Ejemplo n.º 1
0
 public void eventRegistered(EventObject e) {
   if (e.getSource() == model && model.isReady()) {
     setCanPaint(true);
     setWantsPaint(true);
     notifyListeners();
   }
 }
Ejemplo n.º 2
0
  public void paintItem(Graphics2D g, int x1, int y1, int x2, int y2) {
    if (!model.isReady()) {
      return;
    }
    Set<Genome> genomes = model.getGenomes();
    if (genomes == null) {
      g.drawString("No Genomes Yet", x1 + 40, y1 + 40);
      return;
    }
    Genome currentGenome = model.getCurrentGenome();
    if (currentGenome == null) {
      g.drawString("Haven't moved", x1 + 40, y1 + 40);
      return;
    }
    genomes.remove(currentGenome);
    if (genomes.size() == 0) {
      g.drawString("Single genome isn't very interesting", x1 + 40, y1 + 40);
      return;
    }
    cs.reset();
    int h = y2 - y1;
    int midY = y1 + h / 2;
    int rstart = getRegion().getStart();
    int rend = getRegion().getEnd();
    Stroke old = g.getStroke();
    Stroke thin = new BasicStroke(1);
    Stroke medium = new BasicStroke(3);
    Stroke thick = new BasicStroke(6);
    for (Genome genome : genomes) {
      Region best = model.getBestRegion(genome);
      if (best == null) {
        continue;
      }
      String bestc = best.getChrom();
      int ostart = best.getStart();
      int oend = best.getEnd();
      java.util.List<MultiZAlignRegion> alignedRegions = model.getAlignedRegions(genome);
      for (MultiZAlignRegion align : alignedRegions) {
        if (align.getOtherChrom().equals(bestc)) {
          g.setColor(
              cs.colorAt(
                  hashPosPair(
                      align.getStart(),
                      align.getEnd(),
                      align.getOtherStart(),
                      align.getOtherEnd(),
                      cs.colorCount())));
          int rsx = getXPos(align.getStart(), rstart, rend, x1, x2);
          int osx = getXPos(align.getOtherStart(), ostart, oend, x1, x2);
          int rex = getXPos(align.getEnd(), rstart, rend, x1, x2);
          int oex = getXPos(align.getOtherEnd(), ostart, oend, x1, x2);

          g.setStroke(medium);
          if (myGenome == currentGenome) {
            g.drawLine(rsx, midY, rex, midY);
            g.drawLine(rsx, y1, rsx, y2);
            g.drawLine(rex, y1, rex, y2);
            addLabel(rsx, y1, rex - rsx, y2, align.toString());
          } else {
            g.drawLine(osx, midY, oex, midY);
            g.drawLine(osx, y1, osx, y2);
            g.drawLine(oex, y1, oex, y2);
            addLabel(osx, y1, oex - osx, y2, align.toString());
          }
        }
      }
    }
    g.setStroke(old);
    g.setColor(Color.BLACK);
    g.drawString(model.getAlignment(), x1 + 5, y2);
  }
Ejemplo n.º 3
0
 public void cleanup() {
   super.cleanup();
   model.removeEventListener(this);
 }