private void filterChange(final BamView bamView, final JComboBox flagCheck[]) {
int nflags = SAMRecordFlagPredicate.FLAGS.length;
int flagCombined = 0;
Vector<SAMRecordPredicate> predicates = new Vector<SAMRecordPredicate>();
for (int j = 0; j < nflags; j++) {
String opt = (String) flagCheck[j].getSelectedItem();
if (opt.equals("HIDE")) flagCombined = flagCombined | SAMRecordFlagPredicate.FLAGS[j];
else if (opt.equals("SHOW"))
predicates.add(new SAMRecordFlagPredicate(SAMRecordFlagPredicate.FLAGS[j], false));
}
if (flagCombined == 0 && predicates.size() == 0) bamView.setSamRecordFlagPredicate(null);
else {
final SAMRecordPredicate predicate;
if (predicates.size() == 0) predicate = new SAMRecordFlagPredicate(flagCombined);
else if (flagCombined == 0) {
predicate =
new SAMRecordFlagConjunctionPredicate(predicates, SAMRecordFlagConjunctionPredicate.OR);
} else {
SAMRecordFlagPredicate p1 = new SAMRecordFlagPredicate(flagCombined);
SAMRecordFlagConjunctionPredicate p2 =
new SAMRecordFlagConjunctionPredicate(predicates, SAMRecordFlagConjunctionPredicate.OR);
predicate =
new SAMRecordFlagConjunctionPredicate(p1, p2, SAMRecordFlagConjunctionPredicate.OR);
}
bamView.setSamRecordFlagPredicate(predicate);
}
bamView.repaint();
}
private void setQualityCutOff(final JTextField cutOff, final BamView bamView) {
String cutOffStr = cutOff.getText().trim();
if (cutOffStr.equals("")) bamView.setSamRecordMapQPredicate(null);
else {
try {
SAMRecordMapQPredicate predicate = new SAMRecordMapQPredicate(Integer.parseInt(cutOffStr));
bamView.setSamRecordMapQPredicate(predicate);
} catch (NumberFormatException nfe) {
bamView.setSamRecordMapQPredicate(null);
}
}
bamView.repaint();
}
public SAMRecordFilter(final BamView bamView) {
super("Filter Reads");
JPanel pane = (JPanel) getContentPane();
pane.setLayout(new GridBagLayout());
int nflags = SAMRecordFlagPredicate.FLAGS.length;
GridBagConstraints c = new GridBagConstraints();
int nrows = 0;
c.ipadx = 5;
c.ipady = 2;
c.gridx = 0;
c.gridwidth = 2;
c.anchor = GridBagConstraints.WEST;
c.gridy = nrows++;
// MAPQ
pane.add(new JLabel(" By Mappying Quality (mapq) cut-off:"), c);
c.gridy = nrows++;
c.gridwidth = 1;
final JTextField cutOff = new JTextField(12);
if (bamView.getSamRecordMapQPredicate() != null)
cutOff.setText(Integer.toString(bamView.getSamRecordMapQPredicate().cutOff));
cutOff.addKeyListener(
new KeyAdapter() {
public void keyPressed(KeyEvent e) {
if (e.getKeyCode() == KeyEvent.VK_ENTER) setQualityCutOff(cutOff, bamView);
}
});
pane.add(cutOff, c);
c.gridx = 1;
final JButton setCutOff = new JButton("SET");
setCutOff.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
setQualityCutOff(cutOff, bamView);
}
});
pane.add(setCutOff, c);
// FLAGS
c.gridwidth = 2;
c.gridx = 0;
c.gridy = nrows++;
pane.add(new JSeparator(), c);
c.gridy = nrows++;
pane.add(new JLabel(" By SAM FLAG column:"), c);
c.gridy = nrows++;
pane.add(new JLabel(" Select below to show or hide only the reads with "), c);
c.gridy = nrows++;
pane.add(new JLabel(" the flag set."), c);
final JComboBox flagCombo[] = new JComboBox[nflags];
final String[] items = {"", "SHOW", "HIDE"};
c.gridwidth = 1;
for (int j = 0; j < nflags; j++) {
flagCombo[j] = new JComboBox(items);
if (SAMRecordFlagPredicate.FLAGS_DESCRIPTION[j].equalsIgnoreCase("Read Unmapped"))
flagCombo[j].setSelectedItem("HIDE");
flagCombo[j].addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
filterChange(bamView, flagCombo);
}
});
c.gridy = nrows++;
c.gridx = 0;
pane.add(flagCombo[j], c);
c.gridx = 1;
pane.add(new JLabel(SAMRecordFlagPredicate.FLAGS_DESCRIPTION[j]), c);
}
JButton closeFrame = new JButton("Close");
closeFrame.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
setVisible(false);
}
});
c.gridx = 1;
c.gridy = nrows++;
c.fill = GridBagConstraints.NONE;
pane.add(closeFrame, c);
pack();
rightJustifyFrame(this);
setVisible(true);
}