net.maizegenetics.analysis.chart.QQDisplayPlugin Maven / Gradle / Ivy
/*
* QQDisplayPlugin.java
*
* Created on December 13, 2010
*
*/
package net.maizegenetics.analysis.chart;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Frame;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Insets;
import java.awt.event.ActionEvent;
import java.awt.event.KeyEvent;
import java.net.URL;
import java.util.ArrayList;
import javax.swing.ImageIcon;
import net.maizegenetics.plugindef.DataSet;
import java.util.List;
import javax.swing.BorderFactory;
import javax.swing.JButton;
import javax.swing.JDialog;
import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JSlider;
import javax.swing.JTextField;
import javax.swing.ListModel;
import javax.swing.ListSelectionModel;
import javax.swing.event.ChangeEvent;
import net.maizegenetics.util.TableReport;
import net.maizegenetics.plugindef.Datum;
/**
*
* @author yz79
*/
public class QQDisplayPlugin extends AbstractDisplayPlugin {
/**
* Creates a new instance of QQDisplayPlugin
*/
public QQDisplayPlugin(Frame parentFrame, boolean isInteractive) {
super(parentFrame, isInteractive);
}
public DataSet performFunction(DataSet input) {
try {
List tableInList = input.getDataOfType(TableReport.class);
if (tableInList.size() != 1) {
String message = "Invalid selection. Please select one table result.";
if (isInteractive()) {
JOptionPane.showMessageDialog(getParentFrame(), message);
} else {
System.out.println(message);
}
return null;
}
TableReport myTableReport = (TableReport) tableInList.get(0).getData();
if (isInteractive()) {
try {
PlotOptionsQQDialog myOptions = new PlotOptionsQQDialog(this.getParentFrame(), getTraits(myTableReport), splitTable(myTableReport));
myOptions.setLocationRelativeTo(getParentFrame());
myOptions.setVisible(true);
if (myOptions.isCanceled() == false) {
QQDisplayPluginDialog myDialog = new QQDisplayPluginDialog(this.getParentFrame(), this, myTableReport, myOptions.getSliderValue(), splitTable(myTableReport), myOptions.getTraitIndices());
myDialog.setLocationRelativeTo(getParentFrame());
myDialog.setVisible(true);
}
} catch (Exception ex) {
ex.printStackTrace();
JOptionPane.showMessageDialog(this.getParentFrame(), "Unable to create QQ plot " + ex);
} catch (Error er) {
er.printStackTrace();
JOptionPane.showMessageDialog(this.getParentFrame(), "Unable to create QQ plot " + er);
}
}
return null;
} finally {
fireProgress(100);
}
}
private ArrayList splitTable(TableReport table) {
ArrayList indexes = new ArrayList();
int numRows = (int) table.getRowCount();
String previousTrait = "";
for (int i = 0; i < numRows; i++) {
if (!previousTrait.equals((String) table.getValueAt(i, 0))) {
if (!((String) table.getValueAt(i, 1)).equals("None")) {
indexes.add(new Integer(i));
previousTrait = (String) table.getValueAt(i, 0);
if (i > 1) {
indexes.add(new Integer(i));
}
} else if (i != 0) {
indexes.add(new Integer(i));
indexes.add(new Integer(i + 1));
previousTrait = (String) table.getValueAt(i + 1, 0);
}
}
}
indexes.add(new Integer(numRows));
return indexes;
}
private String[] getTraits(TableReport table) {
ArrayList traitArray = new ArrayList();
int numRows = (int) table.getRowCount();
String previousTrait = "";
for (int i = 0; i < numRows; i++) {
if (!previousTrait.equals((String) table.getValueAt(i, 0))) {
previousTrait = (String) table.getValueAt(i, 0);
traitArray.add(previousTrait);
}
}
String[] traits = new String[traitArray.size()];
for (int i = 0; i < traitArray.size(); i++) {
traits[i] = traitArray.get(i);
}
return traits;
}
/**
* Icon for this plugin to be used in buttons, etc.
*
* @return ImageIcon
*/
@Override
public ImageIcon getIcon() {
URL imageURL = QQDisplayPlugin.class.getResource("/net/maizegenetics/analysis/images/QQPlot.gif");
if (imageURL == null) {
return null;
} else {
return new ImageIcon(imageURL);
}
}
/**
* Button name for this plugin to be used in buttons, etc.
