net.maizegenetics.analysis.popgen.LinkageDiseqDisplayPlugin Maven / Gradle / Ivy
/*
* LinkageDiseqDisplayPlugin.java
*
* Created on December 22, 2006, 5:02 PM
*
*/
package net.maizegenetics.analysis.popgen;
import net.maizegenetics.plugindef.DataSet;
import net.maizegenetics.plugindef.Datum;
import javax.swing.*;
import javax.swing.event.ChangeEvent;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.KeyEvent;
import java.awt.event.MouseEvent;
import java.net.URL;
import java.util.List;
import net.maizegenetics.analysis.chart.AbstractDisplayPlugin;
/**
*
* @author Ed Buckler
*/
public class LinkageDiseqDisplayPlugin extends AbstractDisplayPlugin {
private int upperCorner = LinkageDisequilibriumComponent.P_VALUE;
private int lowerCorner = LinkageDisequilibriumComponent.RSQUARE;
private boolean blockSchematic = true;
private boolean chromosomalView = false;
private boolean includeLabels = true;
/** Creates a new instance of LinkageDiseqDisplayPlugin */
public LinkageDiseqDisplayPlugin(Frame parentFrame, boolean isInteractive) {
super(parentFrame, isInteractive);
}
public DataSet performFunction(DataSet input) {
try {
List LDInList = input.getDataOfType(LinkageDisequilibrium.class);
if (LDInList.size() != 1) {
String message = "Invalid selection. Please select one LD result.";
if (isInteractive()) {
JOptionPane.showMessageDialog(getParentFrame(), message);
} else {
System.out.println(message);
}
return null;
}
LinkageDisequilibrium theLD = (LinkageDisequilibrium) LDInList.get(0).getData();
if (isInteractive()) {
try {
LinkageDiseqDisplayDialog myDialog = new LinkageDiseqDisplayDialog(this, theLD);
myDialog.setLocationRelativeTo(getParentFrame());
myDialog.setVisible(true);
} catch (Exception ex) {
ex.printStackTrace();
JOptionPane.showMessageDialog(this.getParentFrame(), "Unable to create LD plot " + ex);
} catch (Error er) {
er.printStackTrace();
JOptionPane.showMessageDialog(this.getParentFrame(), "Unable to create LD plot " + er);
}
} else if (getSaveFile() != null) {
// LinkageDisequilibriumComponent ldc = new LinkageDisequilibriumComponent(theLD, blockSchematic, chromosomalView, theLD.numberOfSites(), Math.max(1, theLD.numberOfSites()), Math.max(1, theLD.numberOfSites()));
LinkageDisequilibriumComponent ldc = new LinkageDisequilibriumComponent(theLD, blockSchematic, chromosomalView, theLD.getSiteCount(), (int)Math.ceil(theLD.getSiteCount()/2.0), (int)Math.ceil(theLD.getSiteCount()/2.0));
ldc.setUpperCorner(upperCorner);
ldc.setLowerCorner(lowerCorner);
ldc.setSize(getImageWidth(), getImageHeight());
ldc.setShowLabels(includeLabels);
saveDataToFile(ldc, getSaveFile());
}
return null;
} finally {
fireProgress(100);
}
}
public int getUpperCorner() {
return upperCorner;
}
public void setUpperCorner(int upperCorner) {
this.upperCorner = upperCorner;
}
public int getLowerCorner() {
return lowerCorner;
}
public void setLowerCorner(int lowerCorner) {
this.lowerCorner = lowerCorner;
}
public boolean isBlockSchematic() {
return blockSchematic;
}
public void setBlockSchematic(boolean blockSchematic) {
this.blockSchematic = blockSchematic;
}
public void setShowLabels(boolean includeLabels) {
this.includeLabels = includeLabels;
}
public boolean isChromosomalView() {
return chromosomalView;
}
public void setChromosomalView(boolean chromosomalView) {
this.chromosomalView = chromosomalView;
}
/**
* Icon for this plugin to be used in buttons, etc.
*
* @return ImageIcon
*/
public ImageIcon getIcon() {
URL imageURL = LinkageDiseqDisplayPlugin.class.getResource("/net/maizegenetics/analysis/images/LDPlot.gif");
if (imageURL == null) {
return null;
} else {
return new ImageIcon(imageURL);
}
}
/**
* Button name for this plugin to be used in buttons, etc.
