/** Constructs a dialog to edit the given gene simulation parameters object. */
public FciIndTestParamsEditorOld(FciIndTestParamsOld params) {
this.params = params;
// set up text and ties them to the parameters object being edited.
alphaField =
new DoubleTextField(indTestParams().getAlpha(), 8, new DecimalFormat("0.0########"));
alphaField.setFilter(
new DoubleTextField.Filter() {
public double filter(double value, double oldValue) {
try {
indTestParams().setAlpha(value);
return value;
} catch (IllegalArgumentException e) {
return oldValue;
}
}
});
depthField = new IntTextField(indTestParams().getDepth(), 5);
depthField.setFilter(
new IntTextField.Filter() {
public int filter(int value, int oldValue) {
try {
indTestParams().setDepth(value);
return value;
} catch (IllegalArgumentException e) {
return oldValue;
}
}
});
buildGui();
}
public void setup() {
this.varNames = params.getVarNames();
for (Object parentModel : parentModels) {
if (parentModel instanceof DataWrapper) {
DataWrapper wrapper = (DataWrapper) parentModel;
DataModel dataModel = wrapper.getSelectedDataModel();
new IndTestChooser().adjustIndTestParams(dataModel, params);
break;
} else if (parentModel instanceof GraphWrapper) {
GraphWrapper wrapper = (GraphWrapper) parentModel;
new IndTestChooser().adjustIndTestParams(wrapper.getGraph(), params);
break;
} else if (parentModel instanceof DagWrapper) {
DagWrapper wrapper = (DagWrapper) parentModel;
new IndTestChooser().adjustIndTestParams(wrapper.getGraph(), params);
break;
} else if (parentModel instanceof SemGraphWrapper) {
SemGraphWrapper wrapper = (SemGraphWrapper) parentModel;
new IndTestChooser().adjustIndTestParams(wrapper.getGraph(), params);
break;
}
}
DataModel dataModel1 = null;
Graph graph = null;
for (Object parentModel1 : parentModels) {
if (parentModel1 instanceof DataWrapper) {
DataWrapper dataWrapper = (DataWrapper) parentModel1;
dataModel1 = dataWrapper.getSelectedDataModel();
}
if (parentModel1 instanceof GraphWrapper) {
GraphWrapper graphWrapper = (GraphWrapper) parentModel1;
graph = graphWrapper.getGraph();
}
if (parentModel1 instanceof DagWrapper) {
DagWrapper dagWrapper = (DagWrapper) parentModel1;
graph = dagWrapper.getDag();
}
if (parentModel1 instanceof SemGraphWrapper) {
SemGraphWrapper semGraphWrapper = (SemGraphWrapper) parentModel1;
graph = semGraphWrapper.getGraph();
}
}
if (dataModel1 != null) {
varNames = new ArrayList(dataModel1.getVariableNames());
} else if (graph != null) {
Iterator it = graph.getNodes().iterator();
varNames = new ArrayList();
Node temp;
while (it.hasNext()) {
temp = (Node) it.next();
if (temp.getNodeType() == NodeType.MEASURED) {
varNames.add(temp.getName());
}
}
} else {
throw new NullPointerException(
"Null model (no graph or data model " + "passed to the search).");
}
params.setVarNames(varNames);
JButton knowledgeButton = new JButton("Edit");
IntTextField depthField = new IntTextField(params.getIndTestParams().getDepth(), 4);
depthField.setFilter(
new IntTextField.Filter() {
public int filter(int value, int oldValue) {
try {
params.getIndTestParams().setDepth(value);
Preferences.userRoot().putInt("depth", value);
return value;
} catch (Exception e) {
return oldValue;
}
}
});
double alpha = params.getIndTestParams().getAlpha();
if (!Double.isNaN(alpha)) {
alphaField = new DoubleTextField(alpha, 4, NumberFormatUtil.getInstance().getNumberFormat());
alphaField.setFilter(
new DoubleTextField.Filter() {
public double filter(double value, double oldValue) {
try {
params.getIndTestParams().setAlpha(value);
Preferences.userRoot().putDouble("alpha", value);
return value;
} catch (Exception e) {
return oldValue;
}
}
});
}
setBorder(new MatteBorder(10, 10, 10, 10, super.getBackground()));
setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
Box b2 = Box.createHorizontalBox();
b2.add(new JLabel("Knowledge:"));
b2.add(Box.createGlue());
b2.add(knowledgeButton);
add(b2);
add(Box.createVerticalStrut(10));
if (!Double.isNaN(alpha)) {
Box b0 = Box.createHorizontalBox();
b0.add(new JLabel("Alpha Value:"));
b0.add(Box.createGlue());
b0.add(alphaField);
add(b0);
add(Box.createVerticalStrut(10));
}
Box b1 = Box.createHorizontalBox();
b1.add(new JLabel("Search Depth:"));
b1.add(Box.createGlue());
b1.add(depthField);
add(b1);
add(Box.createVerticalStrut(10));
knowledgeButton.addActionListener(
new ActionListener() {
public final void actionPerformed(ActionEvent e) {
openKnowledgeEditor();
}
});
}
public BuildPureClustersIndTestParamsEditor(
