package org.cytoscape.ClusterViz.internal.algorithmPanels;
import javax.swing.*;
import org.cytoscape.ClusterViz.internal.ClusterUtil;
import org.cytoscape.ClusterViz.internal.CollapsiblePanel;
import org.cytoscape.ClusterViz.internal.MyTipTool;
import org.cytoscape.ClusterViz.internal.ParameterSet;
import org.cytoscape.application.swing.CySwingApplication;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.text.DecimalFormat;
public class FAGECPanel extends JPanel{
private CySwingApplication desktopApp;
private final ClusterUtil mcodeUtil;
ParameterSet currentParameters;
private DecimalFormat decimal; // used in the formatted text fields
JCheckBox overlapped;
JFormattedTextField fThreshold;
JFormattedTextField cliqueSizeThreshold;
JFormattedTextField complexSizeThreshold;
JRadioButton weak; // use weak module definition
JRadioButton strong; // use strong module definition
JPanel weakPanel;
JPanel cliqueSizePanel;
public FAGECPanel(CySwingApplication swingApplication, ClusterUtil mcodeUtil){
desktopApp=swingApplication;
this.mcodeUtil = mcodeUtil;
this.currentParameters = this.mcodeUtil.getCurrentParameters().getParamsCopy(null);
// currentParameters = ParameterSet.getInstance().getParamsCopy(null);
decimal = new DecimalFormat();
decimal.setParseIntegerOnly(true);
this.setLayout(new BorderLayout());
this.setBorder(BorderFactory.createTitledBorder(""));
//the collapsible panel
CollapsiblePanel collapsiblePanel = new CollapsiblePanel("FAG-EC Options");
JPanel panel = new JPanel();
panel.setLayout(new BoxLayout(panel,BoxLayout.Y_AXIS));
panel.setBorder(BorderFactory.createTitledBorder(""));
//the radio botton panel
JPanel functionPanel=new JPanel();
functionPanel.setLayout(new BorderLayout());
//the radio bottons
weak = new JRadioButton("Weak",true);
weak.setToolTipText("use weak module definition");
strong = new JRadioButton("Strong", false);
strong.setToolTipText("use strong module definition");
ButtonGroup choices = new ButtonGroup();
choices.add(weak);
choices.add(strong);
weak.addActionListener(new FunctionAction());
strong.addActionListener(new FunctionAction());
functionPanel.add(weak,BorderLayout.WEST);
functionPanel.add(strong,BorderLayout.CENTER);
//the weak module definition parameter input Panel
weakPanel = new JPanel();
weakPanel.setLayout(new BorderLayout());
//the label
JLabel label=new JLabel("Threshold"); //Clique Size Threshold input
fThreshold = new JFormattedTextField(decimal) {
public JToolTip createToolTip() {
return new MyTipTool();
}
};
//the input text field
fThreshold.setColumns(3);
fThreshold.addPropertyChangeListener("value", new FAGECPanel.FormattedTextFieldAction());
String tip2 = "threshold to define a module\n" +
"It stands for the proportion of\n"+
"the indegree to the outdegree of a clique";
fThreshold.setToolTipText(tip2);
fThreshold.setText((new Double(currentParameters.getfThreshold()).toString()));
weakPanel.add(fThreshold,BorderLayout.EAST);
weakPanel.add(label,BorderLayout.WEST);
weakPanel.setVisible(true);
//the cliqueSize Panel
cliqueSizePanel=createCliqueSizePanel();
//the ComplexSize Panel
JPanel complexSizePanel=createComplexSizePanel();
//Produce Overlapped Complexes input
JLabel overlapLabel = new JLabel(" Produce Overlapped Complexes");
overlapped = new JCheckBox() {
public JToolTip createToolTip() {
return new MyTipTool();
}
};
overlapped.addItemListener(new overlappedCheckBoxAction());
String overlapTip = "Produce overlapped module.";
overlapped.setToolTipText(overlapTip);
overlapped.setSelected(currentParameters.isOverlapped());
JPanel overlapPanel = new JPanel() {
public JToolTip createToolTip() {
return new MyTipTool();
}
};
overlapPanel.setLayout(new BorderLayout());
overlapPanel.setToolTipText(overlapTip);
overlapPanel.add(overlapLabel, BorderLayout.WEST);
overlapPanel.add(overlapped, BorderLayout.EAST);
panel.add(functionPanel);
panel.add(weakPanel);
panel.add(complexSizePanel);
panel.add(overlapPanel);
panel.add(cliqueSizePanel);
cliqueSizePanel.setVisible(currentParameters.isOverlapped());
collapsiblePanel.getContentPane().add(panel, BorderLayout.NORTH);
collapsiblePanel.setToolTipText("Customize parameters for FAG-EC (Optional)");
this.add(collapsiblePanel);
}
private class FunctionAction extends AbstractAction {
public void actionPerformed(ActionEvent e) {
if (weak.isSelected()) {
currentParameters.setWeak(true);
weakPanel.setVisible(true);
} else {
currentParameters.setWeak(false);
weakPanel.setVisible(false);
}
}
}
/**
* Handles setting for the text field parameters that are numbers.