*
* @return String
*/
public String getButtonName() {
return "LD Plot";
}
/**
* Tool Tip Text for this plugin
*
* @return String
*/
public String getToolTipText() {
return "Display Linkage Disequilibrium";
}
}
class LinkageDiseqDisplayDialog extends JDialog {
final int myDefaultViewableSize = 35;
int maxWindowSize;
int myMaxWindowSize = 1000;
JPanel panel1 = new JPanel();
JButton okButton = new JButton();
JPanel linkPanel = new JPanel();
JPanel mapPanel = new JPanel();
LinkageDisequilibriumComponent ldFigurePanel;
LinkageDisequilibriumMinimapComponent ldMapPanel;
BorderLayout borderLayout1 = new BorderLayout();
LinkageDisequilibrium theLinkageDisequilibrium;
LinkageDiseqDisplayPlugin theLinkageDiseqDisplayPlugin;
BorderLayout borderLayout2 = new BorderLayout();
JPanel jPanel1 = new JPanel();
JButton saveButton = new JButton();
JButton saveAllButton = new JButton();
JLabel upperSqrLabel;
JLabel lowerSqrLabel;
JComboBox upperSqrSelector;
JComboBox lowerSqrSelector;
GridBagLayout gridBagLayout1 = new GridBagLayout();
JCheckBox schematicCheckBox = new JCheckBox();
//locks scroll bars together
JCheckBox myLockScrollBarsCheckBox = new JCheckBox();
boolean myLockedBars = false;
JScrollBar verticalScrollBar = new JScrollBar(Adjustable.VERTICAL);
JScrollBar horizontalScrollBar = new JScrollBar(Adjustable.HORIZONTAL);
// JComboBox formatComboBox = new JComboBox();
// Windowed Viewer
JPanel viewerLocationOptionsPanel = new JPanel();
//window size
JLabel windowSizeLabel = new JLabel();
JSlider windowSizeSlider;
JTextField windowSizeText = new JTextField();
//x axis
JSlider windowXSlider;
// Y axis panel
JPanel yAxisPanel = new JPanel();
//y axis
JSlider windowYSlider;
// remembers current location
int myXPos;
int myYPos;
public LinkageDiseqDisplayDialog(LinkageDiseqDisplayPlugin theQAF, LinkageDisequilibrium theLinkageDisequilibrium) {
super(theQAF.getParentFrame(), "Linkage Disequilibrium", false);
this.theLinkageDiseqDisplayPlugin = theQAF;
this.theLinkageDisequilibrium = theLinkageDisequilibrium;
maxWindowSize = theLinkageDisequilibrium.getSiteCount();
myXPos = (int)Math.ceil(maxWindowSize/2.0);
myYPos = (int)Math.ceil(maxWindowSize/2.0);
try {
jbInit();
if (theLinkageDisequilibrium.getSiteCount() > myDefaultViewableSize) {
ldFigurePanel = new LinkageDisequilibriumComponent(theLinkageDisequilibrium, true, false, myDefaultViewableSize, theLinkageDisequilibrium.getSiteCount()/2, theLinkageDisequilibrium.getSiteCount()/2);
} else {
ldFigurePanel = new LinkageDisequilibriumComponent(theLinkageDisequilibrium, true, false, maxWindowSize, (int)Math.ceil(maxWindowSize/2.0), (int)Math.ceil(maxWindowSize/2.0));
}
linkPanel.add(ldFigurePanel, BorderLayout.CENTER);
pack();
} catch (Exception ex) {
ex.printStackTrace();
JOptionPane.showMessageDialog(this.getParent(), "Unable to create LD plot " + ex);
}
repaint();
}
void jbInit() throws Exception {
jPanel1.setLayout(gridBagLayout1);
jPanel1.setToolTipText("");
// Window Viewer init
if (theLinkageDisequilibrium.getSiteCount() > myDefaultViewableSize) {
viewerLocationOptionsPanel.setLayout(new GridBagLayout());
yAxisPanel.setLayout(new GridBagLayout());
//Window size
windowSizeLabel.setText("Select viewable size");
windowSizeSlider = new JSlider(1, Math.min(maxWindowSize, myMaxWindowSize), myDefaultViewableSize);
windowSizeText.setText(String.valueOf(windowSizeSlider.getValue()));
windowSizeSlider.addMouseListener(new java.awt.event.MouseListener() {