BuildPureClustersIndTestParams paramsPureClusters, boolean discreteData) {
this.paramsPureClusters = paramsPureClusters;
DoubleTextField alphaField =
new DoubleTextField(getParams().getAlpha(), 8, new DecimalFormat("0.0########"));
alphaField.setFilter(
new DoubleTextField.Filter() {
public double filter(double value, double oldValue) {
try {
getParams().setAlpha(value);
return value;
} catch (IllegalArgumentException e) {
return oldValue;
}
}
});
JComboBox testSelector = null;
JComboBox purifySelector = null;
if (!discreteData) {
final String[] descriptions = Bpc.getTestDescriptions();
testSelector = new JComboBox(descriptions);
testSelector.setSelectedIndex(getParams().getTetradTestType());
testSelector.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
JComboBox combo = (JComboBox) e.getSource();
int index = combo.getSelectedIndex();
getParams().setTetradTestType(index);
}
});
final String[] purifyDescriptions = Bpc.getPurifyTestDescriptions();
purifySelector = new JComboBox(purifyDescriptions);
purifySelector.setSelectedIndex(getParams().getPurifyTestType());
purifySelector.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
JComboBox combo = (JComboBox) e.getSource();
int index = combo.getSelectedIndex();
getParams().setPurifyTestType(index);
}
});
}
setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
if (!discreteData) {
Box b1 = Box.createHorizontalBox();
b1.add(new JLabel("Test:"));
b1.add(Box.createHorizontalGlue());
b1.add(testSelector);
add(b1);
add(Box.createHorizontalGlue());
Box b2 = Box.createHorizontalBox();
b2.add(new JLabel("Purify:"));
b2.add(Box.createHorizontalGlue());
b2.add(purifySelector);
add(b2);
add(Box.createHorizontalGlue());
}
Box b3 = Box.createHorizontalBox();
b3.add(new JLabel("Alpha:"));
b3.add(Box.createHorizontalGlue());
b3.add(alphaField);
add(b3);
add(Box.createHorizontalGlue());
// if (discreteData) {
// paramsPureClusters.setPurifyTestType(
// BuildPureClusters.PURIFY_TEST_DISCRETE_LRT);
// paramsPureClusters.setTetradTestType(BuildPureClusters.TEST_DISCRETE);
//
// }
}
/**
* Constructs the Gui used to edit properties; called from each constructor. Constructs labels and
* text fields for editing each property and adds appropriate listeners.
*/
public void setup() {
setLayout(new BorderLayout());
JRadioButton manualRetain = new JRadioButton();
JRadioButton randomRetain = new JRadioButton();
manualRetain.setText("Manually, retaining previous values where possible.");
randomRetain.setText(
"Using a symmetric prior for each row of each conditional" + " probability table.");
ButtonGroup group = new ButtonGroup();
group.add(manualRetain);
group.add(randomRetain);
final DoubleTextField symmetricAlphaField =
new DoubleTextField(
params.getDouble("symmetricAlpha", 1.0),
5,
NumberFormatUtil.getInstance().getNumberFormat());
symmetricAlphaField.setFilter(
new DoubleTextField.Filter() {
public double filter(double value, double oldValue) {
try {
params.set("symmetricAlpha", value);
return value;
} catch (IllegalArgumentException e) {
return oldValue;
}
}
});
if (getParams().getString("initializationMode", "manualRetain").equals("manualRetain")) {
manualRetain.setSelected(true);
symmetricAlphaField.setEnabled(false);
} else if (getParams()
.getString("initializationMode", "manualRetain")
.equals("symmetricPrior")) {
randomRetain.setSelected(true);
symmetricAlphaField.setEnabled(true);
} else {
throw new IllegalStateException();
}
manualRetain.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
getParams().set("initializationMode", "manualRetain");
symmetricAlphaField.setEnabled(false);
}
});
randomRetain.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
getParams().set("initializationMode", "symmetricPrior");
symmetricAlphaField.setEnabled(true);
}
});
// continue workbench construction.
Box b1 = Box.createVerticalBox();
Box b2 = Box.createHorizontalBox();
b2.add(new JLabel("Pseudocounts for this Dirichlet Bayes IM should be initialized:"));
b2.add(Box.createHorizontalGlue());
Box b3 = Box.createHorizontalBox();
b3.add(manualRetain);
b3.add(Box.createHorizontalGlue());
Box b4 = Box.createHorizontalBox();
b4.add(randomRetain);
b4.add(Box.createHorizontalGlue());
Box b5 = Box.createHorizontalBox();
b5.add(Box.createRigidArea(new Dimension(30, 0)));
b5.add(new JLabel("All pseudocounts = "));
b5.add(symmetricAlphaField);
b5.add(Box.createHorizontalGlue());
b1.add(b2);
b1.add(Box.createVerticalStrut(5));
b1.add(b3);
b1.add(b4);
b1.add(b5);
b1.add(Box.createHorizontalGlue());
add(b1, BorderLayout.CENTER);
}
