
        JLabel lblFiringCondition = new JLabel("Firing Condition");
        firingCondition.setText(((Transition) ab).getFiringCondition());
        firingCondition.setName("firingCondition");
        firingCondition.addFocusListener(pwl);

        p.add(lblFiringCondition, "gap 5");
        p.add(firingCondition, "wrap");

        if (ab instanceof DiscreteTransition) {
          DiscreteTransition trans = (DiscreteTransition) ab;
          JTextField delay = new JTextField(4);
          JLabel lbldelay = new JLabel("Delay");
          delay.setText(trans.getDelay() + "");
          delay.setName("delay");
          delay.addFocusListener(pwl);

          p.add(lbldelay, "gap 5");
          p.add(delay, "wrap");
        } else if (ab instanceof StochasticTransition) {
          StochasticTransition trans = (StochasticTransition) ab;
          String[] disStrings = {"norm", "exp"};
          // Create the combo box, select item at index 4.
          // Indices start at 0, so 4 specifies the pig.
          JComboBox<String> distributionList = new JComboBox<String>(disStrings);
          distributionList.setSelectedItem(trans.getDistribution());
          distributionList.setName("disList");
          distributionList.addFocusListener(pwl);
          p.add(new JLabel("Distribution"), "gap 5");
          p.add(distributionList, "wrap");
        } else if (ab instanceof ContinuousTransition) {
          ContinuousTransition trans = (ContinuousTransition) ab;
          JTextField maxSpeed = new JTextField(4);
          JLabel lblMaxSpeed = new JLabel("Maximum Speed");
          maxSpeed.setText(trans.getMaximumSpeed());
          maxSpeed.setName("maximumSpeed");
          maxSpeed.addFocusListener(pwl);

          p.add(lblMaxSpeed, "gap 5");
          p.add(maxSpeed, "wrap");

          if (trans.isKnockedOut()) {
            maxSpeed.setEnabled(false);
          }
        }
      }

    } else if (ab.isEdge()) {
      // System.out.println("edge");
      if (ab instanceof PNEdge) {

        PNEdge e = (PNEdge) ab;
        JTextField prob = new JTextField(4);
        prob.setText(e.getActivationProbability() + "");
        prob.setName("activationProb");
        prob.addFocusListener(pwl);
        JLabel lblProb = new JLabel("activation Probability");
        JTextField function = new JTextField(5);
        function.setText(e.getFunction());
        function.setName("function");
        function.addFocusListener(pwl);
        JLabel lblpassingTokens = new JLabel("Edge Function");
        JTextField lowBoundary = new JTextField(5);
        lowBoundary.setText(e.getLowerBoundary() + "");
        lowBoundary.setName("lowBoundary");
        lowBoundary.addFocusListener(pwl);
        JLabel lblLow = new JLabel("lower Boundary");
        JTextField upBoundary = new JTextField(5);
        upBoundary.setText(e.getUpperBoundary() + "");
        upBoundary.setName("upBoundary");
        upBoundary.addFocusListener(pwl);
        JLabel lblUp = new JLabel("upper Boundary");

        // String[] types = { "discrete", "continuous", "inhibition" };
        // Create the combo box, select item at index 4.
        // Indices start at 0, so 4 specifies the pig.
        // JLabel typeList = new JComboBox(types);

        p.add(new JLabel("Edge Type"), "gap 5 ");
        p.add(new JLabel(e.getType()), "wrap");

        JButton dirChanger = new JButton("Change Direction");
        dirChanger.setActionCommand("dirChanger");
        dirChanger.addActionListener(this);
        p.add(dirChanger, "wrap");

        p.add(lblProb, "gap 5");
        p.add(prob, "wrap");
        p.add(lblpassingTokens, "gap 5");
        p.add(function, "wrap");
        p.add(lblLow, "gap 5");
        p.add(lowBoundary, "wrap");
        p.add(lblUp, "gap 5");
        p.add(upBoundary, "wrap");
      }
    }

