/*
* Copyright (c) 2010 The Jackson Laboratory
*
* This is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This software is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this software. If not, see <http://www.gnu.org/licenses/>.
*/
package org.jax.bham.test;
import java.awt.Frame;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.HashSet;
import java.util.Set;
import javax.swing.JDialog;
import org.jax.bham.project.BhamProject;
import org.jax.haplotype.analysis.HaplotypeAssociationTest;
import org.jax.haplotype.analysis.HaplotypeDataSource;
import org.jax.haplotype.analysis.PhenotypeDataSource;
import org.jax.util.datastructure.SequenceUtilities;
import org.jax.util.gui.MessageDialogUtilities;
/**
* This dialog allows the user to specify the parameters for a haplotype
* association test
* @author <A HREF="mailto:keith.sheppard@jax.org">Keith Sheppard</A>
*/
public class EMMATestDialog extends JDialog
{
/**
* every {@link java.io.Serializable} is supposed to have one of these
*/
private static final long serialVersionUID = -1118077394451572390L;
private final BhamProject project;
/**
* Constructor
* @param parent
* the parent to use for this dialog
* @param project
* the project to create a test for
*/
public EMMATestDialog(
Frame parent,
BhamProject project)
{
super(parent, "Haplotype Association Test", false);
this.project = project;
this.initComponents();
this.postGuiInit();
}
/**
* handle the initialization not done by the GUI builder
*/
private void postGuiInit()
{
for(HaplotypeDataSource hapDataSrc: this.project.getHaplotypeDataSources())
{
this.haplotypeDataSourceComboBox.addItem(hapDataSrc);
}
for(PhenotypeDataSource phenoDataSrc: this.project.getPhenotypeDataSources())
{
this.phenotypeDataSourceComboBox.addItem(phenoDataSrc);
}
this.okButton.addActionListener(new ActionListener()
{
/**
* {@inheritDoc}
*/
public void actionPerformed(ActionEvent e)
{
EMMATestDialog.this.ok();
}
});
this.cancelButton.addActionListener(new ActionListener()
{
/**
* {@inheritDoc}
*/
public void actionPerformed(ActionEvent e)
{
EMMATestDialog.this.cancel();
}
});
this.helpButton.addActionListener(new ActionListener()
{
/**
* {@inheritDoc}
*/
public void actionPerformed(ActionEvent e)
{
EMMATestDialog.this.showHelp();
}
});
}
private void showHelp()
{
MessageDialogUtilities.inform(
this,
"Sorry, no help yet..",
"Help Not Implemented");
}
private void cancel()
{
this.dispose();
}
/**
* Getter for the selected haplotype data source
* @return
* the selected haplotype data source
*/
private HaplotypeDataSource getSelectedHaplotypeDataSource()
{
return (HaplotypeDataSource)this.haplotypeDataSourceComboBox.getSelectedItem();
}
/**
* Getter for the selected phenotype data source
* @return
* the selected phenotype data source
*/
private PhenotypeDataSource getSelectedPhenotypeDataSource()
{
return (PhenotypeDataSource)this.phenotypeDataSourceComboBox.getSelectedItem();
}
private String getSelectedName()
{
return this.nameTextField.getText().trim();
}
private void ok()
{
if(this.validateData())
{
// if(this.cacheResultsCheckBox.isSelected())
// {
// // precompute results and add them to the project
// CachingHaplotypeAssociationTest haplotypeAssociationTest =
// new CachingHaplotypeAssociationTest(
// this.getSelectedName(),
// this.getSelectedHaplotypeDataSource(),
// this.getSelectedPhenotypeDataSource());
// this.project.addHaplotypeAssociationTest(haplotypeAssociationTest);
//
// PrecomputeHaplotypeAssociationTestResultsTask exportTask =
// new PrecomputeHaplotypeAssociationTestResultsTask(
// haplotypeAssociationTest);
// MultiTaskProgressPanel progressTracker =
// BhamApplication.getInstance().getBhamFrame().getMultiTaskProgress();
// progressTracker.trackTaskProgress(exportTask);
// new Thread(exportTask).start();
// }
// else
{
// add test results to the project without precomputing
HaplotypeAssociationTest haplotypeAssociationTest =
new HaplotypeAssociationTest(
this.getSelectedName(),
this.getSelectedHaplotypeDataSource(),
this.getSelectedPhenotypeDataSource());
this.project.addHaplotypeAssociationTest(haplotypeAssociationTest);
}
this.dispose();
}
}
private boolean validateData()
{
String errorMessage = null;
if(this.getSelectedName().length() == 0)
{
errorMessage =
"Please enter a name for the test before continuing";
}
else if(this.getSelectedHaplotypeDataSource() == null)
{
errorMessage =
"You cannot perform a haplotype association test without " +
"any haplotype data sources.";
}
else if(this.getSelectedPhenotypeDataSource() == null)
{
errorMessage =
"You cannot perform a haplotype association test without " +
"any phenotype data sources.";
}
if(errorMessage == null)
{
Set<String> haploStrains = this.getSelectedHaplotypeDataSource().getAvailableStrains();
