public void updateRegulatorsOptions() {
Integer value = (Integer) numRegulators_.getModel().getValue();
if ((Integer) numRegulators_.getModel().getValue()
> (Integer) subnetSize_.getModel().getValue())
value = (Integer) subnetSize_.getModel().getValue();
SpinnerNumberModel model = (SpinnerNumberModel) numRegulators_.getModel();
model.setMinimum(1);
model.setMaximum((Integer) subnetSize_.getModel().getValue());
model.setStepSize(1);
model.setValue(value);
}
public void init() {
setup("Circumference of a Circle");
SpinnerNumberModel snm = (SpinnerNumberModel) (n.getModel());
snm.setMinimum(new Integer(3));
north.setLayout(new BorderLayout());
north.add("West", choice);
JPanel east = new JPanel();
east.add(new JLabel(" n="));
east.add(n);
north.add("East", east);
south.remove(choice);
contentpane.add("North", north);
contentpane.add("Center", graph = new CircleCircumferenceGraph(this, N));
if (getParameter("originX") != null) {
graph.originX = Double.parseDouble(getParameter("originX"));
}
if (getParameter("originY") != null) {
graph.originY = Double.parseDouble(getParameter("originY"));
}
if (getParameter("zoom") != null) {
graph.zoom += Integer.parseInt(getParameter("zoom"));
}
stat2.setVisible(true);
// choice = new Choice();
choice.addItem("Inscribed Polygon");
choice.addItem("Circumscribed Polygon");
choice.addItem("Show Both");
choice.addItem("Show Sequences");
// choice.addItem("Newton-Cotes Rule");
choice.setSelectedItem(getParameter("type"));
graph.repaint();
splash = new SplashPanel(new CircleCircumferenceGraph(this, N));
splash.graph.originX = graph.originX;
splash.graph.originY = graph.originY;
splash.graph.zoom = graph.zoom;
getContentPane().add(splash);
}
/** Constructor */
@SuppressWarnings("serial")
public SubnetExtraction(Frame aFrame, GenericElement item) {
super(aFrame);
item_ = item;
// Set model of "subnet size" spinner
SpinnerNumberModel model = new SpinnerNumberModel();
model.setMinimum(1);
model.setStepSize(1);
int maxSize =
(item instanceof StructureElement)
? ((StructureElement) item).getNetwork().getSize()
: ((DynamicalModelElement) item).getGeneNetwork().getSize();
model.setMaximum(maxSize);
int effectiveSize = (10 <= maxSize) ? 10 : maxSize;
model.setValue(effectiveSize);
subnetSize_.setModel(model);
// Set model of "number of subnets" spinner
model = new SpinnerNumberModel();
model.setMinimum(1);
model.setMaximum(20);
model.setStepSize(1);
model.setValue(10);
numberSubnets_.setModel(model);
// Set model of "random among top" spinner
model = new SpinnerNumberModel();
model.setMinimum(1);
model.setMaximum(100);
model.setStepSize(1);
model.setValue(20);
randomAmongTopSpinner_.setModel(model);
// Set model of "From strongly connected components"
model = new SpinnerNumberModel();
model.setMinimum(1);
model.setMaximum(maxSize);
model.setStepSize(1);
model.setValue(10);
numStronglyConnected_.setModel(model);
// Set model of "From strongly connected components"
model = new SpinnerNumberModel();
model.setMinimum(1);
model.setMaximum((Integer) subnetSize_.getModel().getValue());
model.setStepSize(1);
model.setValue(10);
numRegulators_.setModel(model);
// add tooltips for all elements of the window
addTooltips();
String title1, title2;
title1 = title2 = "";
if (item_ instanceof StructureElement) {
ImodNetwork network = ((StructureElement) item_).getNetwork();
title1 = item_.getLabel();
title2 = network.getSize() + " nodes, " + network.getNumEdges() + " edges";
} else if (item_ instanceof DynamicalModelElement) {
GeneNetwork geneNetwork = ((DynamicalModelElement) item_).getGeneNetwork();
title1 = item_.getLabel();
title2 = geneNetwork.getSize() + " genes, " + geneNetwork.getNumEdges() + " interactions";
}
setGeneralInformation(title1 + " (" + title2 + ")");
/** ACTIONS */
subnetRootNameDocument_ = subnetRootName_.getDocument();
subnetRootNameDocument_.addDocumentListener(
new DocumentListener() {
public void changedUpdate(DocumentEvent arg0) {
runButton_.setEnabled(!subnetRootName_.getText().equals(""));
}
public void insertUpdate(DocumentEvent arg0) {
runButton_.setEnabled(!subnetRootName_.getText().equals(""));
