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");
}
@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();
}