    p.add(new JLabel("Reference"), "gap 5 ");
    p.add(reference, "wrap, span 3");
    if (ab instanceof Transition) {
      knockedOut.setSelected(((Transition) ab).isKnockedOut());
      knockedOut.setToolTipText("Knock out");
      knockedOut.setActionCommand("knockedOut");
      knockedOut.addActionListener(this);
      p.add(new JLabel("Knocked out"), "gap 5 ");
      p.add(knockedOut, "wrap ,span 3");
    }

    if (ab.isVertex()) {
      hideNeighbours.setToolTipText("Sets all Neighbors of the selected Node to Reference");
      hideNeighbours.setActionCommand("hideNeighbours");
      hideNeighbours.addActionListener(this);
      hideNeighbours.setMaximumSize(new Dimension(120, 30));
      showNeighbours.setToolTipText("Delete Reference flag of all Neighbours of the current Node");
      showNeighbours.setActionCommand("showNeighbours");
      showNeighbours.addActionListener(this);
      showNeighbours.setMaximumSize(new Dimension(120, 30));
      p.add(showNeighbours);
      p.add(hideNeighbours);
    }
    parametersButton.setToolTipText("Show all Parameters");
    parametersButton.setActionCommand("showParameters");
    parametersButton.addActionListener(this);
    p.add(parametersButton);

    p.add(colorButton, "gap 5");
  }
Example #4
0
  @Override
  public void actionPerformed(ActionEvent e) {
    MainWindow w = MainWindowSingleton.getInstance();
    String event = e.getActionCommand();

    if ("colour".equals(event)) {

      // TODO fail due to old substance API / Bug in API
      Color newColor = JColorChooser.showDialog(w, "Choose Element Colour", getElementColor());
      JButton b = ((JButton) e.getSource());
      b.setBackground(newColor);

      ab.setColor(newColor);
      ab.setReference(false);
      ab.setHidden(false);
      ab.setVisible(true);
      // reference.setSelected(false);
      // updateReferences(false);

    } else if ("reference".equals(event)) {
      // TODO calculate References properly
      ab.setReference(reference.isSelected());
      if (reference.isSelected()) {
        ab.setHidden(true);
        updateReferences(true);
      } else {
        ab.setHidden(false);
        updateReferences(false);
      }
      colorButton.setBackground(ab.getColor());
    } else if ("pathwayLink".equals(event)) {
      if (JOptionPane.showConfirmDialog(
                  w,
                  "If you delete the PathwayLink the Sub-Pathway (with all eventually made changes within it) will be lost. Do you want to do this?",
                  "Delete the Sub-Pathway...",
                  JOptionPane.YES_NO_OPTION,
                  JOptionPane.QUESTION_MESSAGE)
              == JOptionPane.YES_OPTION
          && ab instanceof PathwayMap) {
        ((PathwayMap) ab).setPathwayLink(null);
        w.updateElementTree();
        w.updatePathwayTree();
        ab.setColor(Color.white);
      }
      w.updateElementProperties();
    } else if (("hideNeighbours".equals(event) || ("showNeighbours".equals(event)))
        && ab instanceof BiologicalNodeAbstract) {
      // TODO visible wird noch nicht gehandelt in transformators
      Pathway pw = graphInstance.getPathway();
      boolean hide = "hideNeighbours".equals(event);
      BiologicalNodeAbstract bna = (BiologicalNodeAbstract) ab;

      Iterator<BiologicalEdgeAbstract> it =
          pw.getGraph().getJungGraph().getIncidentEdges(bna).iterator();
      BiologicalEdgeAbstract bea;

      while (it.hasNext()) {
        // System.out.println(!hide);
        bea = it.next();
        bea.setVisible(!hide);
        // bea.setLabel(!hide+"");
      }

      Iterator<BiologicalNodeAbstract> it2 =
          pw.getGraph().getJungGraph().getNeighbors(bna).iterator();

      BiologicalNodeAbstract node;
      while (it2.hasNext()) {
        // System.out.println("drin");
        node = it2.next();
        node.setVisible(!hide);
        node.setHidden(hide);
      }

    } else if ("dirChanger".equals(event) && ab.isEdge()) {
      Pathway pw = graphInstance.getPathway();
      PNEdge edge = (PNEdge) ab;