* Makes sure that the numbers make sense.
*/
private class FormattedTextFieldAction implements PropertyChangeListener {
public void propertyChange(PropertyChangeEvent e) {
currentParameters=mcodeUtil.getMainPanel().getCurrentParamsCopy();//
JFormattedTextField source = (JFormattedTextField) e.getSource();
String message = "Invaluled input\n";
boolean invalid = false;
if (source == cliqueSizeThreshold) {
Number value = (Number) cliqueSizeThreshold.getValue();
if ((value != null) && (value.intValue() >= 0) && (value.intValue() <= 10)) {
currentParameters.setCliqueSizeThreshold(value.intValue());
} else {
source.setValue(new Double (currentParameters.getCliqueSizeThreshold()));
message += "clique size cutoff should\n" +
"be set between 0 and 10.";
invalid = true;
}
}else if (source == fThreshold) {
Number value = (Number) fThreshold.getValue();
if ((value != null) && (value.doubleValue() >= 1.0) && (value.doubleValue() <= 10.0)) {
currentParameters.setfThreshold(value.doubleValue());
} else {
source.setValue(new Double (currentParameters.getfThreshold()));
message += "module threshold should\n" +
"be set between 1 and 10.";
invalid = true;
}
}else if (source == complexSizeThreshold) {
Number value = (Number) complexSizeThreshold.getValue();
if ((value != null) && (value.intValue() >= 0)) {
currentParameters.setComplexSizeThreshold(value.intValue());
} else {
source.setValue(new Double (currentParameters.getComplexSizeThreshold()));
message += "size of output module cutoff should\n" +
"be greater than 0.";
invalid = true;
}
}
if (invalid) {
JOptionPane.showMessageDialog(desktopApp.getJFrame(), message, "paramter out of boundary", JOptionPane.WARNING_MESSAGE);
}
}
}
private JPanel createCliqueSizePanel(){
JPanel panel;
//the label
JLabel sizeThresholdLabel=new JLabel(" CliqueSize Threshold"); //Clique Size Threshold input
cliqueSizeThreshold = new JFormattedTextField(decimal) {
public JToolTip createToolTip() {
return new MyTipTool();
}
};
//the input text field
cliqueSizeThreshold.setColumns(3);
cliqueSizeThreshold.addPropertyChangeListener("value", new FAGECPanel.FormattedTextFieldAction());
String tip = "size cutoff of maximal clique\n" +
"maximal cliques smaller than this will be\n" +
"regarded as subordinate and filtered\n"+
"the value is recommended to be set 2~5";
cliqueSizeThreshold.setToolTipText(tip);
cliqueSizeThreshold.setText((new Integer(currentParameters.getCliqueSizeThreshold()).toString()));
//the panel
panel = new JPanel() {
public JToolTip createToolTip() {
return new MyTipTool();
}
};
//add the components to the panel
panel.setLayout(new BorderLayout());
panel.setToolTipText(tip);
panel.add(sizeThresholdLabel, BorderLayout.WEST);
panel.add(cliqueSizeThreshold, BorderLayout.EAST);
return panel;
}
private JPanel createComplexSizePanel(){
JPanel panel=new JPanel();
panel.setLayout(new BorderLayout());
//the label
JLabel sizeThresholdLabel2=new JLabel(" ComplexSize Threshold"); //Clique Size Threshold input
//the input text field
complexSizeThreshold = new JFormattedTextField(decimal) {
public JToolTip createToolTip() {
return new MyTipTool();
}
};
complexSizeThreshold.setColumns(3);
complexSizeThreshold.addPropertyChangeListener("value", new FAGECPanel.FormattedTextFieldAction());
String tip3 = "size cutoff of modules to be outputed\n" +
"modules smaller than this will be filtered";
complexSizeThreshold.setToolTipText(tip3);
complexSizeThreshold.setText((new Integer(currentParameters.getComplexSizeThreshold()).toString()));
panel.add(sizeThresholdLabel2,BorderLayout.WEST);
panel.add(complexSizeThreshold,BorderLayout.EAST);
return panel;
}
/**
* Handles setting of the produce-overlapped-complexes parameter
*/
private class overlappedCheckBoxAction implements ItemListener {
public void itemStateChanged(ItemEvent e) {
currentParameters=mcodeUtil.getMainPanel().getCurrentParamsCopy();//
if (e.getStateChange() == ItemEvent.SELECTED) {
currentParameters.setOverlapped(true);
cliqueSizePanel.setVisible(true);
} else {
currentParameters.setOverlapped(false);
cliqueSizePanel.setVisible(false);
}
}
}
}