Set<String> phenoStrains = this.getSelectedPhenotypeDataSource().getPhenotypeData().keySet();
if(haploStrains.equals(phenoStrains))
{
return true;
}
else
{
// make sure that the user is aware that the strain sets do
// not completely overlap
Set<String> haploOnlyStrains = new HashSet<String>(haploStrains);
haploOnlyStrains.removeAll(phenoStrains);
Set<String> phenoOnlyStrains = new HashSet<String>(phenoStrains);
phenoOnlyStrains.removeAll(haploStrains);
Set<String> commonStrains = new HashSet<String>(haploStrains);
commonStrains.retainAll(phenoStrains);
boolean performTest = MessageDialogUtilities.ask(
this,
"[" + SequenceUtilities.toString(haploOnlyStrains, ", ") +
"] are unique to the haplotype data and [" +
SequenceUtilities.toString(phenoOnlyStrains, ", ") +
"] are unique to the phenotype data. Would you " +
"like to perform the test using only the subset of " +
"strains that they have in common: [" +
SequenceUtilities.toString(commonStrains, ", ") +
"]?",
"Strains Do Not Match");
return performTest;
}
}
else
{
MessageDialogUtilities.warn(
this,
errorMessage,
"Validation Failed");
return false;
}
}
/**
* This method is called from within the constructor to
* initialize the form.
* WARNING: Do NOT modify this code. The content of this method is
* always regenerated by the Form Editor.
*/
@SuppressWarnings("all")
// <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
private void initComponents() {
javax.swing.JLabel nameLabel = new javax.swing.JLabel();
nameTextField = new javax.swing.JTextField();
javax.swing.JLabel haplotypeDataSourceLabel = new javax.swing.JLabel();
haplotypeDataSourceComboBox = new javax.swing.JComboBox();
javax.swing.JLabel phenotypeDataSourceLabel = new javax.swing.JLabel();
phenotypeDataSourceComboBox = new javax.swing.JComboBox();
javax.swing.JPanel actionPanel = new javax.swing.JPanel();
okButton = new javax.swing.JButton();
cancelButton = new javax.swing.JButton();
helpButton = new javax.swing.JButton();
setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
nameLabel.setText("Test Name:");
haplotypeDataSourceLabel.setText("Haplotype Data:");
phenotypeDataSourceLabel.setText("Phenotype Data:");
okButton.setText("OK");
actionPanel.add(okButton);
cancelButton.setText("Cancel");
actionPanel.add(cancelButton);
helpButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/images/help-16x16.png"))); // NOI18N
helpButton.setText("Help...");
actionPanel.add(helpButton);
org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane());
getContentPane().setLayout(layout);
layout.setHorizontalGroup(
layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
.add(org.jdesktop.layout.GroupLayout.TRAILING, actionPanel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 362, Short.MAX_VALUE)
.add(layout.createSequentialGroup()
.addContainerGap()
.add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
.add(nameLabel)
.add(haplotypeDataSourceLabel)
.add(phenotypeDataSourceLabel))
.add(19, 19, 19)
.add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
.add(layout.createSequentialGroup()
.add(phenotypeDataSourceComboBox, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
.addContainerGap(174, Short.MAX_VALUE))
.add(layout.createSequentialGroup()
.add(nameTextField, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 194, Short.MAX_VALUE)
.add(27, 27, 27))
.add(layout.createSequentialGroup()
.add(haplotypeDataSourceComboBox, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
.addContainerGap())))
);
layout.setVerticalGroup(
layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
.add(layout.createSequentialGroup()
.addContainerGap()
.add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
.add(nameLabel)
.add(nameTextField, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
.add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
.add(haplotypeDataSourceLabel)
.add(haplotypeDataSourceComboBox, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
.add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
.add(phenotypeDataSourceLabel)
.add(phenotypeDataSourceComboBox, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED, 8, Short.MAX_VALUE)
.add(actionPanel, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
);
pack();
}// </editor-fold>//GEN-END:initComponents
// Variables declaration - do not modify//GEN-BEGIN:variables
private javax.swing.JButton cancelButton;
private javax.swing.JComboBox haplotypeDataSourceComboBox;
private javax.swing.JButton helpButton;
private javax.swing.JTextField nameTextField;
private javax.swing.JButton okButton;
private javax.swing.JComboBox phenotypeDataSourceComboBox;
// End of variables declaration//GEN-END:variables
}