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);
      }
    }
Exemple #2
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  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);
      }
    }