public void mouseClicked(MouseEvent me) {
// throw new UnsupportedOperationException("Not supported yet.");
}
public void mousePressed(MouseEvent me) {
// throw new UnsupportedOperationException("Not supported yet.");
}
public void mouseReleased(MouseEvent me) {
sizeSlider_actionPerformed(me);
}
public void mouseEntered(MouseEvent me) {
// throw new UnsupportedOperationException("Not supported yet.");
}
public void mouseExited(MouseEvent me) {
// throw new UnsupportedOperationException("Not supported yet.");
}
});
windowSizeText.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) {
sizeTextField_keyTyped(ke);
}
});
//X coords
// windowXSlider = new JSlider(myDefaultViewableSize/2, numSites-(myDefaultViewableSize/2+(myDefaultViewableSize%2)+numChroms-1), numSites/2);
windowXSlider = new JSlider((int)Math.ceil(myDefaultViewableSize/2.0), (int)Math.ceil(maxWindowSize-myDefaultViewableSize/2.0), (int)Math.ceil(maxWindowSize/2.0));
windowXSlider.addChangeListener(new javax.swing.event.ChangeListener() {
public void stateChanged(ChangeEvent ce) {
xSlider_actionPerformed(ce);
}
//
});
//Y coords
// windowYSlider = new JSlider(myDefaultViewableSize/2, numSites-(myDefaultViewableSize/2+(myDefaultViewableSize%2)+numChroms-1), numSites/2);
windowYSlider = new JSlider((int)Math.ceil(myDefaultViewableSize/2.0), (int)Math.ceil(maxWindowSize-myDefaultViewableSize/2.0), (int)Math.ceil(maxWindowSize/2.0));
windowYSlider.setOrientation(JSlider.VERTICAL);
windowYSlider.setInverted(true);
windowYSlider.addChangeListener(new javax.swing.event.ChangeListener() {
public void stateChanged(ChangeEvent ce) {
ySlider_actionPerformed(ce);
}
});
//Minimap
ldMapPanel = new LinkageDisequilibriumMinimapComponent(theLinkageDisequilibrium, myDefaultViewableSize, (int)Math.ceil(maxWindowSize/2.0), (int)Math.ceil(maxWindowSize/2.0));
mapPanel.add(ldMapPanel, BorderLayout.CENTER);
mapPanel.setBorder(BorderFactory.createEtchedBorder());
ldMapPanel.addMouseListener(new java.awt.event.MouseListener() {
public void mouseClicked(MouseEvent me) {
// throw new UnsupportedOperationException("Not supported yet.");
}
public void mousePressed(MouseEvent me) {
mapPanel_mouseEvent(me);
}
public void mouseReleased(MouseEvent me) {
// throw new UnsupportedOperationException("Not supported yet.");
}
public void mouseEntered(MouseEvent me) {
// throw new UnsupportedOperationException("Not supported yet.");
}
public void mouseExited(MouseEvent me) {
// throw new UnsupportedOperationException("Not supported yet.");
}
});
ldMapPanel.addMouseMotionListener(new java.awt.event.MouseMotionListener() {
public void mouseDragged(MouseEvent me) {
mapPanel_mouseEvent(me);
}
public void mouseMoved(MouseEvent me) {
// throw new UnsupportedOperationException("Not supported yet.");
}
});
//Add window size to panel
viewerLocationOptionsPanel.add(windowSizeLabel, new GridBagConstraints(0, 0, 1, 1, 0.0, 1.0, GridBagConstraints.LAST_LINE_END, GridBagConstraints.NONE, new Insets(0, 5, 8, 5), 0, 0));
viewerLocationOptionsPanel.add(windowSizeSlider, new GridBagConstraints(1, 0, 2, 1, 0.9, 1.0, GridBagConstraints.PAGE_END, GridBagConstraints.HORIZONTAL, new Insets(0, 0, 0, 0), 0, 0));
viewerLocationOptionsPanel.add(windowSizeText, new GridBagConstraints(3, 0, 1, 1, 0.1, 1.0, GridBagConstraints.LAST_LINE_START, GridBagConstraints.HORIZONTAL, new Insets(0, 5, 0, 5), 0, 0));
