public void analyze(String name, Object data) {
if (!(data instanceof SequenceGroup)) {
ErrorWindow.showErrorWindow(
new Exception("Got a non-sequencegroup object for a dot plot analysis"));
}
SequenceGroup sg = (SequenceGroup) data;
currentSG = sg;
titleLabel.setText(name);
DefaultComboBoxModel cModel1 = new DefaultComboBoxModel();
DefaultComboBoxModel cModel2 = new DefaultComboBoxModel();
for (int j = 0; j < sg.size(); j++) {
cModel1.addElement(sg.get(j).getName());
cModel2.addElement(sg.get(j).getName());
}
seq1Box.setModel(cModel1);
seq2Box.setModel(cModel2);
seq1Box.setSelectedIndex(0);
seq2Box.setSelectedIndex(1);
dotPlot.setBlockWidth((Integer) blockWidthSpinner.getValue());
changeSequences();
}
protected void changeSequences() {
String name1 = (String) seq1Box.getSelectedItem();
Sequence seq1 = currentSG.getSequenceForName(name1);
if (revComp1Box.isSelected()) {
seq1 = seq1.getReverseComplement();
seq1.setName(name1);
}
String name2 = (String) seq2Box.getSelectedItem();
Sequence seq2 = currentSG.getSequenceForName(name2);
if (revComp2Box.isSelected()) {
seq2 = seq2.getReverseComplement();
seq2.setName(name2);
}
dotPlot.setSequences(seq1, seq2);
repaint();
}
private void initializeComponents() {
mainPanel = new JPanel();
mainScrollPane = new JScrollPane(mainPanel);
mainPanel.setLayout(new BorderLayout());
mainPanel.setMinimumSize(new Dimension(300, 300));
mainPanel.setBackground(Color.white);
mainScrollPane.setBackground(Color.white);
this.setLayout(new BorderLayout());
this.add(mainScrollPane, BorderLayout.CENTER);
JPanel leftPanel = new JPanel();
leftPanel.setBackground(Color.white);
leftPanel.setMinimumSize(new Dimension(200, 10));
leftPanel.setPreferredSize(new Dimension(200, 10));
mainPanel.add(leftPanel, BorderLayout.WEST);
leftPanel.setLayout(new BoxLayout(leftPanel, BoxLayout.Y_AXIS));
titleLabel = new JLabel();
titleLabel.setAlignmentX(RIGHT_ALIGNMENT);
leftPanel.add(Box.createVerticalStrut(10));
leftPanel.add(titleLabel);
JPanel buttonPanel = new JPanel();
buttonPanel.setOpaque(false);
buttonPanel.setLayout(new FlowLayout(FlowLayout.LEFT));
JButton saveButton = new JButton("Save");
saveButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
saveImage();
}
});
buttonPanel.add(saveButton);
JButton restoreButton = new JButton("Restore");
restoreButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
restoreDefaultBounds();
}
});
buttonPanel.add(restoreButton);
JButton zoomButton = new JButton("Zoom");
zoomButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
zoomSelectedBounds();
}
});
buttonPanel.add(zoomButton);
leftPanel.add(buttonPanel);
leftPanel.add(Box.createVerticalStrut(50));
seq1Box = new JComboBox();
seq1Box.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
changeSequences();
}
});
leftPanel.add(seq1Box);
seq1Box.setPreferredSize(new Dimension(180, 24));
seq1Box.setMaximumSize(new Dimension(Integer.MAX_VALUE, 28));
seq1Box.setAlignmentX(RIGHT_ALIGNMENT);
revComp1Box = new JCheckBox("Use reverse complement");
revComp1Box.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent evt) {
changeSequences();
}
});
revComp1Box.setAlignmentX(RIGHT_ALIGNMENT);
leftPanel.add(revComp1Box);
leftPanel.add(Box.createVerticalStrut(10));
seq2Box = new JComboBox();
seq2Box.setPreferredSize(new Dimension(180, 24));
seq2Box.setMaximumSize(new Dimension(Integer.MAX_VALUE, 28));
seq2Box.setAlignmentX(RIGHT_ALIGNMENT);
seq2Box.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
changeSequences();
}
});
leftPanel.add(seq2Box);
revComp2Box = new JCheckBox("Use reverse complement");
revComp2Box.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent evt) {
changeSequences();
}
});
revComp2Box.setAlignmentX(RIGHT_ALIGNMENT);
leftPanel.add(revComp2Box);
leftPanel.add(Box.createVerticalStrut(15));
blockWidthSpinner = new JSpinner();