}
public void removeUpdate(DocumentEvent arg0) {
runButton_.setEnabled(!subnetRootName_.getText().equals(""));
}
});
extractAllRegulators_.addActionListener(
new ActionListener() {
public void actionPerformed(final ActionEvent arg0) {
disableExtractionOptions();
}
});
randomVertex_.addActionListener(
new ActionListener() {
public void actionPerformed(final ActionEvent arg0) {
updateSeedControls();
}
});
selectionFromList_.addActionListener(
new ActionListener() {
public void actionPerformed(final ActionEvent arg0) {
updateSeedControls();
}
});
greedy_.addActionListener(
new ActionListener() {
public void actionPerformed(final ActionEvent arg0) {
updateNeighborSelectionControls();
}
});
randomAmongTop_.addActionListener(
new ActionListener() {
public void actionPerformed(final ActionEvent arg0) {
updateNeighborSelectionControls();
}
});
stronglyConnected_.addActionListener(
new ActionListener() {
public void actionPerformed(final ActionEvent arg0) {
updateSeedControls();
}
});
cancelButton.addActionListener(
new ActionListener() {
public void actionPerformed(final ActionEvent arg0) {
GnwSettings.getInstance().stopSubnetExtraction(true);
escapeAction();
}
});
runButton_.addActionListener(
new ActionListener() {
public void actionPerformed(final ActionEvent arg0) {
run();
}
});
subnetSize_.addChangeListener(
new ChangeListener() {
public void stateChanged(ChangeEvent arg0) {
updateRegulatorsOptions();
}
});
numRegulators_.addChangeListener(
new ChangeListener() {
public void stateChanged(ChangeEvent arg0) {
updateRegulatorsOptions();
}
});
useNumRegulators_.addActionListener(
new ActionListener() {
public void actionPerformed(final ActionEvent arg0) {
numRegulators_.setEnabled(useNumRegulators_.isSelected());
}
});
// useNumRegulators_.addChangeListener(new ChangeListener() {
// public void stateChanged(ChangeEvent arg0) {
// numRegulators_.setEnabled(useNumRegulators_.isSelected());
// }
// });
subnetIdProposal();
setListVerticesID();
updateSeedControls();
updateNeighborSelectionControls();
useNumRegulators_.setSelected(false);
numRegulators_.setEnabled(false);
}
/** performs the creation of the dialog and all its components. */
protected void initGUI() {
JPanel panel;
SpinnerNumberModel model;
JPanel panel2;
getContentPane().setLayout(new BorderLayout());
panel = new JPanel(new GridLayout(6, 1));
panel.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
getContentPane().add(panel, BorderLayout.CENTER);
// mean precision
m_MeanPrecSpinner = new JSpinner();
m_MeanPrecSpinner.addChangeListener(
new ChangeListener() {
public void stateChanged(ChangeEvent e) {
getData();
}
});
model = (SpinnerNumberModel) m_MeanPrecSpinner.getModel();
model.setMaximum(new Integer(20));
model.setMinimum(new Integer(0));
m_MeanPrecLabel = new JLabel("Mean Precision");
m_MeanPrecLabel.setDisplayedMnemonic('M');
m_MeanPrecLabel.setLabelFor(m_MeanPrecSpinner);
panel2 = new JPanel(new FlowLayout(FlowLayout.LEFT));
panel2.add(m_MeanPrecLabel);
panel2.add(m_MeanPrecSpinner);
panel.add(panel2);
// stddev precision
m_StdDevPrecSpinner = new JSpinner();
m_StdDevPrecSpinner.addChangeListener(
new ChangeListener() {
public void stateChanged(ChangeEvent e) {
getData();
}
});
model = (SpinnerNumberModel) m_StdDevPrecSpinner.getModel();
model.setMaximum(new Integer(20));
model.setMinimum(new Integer(0));
m_StdDevPrecLabel = new JLabel("StdDev. Precision");
m_StdDevPrecLabel.setDisplayedMnemonic('S');
m_StdDevPrecLabel.setLabelFor(m_StdDevPrecSpinner);
panel2 = new JPanel(new FlowLayout(FlowLayout.LEFT));
panel2.add(m_StdDevPrecLabel);
panel2.add(m_StdDevPrecSpinner);
panel.add(panel2);
// Format
m_OutputFormatComboBox = new JComboBox(m_OutputFormatNames);
m_OutputFormatComboBox.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
getData();
}
});
m_OutputFormatLabel = new JLabel("Output Format");
m_OutputFormatLabel.setDisplayedMnemonic('F');
m_OutputFormatLabel.setLabelFor(m_OutputFormatComboBox);
panel2 = new JPanel(new FlowLayout(FlowLayout.LEFT));
panel2.add(m_OutputFormatLabel);
panel2.add(m_OutputFormatComboBox);