viewerLocationOptionsPanel.add(mapPanel, new GridBagConstraints(4, 0, 1, 1, 0.2, 0.2, GridBagConstraints.CENTER, GridBagConstraints.NONE, new Insets(5, 5, 5, 5), 0, 0));
//Add X coords to panel
jPanel1.add(windowXSlider, new GridBagConstraints(0, 0, 6, 1, 1.0, 1.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL, new Insets(0, 172, 0, 85), 0, 0));
//Add Y coords to panel
yAxisPanel.add(windowYSlider, new GridBagConstraints(0, 0, 1, 1, 0.0, 1.0, GridBagConstraints.CENTER, GridBagConstraints.VERTICAL, new Insets(10, 0, 30, 0), 0, 0));
getContentPane().add(viewerLocationOptionsPanel, BorderLayout.NORTH);
getContentPane().add(mapPanel, BorderLayout.LINE_START);
getContentPane().add(yAxisPanel, BorderLayout.LINE_END);
}
String[] valueOptions = {"P-Value", "R Squared", "D Prime"};
upperSqrLabel = new JLabel("Upper triangle:");
upperSqrSelector = new JComboBox<>(valueOptions);
upperSqrSelector.setSelectedIndex(1);
upperSqrSelector.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
upperSqrSelector_actionPerformed(e);
}
});
lowerSqrLabel = new JLabel("Lower triangle:");
lowerSqrSelector = new JComboBox<>(valueOptions);
lowerSqrSelector.setSelectedIndex(0);
lowerSqrSelector.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
lowerSqrSelector_actionPerformed(e);
}
});
panel1.setLayout(borderLayout2);
okButton.setText("Close");
okButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
okButton_actionPerformed(e);
}
});
linkPanel.setBorder(BorderFactory.createEtchedBorder());
linkPanel.setLayout(borderLayout1);
panel1.setPreferredSize(new Dimension(600, 600));
saveButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
saveButton_actionPerformed(e);
}
});
saveButton.setText("Save");
saveAllButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
saveAllButton_actionPerformed(e);
}
});
saveAllButton.setText("Save All");
schematicCheckBox.setSelected(true);
schematicCheckBox.setText("Schematic");
schematicCheckBox.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
schematicCheckBox_actionPerformed(e);
}
});
myLockScrollBarsCheckBox.setSelected(false);
myLockScrollBarsCheckBox.setText("Lock Y Axis to X");
myLockScrollBarsCheckBox.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
lockScrollBarsCheckBox_actionPerformed(e);
}
});
getContentPane().add(panel1, BorderLayout.CENTER);
panel1.add(linkPanel, BorderLayout.CENTER);
this.getContentPane().add(jPanel1, BorderLayout.SOUTH);
jPanel1.add(upperSqrLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0, GridBagConstraints.LINE_END, GridBagConstraints.NONE, new Insets(0, 10, 0, 0), 5, 0));
jPanel1.add(lowerSqrLabel, new GridBagConstraints(0, 2, 1, 1, 0.0, 0.0, GridBagConstraints.LINE_END, GridBagConstraints.NONE, new Insets(0, 10, 0, 0), 5, 0));
jPanel1.add(upperSqrSelector, new GridBagConstraints(1, 1, 1, 1, 0.5, 0.5, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL, new Insets(0, 0, 0, 0), 0, 0));
jPanel1.add(lowerSqrSelector, new GridBagConstraints(1, 2, 1, 1, 0.5, 0.5, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL, new Insets(0, 0, 0, 0), 0, 0));
jPanel1.add(okButton, new GridBagConstraints(5, 2, 1, 1, 0.0, 0.0, GridBagConstraints.LINE_END, GridBagConstraints.NONE, new Insets(0, 0, 0, 15), 0, 0));
jPanel1.add(myLockScrollBarsCheckBox, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0, GridBagConstraints.LINE_START, GridBagConstraints.NONE, new Insets(0, 0, 0, 0), 0, 0));
jPanel1.add(saveButton, new GridBagConstraints(4, 1, 1, 1, 0.0, 0.0, GridBagConstraints.CENTER, GridBagConstraints.NONE, new Insets(0, 0, 0, 0), 0, 0));