*
* @return String
*/
@Override
public String getButtonName() {
return "QQ Plot";
}
/**
* Tool Tip Text for this plugin
*
* @return String
*/
@Override
public String getToolTipText() {
return "Display QQ Plot";
}
}
class QQDisplayPluginDialog extends JDialog {
XYScatterAndLinePanel myQQPlot;
TableReport myTableReport;
JButton myCloseButton = new JButton();
JPanel myMainPanel;
JPanel myOptionPanel = new JPanel();
public QQDisplayPluginDialog(Frame f, QQDisplayPlugin plugin, TableReport theTableReport, int countToDisplay, ArrayList tableIndices, int[] indices) {
super(f, "QQ Plot", false);
myTableReport = theTableReport;
try {
jbInit();
myQQPlot = new XYScatterAndLinePanel(plugin, theTableReport, countToDisplay, tableIndices, indices);
// myQQFigurePanel = new QQComponent(theTableReport);
getContentPane().add(myQQPlot, BorderLayout.CENTER);
pack();
} catch (Exception ex) {
ex.printStackTrace();
JOptionPane.showMessageDialog(this.getParent(), "Unable to create QQ plot " + ex);
}
repaint();
}
void jbInit() throws Exception {
myCloseButton.setText("Close");
myCloseButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
closeButton_actionPerformed(e);
}
});
myOptionPanel.add(myCloseButton, new GridBagConstraints(0, 0, 0, 0, 0.0, 0.0, GridBagConstraints.SOUTHEAST, GridBagConstraints.NONE, new Insets(0, 0, 0, 0), 0, 0));
getContentPane().add(myOptionPanel);
}
void closeButton_actionPerformed(ActionEvent e) {
dispose();
}
}
class PlotOptionsQQDialog extends JDialog {
boolean isCanceled = true;
String[] myTraits;
private JPanel mainPanel = new JPanel();
private JButton okayButton = new JButton();
private JButton cancelButton = new JButton();
private JLabel sliderLabel1 = new JLabel();
private JSlider slider = new JSlider();
private JLabel countLabel1 = new JLabel();
private JLabel listLabel1 = new JLabel();
private JLabel listLabel2 = new JLabel();
private JTextField countTextField = new JTextField();
private GridBagLayout gridBagLayout2 = new GridBagLayout();
private JList list1 = new JList();
private JList list2 = new JList();
private JButton addAllButton = new JButton();
private JButton addOneButton = new JButton();
private JButton removeAllButton = new JButton();
private JButton removeOneButton = new JButton();
public PlotOptionsQQDialog(Frame f, String[] traits, ArrayList indexes) {
super(f, "QQ Plot Options", true);
myTraits = traits;
int numSites = indexes.get(1) - indexes.get(0);
slider.setMinimum(1);
slider.setMaximum(numSites);
slider.setValue((int) (numSites * 0.01));
countTextField.setText("" + (int) (numSites * 0.01));
try {
initUI();
pack();
} catch (Exception ex) {
ex.printStackTrace();
}
}
void initUI() throws Exception {
mainPanel.setMinimumSize(new Dimension(400, 230));
mainPanel.setPreferredSize(new Dimension(400, 230));
mainPanel.setLayout(gridBagLayout2);
listLabel1.setText("Available Traits");
listLabel2.setText("Traits to Plot");
list1.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
list1.setLayoutOrientation(JList.VERTICAL);
list1.setVisibleRowCount(5);
list1.setMinimumSize(new Dimension(100, 104));
list1.setBackground(Color.white);
list1.setBorder(BorderFactory.createLineBorder(Color.black));
list2.setListData(myTraits);
list2.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
list2.setLayoutOrientation(JList.VERTICAL);
list2.setVisibleRowCount(5);
list2.setMinimumSize(new Dimension(100, 104));
list2.setBorder(BorderFactory.createLineBorder(Color.black));
addAllButton.setText(">>");
addAllButton.setMaximumSize(new Dimension(63, 27));
addAllButton.setMinimumSize(new Dimension(63, 27));
addAllButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
addAllButton_actionPerformed(e);
}
});
addOneButton.setText(">");
addOneButton.setMaximumSize(new Dimension(63, 27));
addOneButton.setMinimumSize(new Dimension(63, 27));
addOneButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
addOneButton_actionPerformed(e);
}
});