panel.add(panel2);
// Average
m_ShowAverageCheckBox = new JCheckBox("");
m_ShowAverageCheckBox.addChangeListener(
new ChangeListener() {
public void stateChanged(ChangeEvent e) {
getData();
}
});
m_ShowAverageLabel = new JLabel("Show Average");
m_ShowAverageLabel.setDisplayedMnemonic('A');
m_ShowAverageLabel.setLabelFor(m_ShowAverageCheckBox);
panel2 = new JPanel(new FlowLayout(FlowLayout.LEFT));
panel2.add(m_ShowAverageLabel);
panel2.add(m_ShowAverageCheckBox);
panel.add(panel2);
// Remove filter classname
m_RemoveFilterNameCheckBox = new JCheckBox("");
m_RemoveFilterNameCheckBox.addChangeListener(
new ChangeListener() {
public void stateChanged(ChangeEvent e) {
getData();
}
});
m_RemoveFilterNameLabel = new JLabel("Remove filter classnames");
m_RemoveFilterNameLabel.setDisplayedMnemonic('R');
m_RemoveFilterNameLabel.setLabelFor(m_RemoveFilterNameCheckBox);
panel2 = new JPanel(new FlowLayout(FlowLayout.LEFT));
panel2.add(m_RemoveFilterNameLabel);
panel2.add(m_RemoveFilterNameCheckBox);
panel.add(panel2);
// Advanced setup
m_ResultMatrix = ExperimenterDefaults.getOutputFormat();
m_ResultMatrixEditor = new GenericObjectEditor(true);
m_ResultMatrixEditor.setClassType(ResultMatrix.class);
m_ResultMatrixEditor.setValue(m_ResultMatrix);
m_ResultMatrixEditor.addPropertyChangeListener(
new PropertyChangeListener() {
public void propertyChange(PropertyChangeEvent e) {
// user selected different class?
if (!m_ResultMatrix.getClass().equals(m_ResultMatrixEditor.getValue().getClass())) {
// if it's the preferred class, then automaticallly use the Experimenter defaults
if (m_ResultMatrixEditor
.getValue()
.getClass()
.equals(ExperimenterDefaults.getOutputFormat().getClass())) {
m_ResultMatrix = ExperimenterDefaults.getOutputFormat();
m_ResultMatrixEditor.setValue(ExperimenterDefaults.getOutputFormat());
} else {
m_ResultMatrix = (ResultMatrix) m_ResultMatrixEditor.getValue();
}
setData();
}
repaint();
}
});
((GenericObjectEditor.GOEPanel) m_ResultMatrixEditor.getCustomEditor())
.addOkListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
m_ResultMatrix = (ResultMatrix) m_ResultMatrixEditor.getValue();
setData();
}
});
m_ResultMatrixPanel = new PropertyPanel(m_ResultMatrixEditor, false);
m_ResultMatrixLabel = new JLabel("Advanced setup");
panel2 = new JPanel(new FlowLayout(FlowLayout.LEFT));
panel2.add(m_ResultMatrixLabel);
panel2.add(m_ResultMatrixPanel);
panel.add(panel2);
// Buttons
panel = new JPanel(new FlowLayout(FlowLayout.RIGHT));
getContentPane().add(panel, BorderLayout.SOUTH);
m_CancelButton = new JButton("Cancel");
m_CancelButton.setMnemonic('C');
m_CancelButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
m_Result = CANCEL_OPTION;
setVisible(false);
}
});
m_OkButton = new JButton("OK");
m_OkButton.setMnemonic('O');
m_OkButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
getData();
m_Result = APPROVE_OPTION;
setVisible(false);
}
});
panel.add(m_OkButton);
panel.add(m_CancelButton);
// default button
getRootPane().setDefaultButton(m_OkButton);
// initial layout (to get widths and heights)
pack();
// adjust dimensions
m_MeanPrecLabel.setPreferredSize(
new Dimension(m_RemoveFilterNameLabel.getWidth(), m_MeanPrecLabel.getHeight()));
m_MeanPrecSpinner.setPreferredSize(
new Dimension(m_MeanPrecSpinner.getWidth() * 3, m_MeanPrecSpinner.getHeight()));
m_StdDevPrecLabel.setPreferredSize(
new Dimension(m_RemoveFilterNameLabel.getWidth(), m_StdDevPrecLabel.getHeight()));
m_StdDevPrecSpinner.setPreferredSize(
new Dimension(m_StdDevPrecSpinner.getWidth() * 3, m_StdDevPrecSpinner.getHeight()));
m_OutputFormatLabel.setPreferredSize(
new Dimension(m_RemoveFilterNameLabel.getWidth(), m_OutputFormatLabel.getHeight()));
m_ShowAverageLabel.setPreferredSize(
new Dimension(m_RemoveFilterNameLabel.getWidth(), m_ShowAverageLabel.getHeight()));
m_ResultMatrixLabel.setPreferredSize(
new Dimension(m_RemoveFilterNameLabel.getWidth(), m_ResultMatrixLabel.getHeight()));
m_ResultMatrixPanel.setPreferredSize(
new Dimension(
(int) (m_ResultMatrixPanel.getWidth() * 1.5), m_ResultMatrixPanel.getHeight()));
// final layout
pack();
}