jPanel1.add(saveAllButton, new GridBagConstraints(5, 1, 1, 1, 0.0, 0.0, GridBagConstraints.LINE_END, GridBagConstraints.NONE, new Insets(0, 0, 0, 15), 0, 0));
jPanel1.add(schematicCheckBox, new GridBagConstraints(3, 1, 1, 1, 0.0, 0.0, GridBagConstraints.CENTER, GridBagConstraints.NONE, new Insets(0, 0, 0, 0), 0, 0));
}
void okButton_actionPerformed(ActionEvent e) {
dispose();
}/////////end calculateDisequilibrium
void saveButton_actionPerformed(ActionEvent e) {
// String s=formatComboBox.getSelectedItem().toString();
this.theLinkageDiseqDisplayPlugin.saveDataToFile(ldFigurePanel);
}
void saveAllButton_actionPerformed(ActionEvent e) {
LinkageDisequilibriumComponent newGraph = new LinkageDisequilibriumComponent(theLinkageDisequilibrium, true, false, maxWindowSize, (int)Math.ceil(maxWindowSize/2.0), (int)Math.ceil(maxWindowSize/2.0));
if (upperSqrSelector.getSelectedIndex() == 0) {
newGraph.setUpperCorner(LinkageDisequilibriumComponent.P_VALUE);
} else if (upperSqrSelector.getSelectedIndex() == 1) {
newGraph.setUpperCorner(LinkageDisequilibriumComponent.RSQUARE);
} else if (upperSqrSelector.getSelectedIndex() == 2) {
newGraph.setUpperCorner(LinkageDisequilibriumComponent.DPRIME);
}
if (lowerSqrSelector.getSelectedIndex() == 0) {
newGraph.setLowerCorner(LinkageDisequilibriumComponent.P_VALUE);
} else if (lowerSqrSelector.getSelectedIndex() == 1) {
newGraph.setLowerCorner(LinkageDisequilibriumComponent.RSQUARE);
} else if (lowerSqrSelector.getSelectedIndex() == 2) {
newGraph.setLowerCorner(LinkageDisequilibriumComponent.DPRIME);
}
newGraph.setGraphSize(4096, 4096);
theLinkageDiseqDisplayPlugin.saveDataToFile(newGraph);
}
void upperSqrSelector_actionPerformed(ActionEvent e) {
if (upperSqrSelector.getSelectedIndex() == 0) {
ldFigurePanel.setUpperCorner(LinkageDisequilibriumComponent.P_VALUE);
} else if (upperSqrSelector.getSelectedIndex() == 1) {
ldFigurePanel.setUpperCorner(LinkageDisequilibriumComponent.RSQUARE);
} else if (upperSqrSelector.getSelectedIndex() == 2) {
ldFigurePanel.setUpperCorner(LinkageDisequilibriumComponent.DPRIME);
}
repaint();
}
void lowerSqrSelector_actionPerformed(ActionEvent e) {
if (lowerSqrSelector.getSelectedIndex() == 0) {
ldFigurePanel.setLowerCorner(LinkageDisequilibriumComponent.P_VALUE);
} else if (lowerSqrSelector.getSelectedIndex() == 1) {
ldFigurePanel.setLowerCorner(LinkageDisequilibriumComponent.RSQUARE);
} else if (lowerSqrSelector.getSelectedIndex() == 2) {
ldFigurePanel.setLowerCorner(LinkageDisequilibriumComponent.DPRIME);
}
repaint();
}
void upDPrimeRadioButton_actionPerformed(ActionEvent e) {
ldFigurePanel.setUpperCorner(LinkageDisequilibriumComponent.DPRIME);
repaint();
}
void upRSqrRadioButton_actionPerformed(ActionEvent e) {
ldFigurePanel.setUpperCorner(LinkageDisequilibriumComponent.RSQUARE);
repaint();
}
void upPRadioButton_actionPerformed(ActionEvent e) {
ldFigurePanel.setUpperCorner(LinkageDisequilibriumComponent.P_VALUE);
repaint();
}
void lowRSqrRadioButton_actionPerformed(ActionEvent e) {
ldFigurePanel.setLowerCorner(LinkageDisequilibriumComponent.RSQUARE);
repaint();
}
void lowPRadioButton_actionPerformed(ActionEvent e) {
ldFigurePanel.setLowerCorner(LinkageDisequilibriumComponent.P_VALUE);
repaint();
}
void lowDPrimeRadioButton_actionPerformed(ActionEvent e) {
ldFigurePanel.setLowerCorner(LinkageDisequilibriumComponent.DPRIME);
repaint();
}
void geneRadioButton_actionPerformed(ActionEvent e) {
