ScanPermutationsPanel.java

/*
 * Copyright (c) 2009 The Jackson Laboratory
 * 
 * This software was developed by Gary Churchill's Lab at The Jackson
 * Laboratory (see http://research.jax.org/faculty/churchill).
 *
 * 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.qtl.scan.gui;

import java.awt.event.ItemEvent;

import javax.swing.SpinnerNumberModel;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;

import org.jax.qtl.scan.ScanCommandBuilder;
import org.jax.qtl.scan.ScanType;

/**
 * Panel that edits the permutations portion of a scan command
 * @author <A HREF="mailto:keith.sheppard@jax.org">Keith Sheppard</A>
 */
public class ScanPermutationsPanel extends ScanCommandEditorPanel
{
    /**
     * every {@link java.io.Serializable} is supposed to have one of these
     */
    private static final long serialVersionUID = -5503455594080368863L;
    
    /**
     * the scan command that this panel edits
     */
    private final ScanCommandBuilder scanCommand;
    
    /**
     * the spinner model for permutation counts
     */
    private final SpinnerNumberModel permutationsCountModel;
    
    /**
     * Constructor
     * @param scanCommand
     *          the command to edit
     */
    public ScanPermutationsPanel(ScanCommandBuilder scanCommand)
    {
        this.scanCommand = scanCommand;
        this.permutationsCountModel = new SpinnerNumberModel(
                0,
                0,
                Integer.MAX_VALUE,
                500);
        this.initComponents();
        this.postGuiInit();
    }
    
    /**
     * Initialization code to run after the GUI builder code has completed
     */
    private void postGuiInit()
    {
        // update the spinner model to behave how we want it to
        this.permutationsCountSpinner.setModel(this.permutationsCountModel);
        this.permutationsCountModel.addChangeListener(
                new ChangeListener()
                {
                    public void stateChanged(ChangeEvent e)
                    {
                        ScanPermutationsPanel.this.permutationsCountChanged();
                    }
                });
        this.permutationsCountChanged();
    }

    /**
     * react to a change in the permutations count
     */
    private void permutationsCountChanged()
    {
        int permutationsCount =
            this.permutationsCountModel.getNumber().intValue();
        this.scanCommand.setNumberOfPermutations(
                permutationsCount);
        this.refreshGui();
        this.fireCommandModified();
    }
    
    /**
     * This function tells this panel that a component other than itself
     * has edited the {@link ScanCommandBuilder} and that we need to refresh
     * our graphics to reflect those changes.
     */
    public void refreshGui()
    {
        // this seperate x chromo option is only available for scan one
        this.seperateXChromosomePermutationsCheckBox.setVisible(
                this.scanCommand.getScanType() == ScanType.SCANONE);
        
        // update the enabled property of the other check boxes based on
        // whether or not we're performing permutations
        int permutationsCount =
            this.scanCommand.getNumberOfPermutations();
        
        this.seperateXChromosomePermutationsCheckBox.setEnabled(
                permutationsCount > 0);
        this.verboseOutputCheckBox.setEnabled(
                permutationsCount > 0);
    }

    /**
     * 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() {

        permutationsCountLabel = new javax.swing.JLabel();
        permutationsCountSpinner = new javax.swing.JSpinner();
        verboseOutputCheckBox = new javax.swing.JCheckBox();
        seperateXChromosomePermutationsCheckBox = new javax.swing.JCheckBox();

        permutationsCountLabel.setText("Number of Permutations to Perform:");

        permutationsCountSpinner.setMinimumSize(new java.awt.Dimension(100, 24));
        permutationsCountSpinner.setPreferredSize(new java.awt.Dimension(100, 24));

        verboseOutputCheckBox.setText("Print Permutations Progress to Console");
        verboseOutputCheckBox.addItemListener(new java.awt.event.ItemListener() {
            public void itemStateChanged(java.awt.event.ItemEvent evt) {
                verboseOutputCheckBoxItemStateChanged(evt);
            }
        });

        seperateXChromosomePermutationsCheckBox.setText("Seperate Permutations for X Chromosome");
        seperateXChromosomePermutationsCheckBox.addItemListener(new java.awt.event.ItemListener() {
            public void itemStateChanged(java.awt.event.ItemEvent evt) {
                seperateXChromosomePermutationsCheckBoxItemStateChanged(evt);
            }
        });

        org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(this);
        this.setLayout(layout);
        layout.setHorizontalGroup(
            layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
            .add(layout.createSequentialGroup()
                .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
                    .add(layout.createSequentialGroup()
                        .add(permutationsCountLabel)
                        .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
                        .add(permutationsCountSpinner, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
                    .add(seperateXChromosomePermutationsCheckBox)
                    .add(verboseOutputCheckBox))
                .addContainerGap(227, Short.MAX_VALUE))
        );
        layout.setVerticalGroup(
            layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
            .add(layout.createSequentialGroup()
                .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
                    .add(permutationsCountLabel)
                    .add(permutationsCountSpinner, 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(seperateXChromosomePermutationsCheckBox)
                .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
                .add(verboseOutputCheckBox))
        );
    }// </editor-fold>//GEN-END:initComponents

    private void seperateXChromosomePermutationsCheckBoxItemStateChanged(java.awt.event.ItemEvent evt) {//GEN-FIRST:event_seperateXChromosomePermutationsCheckBoxItemStateChanged
        this.scanCommand.setSeperatePermutationsForAutosome(
                evt.getStateChange() == ItemEvent.SELECTED);
        this.fireCommandModified();
    }//GEN-LAST:event_seperateXChromosomePermutationsCheckBoxItemStateChanged

    private void verboseOutputCheckBoxItemStateChanged(java.awt.event.ItemEvent evt) {//GEN-FIRST:event_verboseOutputCheckBoxItemStateChanged
        this.scanCommand.setVerbosePermutationsOutput(
                evt.getStateChange() == ItemEvent.SELECTED);
        this.fireCommandModified();
    }//GEN-LAST:event_verboseOutputCheckBoxItemStateChanged
    
    
    // Variables declaration - do not modify//GEN-BEGIN:variables
    private javax.swing.JLabel permutationsCountLabel;
    private javax.swing.JSpinner permutationsCountSpinner;
    private javax.swing.JCheckBox seperateXChromosomePermutationsCheckBox;
    private javax.swing.JCheckBox verboseOutputCheckBox;
    // End of variables declaration//GEN-END:variables

    /**
     * {@inheritDoc}
     */
    @Override
    protected ScanCommandBuilder getScanCommand()
    {
        return this.scanCommand;
    }
    
}