removeOneButton.setText("<");
removeOneButton.setMaximumSize(new Dimension(63, 27));
removeOneButton.setMinimumSize(new Dimension(63, 27));
removeOneButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
removeOneButton_actionPerformed(e);
}
});
removeAllButton.setText("<<");
removeAllButton.setMaximumSize(new Dimension(63, 27));
removeAllButton.setMinimumSize(new Dimension(63, 27));
removeAllButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
removeAllButton_actionPerformed(e);
}
});
sliderLabel1.setText("Plot Density:");
sliderLabel1.setToolTipText("Plot Density is then number of Significant Points plotted without removing data. The rest of the data is plotted at a regular interval to maintain the trend without drawing all the points.");
slider.addChangeListener(new javax.swing.event.ChangeListener() {
public void stateChanged(ChangeEvent ce) {
slider_actionPerformed(ce);
}
});
if (myTraits.length == 1) {
mainPanel.setMinimumSize(new Dimension(400, 100));
mainPanel.setPreferredSize(new Dimension(400, 100));
listLabel1.setVisible(false);
listLabel2.setVisible(false);
list1.setVisible(false);
list2.setVisible(false);
addAllButton.setVisible(false);
addOneButton.setVisible(false);
removeOneButton.setVisible(false);
removeAllButton.setVisible(false);
}
countTextField.addKeyListener(new java.awt.event.KeyListener() {
public void keyTyped(KeyEvent ke) {
// countTextField_keyTyped(ke);
}
public void keyPressed(KeyEvent ke) {
// throw new UnsupportedOperationException("Not supported yet.");
}
public void keyReleased(KeyEvent ke) {
countTextField_keyTyped(ke);
}
});
countLabel1.setText("of " + slider.getMaximum() + " points per trait.");
okayButton.setMaximumSize(new Dimension(95, 27));
okayButton.setMinimumSize(new Dimension(95, 27));
okayButton.setText("Okay");
okayButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
okayButton_actionPerformed(e);
}
});
cancelButton.setMaximumSize(new Dimension(95, 27));
cancelButton.setMinimumSize(new Dimension(95, 27));
cancelButton.setText("Cancel");
cancelButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
cancelButton_actionPerformed(e);
}
});
mainPanel.add(listLabel1, new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0, GridBagConstraints.CENTER, GridBagConstraints.NONE, new Insets(10, 0, 5, 0), 0, 0));
mainPanel.add(listLabel2, new GridBagConstraints(2, 0, 1, 1, 0.0, 0.0, GridBagConstraints.CENTER, GridBagConstraints.NONE, new Insets(10, 0, 5, 0), 0, 0));
mainPanel.add(new JScrollPane(list1), new GridBagConstraints(0, 1, 1, 4, 1.0, 1.0, GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0, 5, 0, 0), 0, 0));
mainPanel.add(new JScrollPane(list2), new GridBagConstraints(2, 1, 1, 4, 1.0, 1.0, GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0, 0, 0, 5), 0, 0));
mainPanel.add(addAllButton, new GridBagConstraints(1, 1, 1, 1, 0.0, 0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL, new Insets(0, 0, 0, 0), 0, 0));
mainPanel.add(addOneButton, new GridBagConstraints(1, 2, 1, 1, 0.0, 0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL, new Insets(0, 0, 0, 0), 0, 0));
mainPanel.add(removeOneButton, new GridBagConstraints(1, 3, 1, 1, 0.0, 0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL, new Insets(0, 0, 0, 0), 0, 0));
mainPanel.add(removeAllButton, new GridBagConstraints(1, 4, 1, 1, 0.0, 0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL, new Insets(0, 0, 0, 0), 0, 0));
mainPanel.add(sliderLabel1, new GridBagConstraints(0, 5, 1, 2, 0.0, 0.0, GridBagConstraints.LINE_END, GridBagConstraints.NONE, new Insets(0, 0, 5, 0), 0, 0));
mainPanel.add(slider, new GridBagConstraints(1, 5, 2, 1, 1.0, 1.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL, new Insets(0, 5, 0, 0), 0, 0));
mainPanel.add(countTextField, new GridBagConstraints(1, 6, 1, 1, 0.7, 0.7, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL, new Insets(0, 0, 0, 0), 0, 0));