ldFigurePanel.setScaleOfView(false);
repaint();
}
void chromoRadioButton_actionPerformed(ActionEvent e) {
ldFigurePanel.setScaleOfView(true);
repaint();
}
void schematicCheckBox_actionPerformed(ActionEvent e) {
ldFigurePanel.setShowSchematic(schematicCheckBox.isSelected());
repaint();
}
void lockScrollBarsCheckBox_actionPerformed(ActionEvent e) {
if ( myLockScrollBarsCheckBox.isSelected() ) {
myLockedBars = true;
} else {
myLockedBars = false;
}
}
void sizeSlider_actionPerformed(MouseEvent me) {
windowSizeText.setText(String.valueOf(windowSizeSlider.getValue()));
// windowXSlider.setValue((int)Math.ceil(maxWindowSize/2.0));
windowXSlider.setMinimum((int)Math.ceil(windowSizeSlider.getValue()/2.0));
windowXSlider.setMaximum((int)Math.ceil(maxWindowSize-windowSizeSlider.getValue()/2.0));
windowXSlider.setValue(Math.min(windowXSlider.getMaximum(), Math.max(windowXSlider.getMinimum(), myXPos)));
// windowYSlider.setValue((int)Math.ceil(maxWindowSize/2.0));
windowYSlider.setMinimum((int)Math.ceil(windowSizeSlider.getValue()/2.0));
windowYSlider.setMaximum((int)Math.ceil(maxWindowSize-windowSizeSlider.getValue()/2.0));
windowYSlider.setValue(Math.min(windowYSlider.getMaximum(), Math.max(windowYSlider.getMinimum(), myYPos)));
int ldMeasureLower = 0;
int ldMeasureUpper = 0;
if (lowerSqrSelector.getSelectedIndex() == 0) {
ldMeasureLower = LinkageDisequilibriumComponent.P_VALUE;
} else if (lowerSqrSelector.getSelectedIndex() == 1) {
ldMeasureLower = LinkageDisequilibriumComponent.RSQUARE;
} else {
ldMeasureLower = LinkageDisequilibriumComponent.DPRIME;
}
if (upperSqrSelector.getSelectedIndex() == 0) {
ldMeasureUpper = LinkageDisequilibriumComponent.P_VALUE;
} else if (upperSqrSelector.getSelectedIndex() == 1) {
ldMeasureUpper = LinkageDisequilibriumComponent.RSQUARE;
} else {
ldMeasureUpper = LinkageDisequilibriumComponent.DPRIME;
}
ldFigurePanel.setWindowSize(windowSizeSlider.getValue(), windowXSlider.getValue(), windowYSlider.getValue(), ldMeasureLower, ldMeasureUpper);
ldMapPanel.setWindowSize(windowSizeSlider.getValue(), windowXSlider.getValue(), windowYSlider.getValue());
repaint();
}
void sizeTextField_keyTyped(KeyEvent ke) {
try {
if (!windowSizeText.getText().equals("")) {
int value = Integer.valueOf(windowSizeText.getText());
if (value >= windowSizeSlider.getMinimum() && value <= windowSizeSlider.getMaximum()) {
windowSizeSlider.setValue(value);
} else if (value <= windowSizeSlider.getMinimum()) {
windowSizeSlider.setValue(windowSizeSlider.getMinimum());
windowSizeText.setText(String.valueOf(windowSizeSlider.getMinimum()));
} else if (value >= windowSizeSlider.getMaximum()) {
windowSizeSlider.setValue(windowSizeSlider.getMaximum());
windowSizeText.setText(String.valueOf(windowSizeSlider.getMaximum()));
}
}
} catch (NumberFormatException nfe) {
windowSizeText.setText(String.valueOf(windowSizeSlider.getValue()));
}
}
void xSlider_actionPerformed(ChangeEvent ce) {
int ldMeasureLower = 0;
int ldMeasureUpper = 0;
if (lowerSqrSelector.getSelectedIndex() == 0) {
ldMeasureLower = LinkageDisequilibriumComponent.P_VALUE;
} else if (lowerSqrSelector.getSelectedIndex() == 1) {
ldMeasureLower = LinkageDisequilibriumComponent.RSQUARE;
} else {
ldMeasureLower = LinkageDisequilibriumComponent.DPRIME;
}
if (upperSqrSelector.getSelectedIndex() == 0) {
ldMeasureUpper = LinkageDisequilibriumComponent.P_VALUE;
} else if (upperSqrSelector.getSelectedIndex() == 1) {
