public void set(MouseEvent e, SAMRecord sr) {
if (sr == null) return;
StringBuffer text = new StringBuffer();
text.append("<html>");
if (sr != null) {
text.append(
MessageManager.getString("shortreadtrack.name") + " " + sr.getReadName() + "<br/>");
text.append(
MessageManager.getString("shortreadtrack.len") + " " + sr.getReadLength() + "<br/>");
text.append(
MessageManager.getString("shortreadtrack.cigar") + " " + sr.getCigarString() + "<br/>");
text.append(
MessageManager.getString("shortreadtrack.sequence")
+ " "
+ rerun(sr.getReadString())
+ "<br/>");
text.append(
MessageManager.getString("shortreadtrack.paired")
+ " "
+ sr.getReadPairedFlag()
+ "<br/>");
if (sr.getReadPairedFlag()) {
if (!sr.getMateUnmappedFlag())
text.append(
MessageManager.getString("shortreadtrack.mate")
+ " "
+ sr.getMateReferenceName()
+ ":"
+ sr.getMateAlignmentStart()
+ "<br/>");
else text.append(MessageManager.getString("shortreadtrack.mate_missing") + "<br/>");
text.append(
MessageManager.getString("shortreadtrack.second") + " " + sr.getFirstOfPairFlag());
}
// text.append("<br/>");
}
text.append("</html>");
if (!text.toString().equals(floater.getText())) {
floater.setText(text.toString());
this.pack();
}
setLocation(e.getXOnScreen() + 5, e.getYOnScreen() + 5);
if (!isVisible()) {
setVisible(true);
}
}
protected TrackConfig(Model model, DataKey dataKey) {
this.dataKey = dataKey;
this.model = model;
guicontainer.add(
new JLabel(MessageManager.getString("trackconfig.track_key") + " \n" + dataKey),
guicontainer.gc);
guicontainer.gc.gridy++;
guicontainer.add(
new StringConfig(
"track:alias:" + dataKey, MessageManager.getString("trackconfig.track_alias"), model),
guicontainer.gc);
guicontainer.gc.gridy++;
Configuration.getVisible(dataKey);
guicontainer.add(
new BooleanConfig(
"track:visible:" + dataKey,
MessageManager.getString("trackconfig.track_visible"),
model),
guicontainer.gc);
guicontainer.gc.gridy++;
guicontainer.add(
new BooleanConfig(
"track:highlight:" + dataKey,
MessageManager.getString("trackconfig.track_highlight"),
model),
guicontainer.gc);
if (isCollapsible()) {
guicontainer.gc.gridy++;
guicontainer.add(
new BooleanConfig(
"track:collapsed:" + dataKey,
MessageManager.getString("trackconfig.track_collapsed"),
model),
guicontainer.gc);
}
}
public void set(MouseEvent e, ShortReadInsertion sri) {
if (sri == null) return;
StringBuffer text = new StringBuffer();
text.append("<html>");
if (sri != null) {
text.append(MessageManager.getString("shortreadtrack.insertion") + " ");
byte[] bases = sri.esr.getReadBases();
for (int i = sri.start; i < sri.start + sri.len; i++) {
text.append((char) bases[i]);
}
text.append("<br/>");
}
text.append("</html>");
if (!text.toString().equals(floater.getText())) {
floater.setText(text.toString());
this.pack();
}
setLocation(e.getXOnScreen() + 5, e.getYOnScreen() + 5);
if (!isVisible()) {
setVisible(true);
}
}