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();
}