ldMeasureUpper = LinkageDisequilibriumComponent.RSQUARE;
} else {
ldMeasureUpper = LinkageDisequilibriumComponent.DPRIME;
}
ldFigurePanel.setWindowX(windowXSlider.getValue(), ldMeasureLower, ldMeasureUpper);
ldMapPanel.setWindowX(windowXSlider.getValue());
if ( myLockedBars ) {
int diff = myXPos - windowXSlider.getValue();
if ( diff < 0) {
windowYSlider.setValue(Math.max(windowYSlider.getMinimum(), windowYSlider.getValue() - diff));
} else {
windowYSlider.setValue(Math.min(windowYSlider.getMaximum(), windowYSlider.getValue() - diff));
}
ldFigurePanel.setWindowY(windowYSlider.getValue(), ldMeasureLower, ldMeasureUpper);
ldMapPanel.setWindowY(windowYSlider.getValue());
myYPos = windowYSlider.getValue();
}
myXPos = windowXSlider.getValue();
repaint();
}
void ySlider_actionPerformed(ChangeEvent ce) {
int ldMeasureLower = 0;
int ldMeasureUpper = 0;
if (lowerSqrSelector.getSelectedIndex() == 0) {
ldMeasureLower = LinkageDisequilibriumComponent.P_VALUE;
} else if (lowerSqrSelector.getSelectedIndex() == 1) {
ldMeasureLower = LinkageDisequilibriumComponent.RSQUARE;
} else {
ldMeasureLower = LinkageDisequilibriumComponent.DPRIME;
}
if (upperSqrSelector.getSelectedIndex() == 0) {
ldMeasureUpper = LinkageDisequilibriumComponent.P_VALUE;
} else if (upperSqrSelector.getSelectedIndex() == 1) {
ldMeasureUpper = LinkageDisequilibriumComponent.RSQUARE;
} else {
ldMeasureUpper = LinkageDisequilibriumComponent.DPRIME;
}
ldFigurePanel.setWindowY(windowYSlider.getValue(), ldMeasureLower, ldMeasureUpper);
ldMapPanel.setWindowY(windowYSlider.getValue());
myYPos = windowYSlider.getValue();
repaint();
}
void mapPanel_mouseEvent(MouseEvent me) {
double mouseX = me.getLocationOnScreen().getX();
double mouseY = me.getLocationOnScreen().getY();
double panelX = ldMapPanel.getLocationOnScreen().getX();
double panelY = ldMapPanel.getLocationOnScreen().getY();
int mapSize = ldMapPanel.getMapSize();
double newX = (mouseX-panelX)/mapSize;
double newY = (mouseY-panelY)/mapSize;
int newXPos = Math.min(Math.max((int)(maxWindowSize*newX), windowXSlider.getMinimum()), windowXSlider.getMaximum());
int newYPos = Math.min(Math.max((int)(maxWindowSize*newY), windowYSlider.getMinimum()), windowYSlider.getMaximum());
int ldMeasureLower = 0;
int ldMeasureUpper = 0;
if (lowerSqrSelector.getSelectedIndex() == 0) {
ldMeasureLower = LinkageDisequilibriumComponent.P_VALUE;
} else if (lowerSqrSelector.getSelectedIndex() == 1) {
ldMeasureLower = LinkageDisequilibriumComponent.RSQUARE;
} else {
ldMeasureLower = LinkageDisequilibriumComponent.DPRIME;
}
if (upperSqrSelector.getSelectedIndex() == 0) {
ldMeasureUpper = LinkageDisequilibriumComponent.P_VALUE;
} else if (upperSqrSelector.getSelectedIndex() == 1) {
ldMeasureUpper = LinkageDisequilibriumComponent.RSQUARE;
} else {
ldMeasureUpper = LinkageDisequilibriumComponent.DPRIME;
}
windowXSlider.setValue(newXPos);
windowYSlider.setValue(newYPos);
ldFigurePanel.setWindowX(newXPos, ldMeasureLower, ldMeasureUpper);
ldFigurePanel.setWindowY(newYPos, ldMeasureLower, ldMeasureUpper);
ldMapPanel.setWindowX(newXPos);
ldMapPanel.setWindowY(newYPos);
myXPos = windowXSlider.getValue();
myYPos = windowYSlider.getValue();
repaint();
}
public int getWindowSizeSelection() {
return windowSizeSlider.getValue();
}
public int getWindowXSelection() {
return windowXSlider.getValue();
}
public int getWindowYSelection() {
return windowYSlider.getValue();
}
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