/*
* 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.cross.gui;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.event.ItemEvent;
import java.util.logging.Logger;
import javax.swing.DefaultListModel;
import javax.swing.JList;
import javax.swing.ListSelectionModel;
import org.jax.analyticgraph.data.NamedDataMatrix;
import org.jax.analyticgraph.data.ReorderedNamedDataMatrix;
import org.jax.analyticgraph.framework.GraphCoordinateConverter;
import org.jax.analyticgraph.framework.SimpleGraphCoordinateConverter;
import org.jax.analyticgraph.graph.AxisRenderingGraph;
import org.jax.analyticgraph.graph.scatterplot.ScatterPlot;
import org.jax.qtl.QTL;
import org.jax.qtl.cross.Cross;
import org.jax.qtl.gui.SimpleGraphContainerPanel;
/**
* Dialog for choosing which phenotypes to show in a scatterplot.
*/
public class ShowScatterPlotDialog extends javax.swing.JDialog
{
/**
* every {@link java.io.Serializable} is supposed to have one of these
*/
private static final long serialVersionUID = -3852079975247381225L;
private volatile Cross selectedCross;
private final Cross[] availableCrosses;
private static final Logger LOG = Logger.getLogger(
ShowScatterPlotDialog.class.getName());
/**
* Constructor
* @param parent
* the parent frame for this dialog
* @param selectedCross
* the selected cross
* @param availableCrosses
* the available crosses
*/
public ShowScatterPlotDialog(
java.awt.Frame parent,
Cross selectedCross,
Cross[] availableCrosses)
{
super(parent, true);
this.selectedCross = selectedCross;
this.availableCrosses = availableCrosses;
this.initComponents();
this.postGuiInit();
}
/**
* take care of any GUI initialization that isn't handled by the
* GUI builder
*/
private void postGuiInit()
{
this.xPhenotypeList.setModel(
new DefaultListModel());
this.xPhenotypeList.setSelectionMode(
ListSelectionModel.SINGLE_SELECTION);
this.yPhenotypeList.setModel(
new DefaultListModel());
this.yPhenotypeList.setSelectionMode(
ListSelectionModel.SINGLE_SELECTION);
Cross selectedCross = this.selectedCross;
for(Cross currCross: this.availableCrosses)
{
this.crossComboBox.addItem(currCross);
}
if(selectedCross != null)
{
this.crossComboBox.setSelectedItem(selectedCross);
}
}
/**
* Rebuild the phenotype lists using the selected cross
*/
private void rebuildPhenotypeLists()
{
Cross selectedCross = this.selectedCross;
if(selectedCross != null)
{
ShowScatterPlotDialog.fillListWithPhenotypes(
selectedCross,
this.xPhenotypeList);
ShowScatterPlotDialog.fillListWithPhenotypes(
selectedCross,
this.yPhenotypeList);
if(this.xPhenotypeList.getModel().getSize() >= 2 &&
this.yPhenotypeList.getModel().getSize() >= 2)
{
this.xPhenotypeList.setSelectedIndex(0);
this.yPhenotypeList.setSelectedIndex(1);
}
}
}
/**
* Fill in the given list with phenotype name strings from the given cross
* @param selectedCross
* the source of the phenotype
* @param phenotypeList
* the list
*/
private static void fillListWithPhenotypes(
Cross selectedCross,
JList phenotypeList)
{
DefaultListModel listModel = (DefaultListModel)phenotypeList.getModel();
listModel.removeAllElements();
for(String phenotypeName:
selectedCross.getPhenotypeData().getDataNames())
{
listModel.addElement(phenotypeName);
}
}
/**
* 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() {
actionPanel = new javax.swing.JPanel();
okButton = new javax.swing.JButton();
cancelButton = new javax.swing.JButton();
crossLabel = new javax.swing.JLabel();
crossComboBox = new javax.swing.JComboBox();
xPhenotypeLabel = new javax.swing.JLabel();
xPhenotypeScrollPane = new javax.swing.JScrollPane();
xPhenotypeList = new javax.swing.JList();
yPhenotypeLabel = new javax.swing.JLabel();
yPhenotypeScrollPane = new javax.swing.JScrollPane();
yPhenotypeList = new javax.swing.JList();
setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
okButton.setText("OK");
okButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
okButtonActionPerformed(evt);
}
});
actionPanel.add(okButton);
cancelButton.setText("Cancel");
cancelButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
cancelButtonActionPerformed(evt);
}
});
actionPanel.add(cancelButton);
crossLabel.setText("Cross:");
crossComboBox.addItemListener(new java.awt.event.ItemListener() {
public void itemStateChanged(java.awt.event.ItemEvent evt) {
crossComboBoxItemStateChanged(evt);
}
});
xPhenotypeLabel.setText("X Axis Phenotype:");
xPhenotypeScrollPane.setViewportView(xPhenotypeList);
yPhenotypeLabel.setText("Y Axis Phenotype:");
yPhenotypeScrollPane.setViewportView(yPhenotypeList);
org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane());
getContentPane().setLayout(layout);
layout.setHorizontalGroup(
layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
.add(actionPanel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 400, Short.MAX_VALUE)