mainPanel.add(countLabel1, new GridBagConstraints(2, 6, 1, 1, 0.0, 0.0, GridBagConstraints.LINE_START, GridBagConstraints.NONE, new Insets(0, 5, 0, 0), 0, 0));
mainPanel.add(okayButton, new GridBagConstraints(1, 7, 1, 1, 0.0, 0.0, GridBagConstraints.LINE_END, GridBagConstraints.NONE, new Insets(0, 0, 0, 0), 0, 0));
mainPanel.add(cancelButton, new GridBagConstraints(2, 7, 1, 1, 0.0, 0.0, GridBagConstraints.LINE_START, GridBagConstraints.NONE, new Insets(0, 5, 0, 0), 0, 0));
this.add(mainPanel, BorderLayout.CENTER);
}
private void addAllButton_actionPerformed(ActionEvent e) {
list1.setListData(new Object[0]);
list2.setListData(myTraits);
okayButton.setEnabled(true);
}
private void addOneButton_actionPerformed(ActionEvent e) {
Object[] selected = list1.getSelectedValues();
ListModel listModel = list2.getModel();
String[] toList = new String[listModel.getSize() + selected.length];
String[] fromList = new String[myTraits.length - toList.length];
int j = 0;
int k = 0;
int l = 0;
int m = 0;
for (int i = 0; i < myTraits.length; i++) {
if (j < selected.length && myTraits[i].equals(selected[j])) {
toList[l] = myTraits[i];
j++;
l++;
} else if (k < listModel.getSize() && myTraits[i].equals(listModel.getElementAt(k))) {
toList[l] = myTraits[i];
k++;
l++;
} else {
fromList[m] = myTraits[i];
m++;
}
}
list1.setListData(fromList);
list2.setListData(toList);
if (toList.length > 0) {
okayButton.setEnabled(true);
}
}
private void removeOneButton_actionPerformed(ActionEvent e) {
Object[] selected = list2.getSelectedValues();
ListModel listModel = list1.getModel();
String[] toList = new String[listModel.getSize() + selected.length];
String[] fromList = new String[myTraits.length - toList.length];
int j = 0;
int k = 0;
int l = 0;
int m = 0;
for (int i = 0; i < myTraits.length; i++) {
if (j < selected.length && myTraits[i].equals(selected[j])) {
toList[l] = myTraits[i];
j++;
l++;
} else if (k < listModel.getSize() && myTraits[i].equals(listModel.getElementAt(k))) {
toList[l] = myTraits[i];
k++;
l++;
} else {
fromList[m] = myTraits[i];
m++;
}
}
list2.setListData(fromList);
list1.setListData(toList);
if (fromList.length < 1) {
okayButton.setEnabled(false);
}
}
private void removeAllButton_actionPerformed(ActionEvent e) {
list2.setListData(new Object[0]);
list1.setListData(myTraits);
okayButton.setEnabled(false);
}
private void okayButton_actionPerformed(ActionEvent e) {
isCanceled = false;
setVisible(false);
}
private void cancelButton_actionPerformed(ActionEvent e) {
isCanceled = true;
setVisible(false);
}
private void slider_actionPerformed(ChangeEvent cd) {
countTextField.setText("" + slider.getValue());
}
private void countTextField_keyTyped(KeyEvent e) {
try {
if (!countTextField.getText().equals("")) {
int value = Integer.valueOf(countTextField.getText());
if (value >= slider.getMinimum() && value <= slider.getMaximum()) {
slider.setValue(value);
} else if (value <= slider.getMinimum()) {
slider.setValue(slider.getMinimum());
countTextField.setText("" + slider.getMinimum());
} else if (value >= slider.getMaximum()) {
slider.setValue(slider.getMaximum());
countTextField.setText("" + slider.getMaximum());
}
}
} catch (NumberFormatException nfe) {
countTextField.setText("" + slider.getValue());
}
}
public boolean isCanceled() {
return isCanceled;
}
public int getSliderValue() {
return slider.getValue();
}
public Dimension getMinimumSize() {
return new Dimension(600, 600);
}
public String[] getSelectedTraits() {
ListModel list = list2.getModel();
String[] traits = new String[list.getSize()];
for (int i = 0; i < traits.length; i++) {
traits[i] = list.getElementAt(i).toString();
}
return traits;
}
public int[] getTraitIndices() {
ListModel list = list2.getModel();
int[] indices = new int[list.getSize()];
int j = 0;
for (int i = 0; i < myTraits.length; i++) {
if (j < list.getSize() && myTraits[i].equals(list.getElementAt(j))) {
indices[j] = i;
j++;
}
}
return indices;
}
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