blockWidthSpinner.setModel(new SpinnerNumberModel(3, 1, 100, 1));
blockWidthSpinner.setToolTipText("The number of sites used per rectangle");
blockWidthSpinner.addChangeListener(
new ChangeListener() {
public void stateChanged(ChangeEvent e) {
updateBlockWidth();
}
});
JPanel bwPanel = new JPanel();
bwPanel.setOpaque(false);
bwPanel.setLayout(new FlowLayout(FlowLayout.LEFT));
JLabel lab = new JLabel("Block width : ");
bwPanel.add(lab);
bwPanel.add(blockWidthSpinner);
bwPanel.setAlignmentX(RIGHT_ALIGNMENT);
leftPanel.add(bwPanel);
leftPanel.add(Box.createVerticalGlue());
dotPlot = new DotPlotFigure();
dotPlot.setPreferredSize(new Dimension(300, 300));
mainPanel.add(dotPlot, BorderLayout.CENTER);
}
protected void updateBlockWidth() {
dotPlot.setBlockWidth((Integer) blockWidthSpinner.getValue());
dotPlot.repaint();
}
protected void restoreDefaultBounds() {
dotPlot.restoreDefaultBounds();
}
/** Zoom in to the selection box */
protected void zoomSelectedBounds() {
dotPlot.zoomToSelection();
}
public void paint(Graphics2D g) {
if (sequenceOne == null || sequenceTwo == null) {
System.out.println("Not drawing plot since one of the sequences is null");
return;
}
redrawImage = redrawImage || getVariablesHaveChanged();
if (redrawImage) drawImage();
int imageX = (int) Math.round(bounds.x * xFactor);
int imageY = (int) Math.round(bounds.y * yFactor);
if (imageIsBeingRedrawn) {
g.drawString("Please wait", 20, 20);
} else {
if (useZoom) {
// g.drawImage(dotPlotImage, imageX, imageY, dotPlotImage.getWidth(),
// dotPlotImage.getHeight(), null);
g.drawImage(
dotPlotImage,
imageX,
imageY,
imageX + dotPlotImage.getWidth(),
imageY + dotPlotImage.getHeight(),
sx1,
sy1,
sx2,
sy2,
null);
// g.setColor(Color.RED);
// g.drawRect(imageX+ sx1, imageY + sy1, sx2-sx1, sy2-sy1);
// g.setColor(Color.black);
} else
g.drawImage(
dotPlotImage, imageX, imageY, dotPlotImage.getWidth(), dotPlotImage.getHeight(), null);
// Draw x-axis
g.setColor(Color.black);
int xAxisY = imageY + dotPlotImage.getHeight() + 1; // y-value in pixels of x-axis
g.drawLine(imageX, xAxisY, imageX + dotPlotImage.getWidth(), xAxisY);
g.setFont(labelFont);
FontMetrics fm = g.getFontMetrics();
double tickStep = dotPlotImage.getWidth() / ((double) xAxisTicks - 1);
for (int i = 0; i < xAxisTicks; i++) {
int tickX = (int) Math.round(imageX + i * tickStep);
g.drawLine(tickX, xAxisY, tickX, xAxisY + 4);
String label = formatter.format(dataXForPixelX(tickX));
g.drawString(label, tickX - fm.stringWidth(label) / 2, xAxisY + 5 + fm.getHeight());
}
// Draw the y-axis
int yAxisX = (int) Math.round(bounds.x * xFactor);
g.drawLine(yAxisX, imageY, yAxisX, imageY + dotPlotImage.getHeight());
tickStep = dotPlotImage.getHeight() / ((double) yAxisTicks - 1);
for (int i = 0; i < yAxisTicks; i++) {
int tickY = (int) Math.round(imageY + i * tickStep);
g.drawLine(yAxisX - 4, tickY, yAxisX, tickY);
String label = formatter.format(dataYForPixelY(tickY));
g.drawString(label, yAxisX - fm.stringWidth(label) - 6, tickY + 5);
}
if (yMarkerMax > 0
&& (dotPlotParent.isCurrentlyRectSelecting()
|| dotPlotParent.isSelectionRectIsPreserved())) {
g.setColor(Color.GRAY);
g.drawLine(yAxisX - 6, yMarkerMax, yAxisX - 1, yMarkerMax);
g.drawLine(yAxisX - 6, yMarkerMin, yAxisX - 1, yMarkerMin);
g.drawLine(xMarkerMin, xAxisY + 1, xMarkerMin, xAxisY + 6);
g.drawLine(xMarkerMax, xAxisY + 1, xMarkerMax, xAxisY + 6);
g.drawString(formatter.format(dataXForPixelX(xMarkerMin)), xMarkerMin - 6, xAxisY + 17);
g.drawString(formatter.format(dataXForPixelX(xMarkerMax)), xMarkerMax - 6, xAxisY + 17);
String lab = formatter.format(dataYForPixelY(yMarkerMin));
g.drawString(lab, yAxisX - fm.stringWidth(lab) - 6, yMarkerMin + 4);
lab = formatter.format(dataYForPixelY(yMarkerMax));
g.drawString(lab, yAxisX - fm.stringWidth(lab) - 6, yMarkerMax + 4);
}
}
}