      PNEdge newEdge =
          new PNEdge(
              edge.getTo(),
              edge.getFrom(),
              edge.getLabel(),
              edge.getName(),
              edge.getBiologicalElement(),
              edge.getFunction());
      newEdge.setUpperBoundary(edge.getUpperBoundary());
      newEdge.setLowerBoundary(edge.getLowerBoundary());
      newEdge.setActivationProbability(edge.getActivationProbability());
      newEdge.setDirected(true);
      // pw = graphInstance.getPathway();
      MyGraph g = pw.getGraph();
      g.getJungGraph().removeEdge(edge);
      // g.getEdgeStringer().removeEdge(edge.getEdge());
      pw.removeElement(edge);
      pw.addEdge(newEdge);
      // g.getVisualizationViewer().getPickedState().clearPickedEdges();
      graphInstance.setSelectedObject(newEdge);

      ab = newEdge;
    } else if ("chooseRef".equals(event)) {
      BiologicalNodeAbstract bna = (BiologicalNodeAbstract) original;
      ReferenceDialog dialog = new ReferenceDialog(bna);
      BiologicalNodeAbstract node = dialog.getAnswer();
      if (node != null) {
        bna.setRef(node);
        this.revalidateView();
        w.updateElementTree();
        // System.out.println("node: "+node.getID());
      }
    } else if ("deleteRef".equals(event)) {
      BiologicalNodeAbstract bna = (BiologicalNodeAbstract) original;
      bna.deleteRef();

      this.revalidateView();
      w.updateElementTree();

    } else if ("pickOrigin".equals(event)) {
      BiologicalNodeAbstract bna = (BiologicalNodeAbstract) original;

      Pathway pw = graphInstance.getPathway();
      pw = graphInstance.getPathway();
      MyGraph g = pw.getGraph();
      g.getVisualizationViewer().getPickedVertexState().pick(bna.getRef(), true);

      this.revalidateView();

    } else if ("pickRefs".equals(event)) {
      BiologicalNodeAbstract bna = (BiologicalNodeAbstract) original;

      Pathway pw = graphInstance.getPathway();
      pw = graphInstance.getPathway();
      MyGraph g = pw.getGraph();
      // System.out.println("c: "+g.getJungGraph().getVertexCount());
      BiologicalNodeAbstract pick;
      Iterator<BiologicalNodeAbstract> it = bna.getRefs().iterator();
      // System.out.println("size: "+bna.getRefs().size());
      while (it.hasNext()) {
        pick = it.next();
        // System.out.println(pick.getLabel());
        // System.out.println(pick);
        g.getVisualizationViewer().getPickedVertexState().pick(pick, true);
      }
      // System.out.println(g.getVisualizationViewer().getPickedVertexState().getPicked().size());
      this.revalidateView();
    } else if ("showParameters".equals(event)) {
      // System.out.println("show parameters");
      new ParameterWindow(ab);
      this.updateWindow(ab);
      p.revalidate();
    } else if ("showLabels".equals(event)) {
      // System.out.println("click");
      new LabelsWindow(ab);
    } else if ("knockedOut".equals(event)) {

      ((Transition) ab).setKnockedOut(knockedOut.isSelected());
      this.updateWindow(ab);
      p.revalidate();
      // p.repaint();
      Pathway pw = new GraphInstance().getPathway();
      pw.handleChangeFlags(ChangedFlags.PNPROPERTIES_CHANGED);

      // System.out.println("knocked out");
    } else if ("constCheck".equals(event)) {
      if (ab instanceof BiologicalNodeAbstract) {
        BiologicalNodeAbstract bna = (BiologicalNodeAbstract) ab;
        if (constCheck.isSelected()) {
          this.tokenMin.setEnabled(false);
          this.tokenMax.setEnabled(false);
          bna.setConstant(true);
        } else {
          this.tokenMin.setEnabled(true);
          this.tokenMax.setEnabled(true);
          bna.setConstant(false);
        }
        Pathway pw = new GraphInstance().getPathway();
        pw.handleChangeFlags(ChangedFlags.EDGEWEIGHT_CHANGED);
      }
      // System.out.println(this.constCheck.isSelected());

    }

    GraphInstance.getMyGraph().updateGraph();
  }