.add(layout.createSequentialGroup()
.addContainerGap()
.add(crossLabel)
.addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
.add(crossComboBox, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
.addContainerGap(289, Short.MAX_VALUE))
.add(org.jdesktop.layout.GroupLayout.TRAILING, layout.createSequentialGroup()
.addContainerGap()
.add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
.add(layout.createSequentialGroup()
.add(xPhenotypeScrollPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 177, Short.MAX_VALUE)
.addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED))
.add(layout.createSequentialGroup()
.add(xPhenotypeLabel)
.add(74, 74, 74)))
.add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
.add(yPhenotypeLabel)
.add(org.jdesktop.layout.GroupLayout.TRAILING, yPhenotypeScrollPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 173, Short.MAX_VALUE))
.addContainerGap())
);
layout.setVerticalGroup(
layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
.add(layout.createSequentialGroup()
.addContainerGap()
.add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
.add(crossLabel)
.add(crossComboBox, 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(xPhenotypeLabel)
.add(yPhenotypeLabel))
.addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
.add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING)
.add(yPhenotypeScrollPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 180, Short.MAX_VALUE)
.add(xPhenotypeScrollPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 180, Short.MAX_VALUE))
.addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
.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
private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_okButtonActionPerformed
Cross selectedCross = this.selectedCross;
int selectedPhenoIndex1 = this.xPhenotypeList.getSelectedIndex();
int selectedPhenoIndex2 = this.yPhenotypeList.getSelectedIndex();
if(selectedCross != null && selectedPhenoIndex1 != -1 && selectedPhenoIndex2 != -1)
{
NamedDataMatrix<Number> allPhenoData = selectedCross.getPhenotypeData();
NamedDataMatrix<Number> selectedPhenoData =
new ReorderedNamedDataMatrix<Number>(
allPhenoData,
new int[] {selectedPhenoIndex1, selectedPhenoIndex2});
GraphCoordinateConverter coordinateConverter = new SimpleGraphCoordinateConverter(
0.0, 0.0,
1.0, 1.0);
ScatterPlot scatterPlotInterior = new ScatterPlot(coordinateConverter);
scatterPlotInterior.plotData(selectedPhenoData);
SimpleGraphCoordinateConverter coordinateConverter2 = new SimpleGraphCoordinateConverter(
0.0, 0.0,
1.0, 1.0);
AxisRenderingGraph scatterPlotWithAxes =
new AxisRenderingGraph(coordinateConverter2);
scatterPlotWithAxes.setInteriorGraph(scatterPlotInterior);
org.jax.analyticgraph.framework.Graph2DComponent graphComponent =
new org.jax.analyticgraph.framework.Graph2DComponent();
graphComponent.setBackground(Color.WHITE);
graphComponent.addGraph2D(scatterPlotWithAxes);
graphComponent.setPreferredSize(new Dimension(400, 400));
SimpleGraphContainerPanel simpleGraphContainerPanel =
new SimpleGraphContainerPanel(
graphComponent,
scatterPlotInterior);
QTL.getInstance().getDesktop().createInternalFrame(
simpleGraphContainerPanel,
"Scatter Plot: x = " +
this.xPhenotypeList.getSelectedValue().toString() +
", y = " +
this.yPhenotypeList.getSelectedValue().toString() +
" (" + selectedCross.toString() +")",
null,
this.xPhenotypeList.getSelectedValue().toString() +
"x" +
this.yPhenotypeList.getSelectedValue().toString());
}
else
{
LOG.severe(
"failed to show scatter plot: " +
"pheno 1 index: " + selectedPhenoIndex1 +
" pheno 2 index: " + selectedPhenoIndex2 +
" cross: " + selectedCross);
}
this.dispose();
}//GEN-LAST:event_okButtonActionPerformed
private void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_cancelButtonActionPerformed
this.dispose();
}//GEN-LAST:event_cancelButtonActionPerformed
private void crossComboBoxItemStateChanged(java.awt.event.ItemEvent evt) {//GEN-FIRST:event_crossComboBoxItemStateChanged
if(evt.getStateChange() == ItemEvent.SELECTED)
{
this.selectedCross = (Cross)evt.getItem();
this.rebuildPhenotypeLists();
}
}//GEN-LAST:event_crossComboBoxItemStateChanged
// Variables declaration - do not modify//GEN-BEGIN:variables
private javax.swing.JPanel actionPanel;
private javax.swing.JButton cancelButton;
private javax.swing.JComboBox crossComboBox;
private javax.swing.JLabel crossLabel;
private javax.swing.JButton okButton;
private javax.swing.JLabel xPhenotypeLabel;
private javax.swing.JList xPhenotypeList;
private javax.swing.JScrollPane xPhenotypeScrollPane;
private javax.swing.JLabel yPhenotypeLabel;
private javax.swing.JList yPhenotypeList;
private javax.swing.JScrollPane yPhenotypeScrollPane;
// End of variables declaration//GEN-END:variables
}