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();
}