예제 #1
0
  @Override
  public void renderBorder(Track track, RenderContext context, Rectangle arect) {

    Rectangle adjustedRect = calculateDrawingRect(arect);

    // Draw boundaries if there is room
    if (adjustedRect.getHeight() >= 10) {

      /// TrackProperties pros = track.getProperties();

      // midline

      DataRange axisDefinition = track.getDataRange();
      float maxValue = axisDefinition.getMaximum();
      float baseValue = axisDefinition.getBaseline();
      float minValue = axisDefinition.getMinimum();

      double maxX = adjustedRect.getMaxX();
      double x = adjustedRect.getX();
      double y = adjustedRect.getY();

      if ((baseValue > minValue) && (baseValue < maxValue)) {
        int baseY = computeYPixelValue(adjustedRect, axisDefinition, baseValue);

        getBaselineGraphics(context).drawLine((int) x, baseY, (int) maxX, baseY);
      }

      PreferenceManager prefs = PreferenceManager.getInstance();

      Color altColor = track.getAltColor();
      Color borderColor =
          (prefs.getAsBoolean(PreferenceManager.CHART_COLOR_BORDERS)
                  && altColor != null
                  && altColor.equals(track.getColor()))
              ? track.getColor()
              : Color.lightGray;
      Graphics2D borderGraphics = context.getGraphic2DForColor(borderColor);

      // Draw the baseline -- todo, this is a wig track option?
      double zeroValue = axisDefinition.getBaseline();
      int zeroY = computeYPixelValue(adjustedRect, axisDefinition, zeroValue);
      borderGraphics.drawLine(adjustedRect.x, zeroY, adjustedRect.x + adjustedRect.width, zeroY);

      // Optionally draw "Y" line  (UCSC track line option)
      if (track.isDrawYLine()) {
        Graphics2D yLineGraphics = context.getGraphic2DForColor(Color.gray);
        int yLine = computeYPixelValue(adjustedRect, axisDefinition, track.getYLine());
        GraphicUtils.drawDashedLine(
            borderGraphics, adjustedRect.x, yLine, adjustedRect.x + adjustedRect.width, yLine);
      }

      // If the chart has + and - numbers draw both borders or none. This
      // needs documented somewhere.
      boolean drawBorders = true;

      if (minValue * maxValue < 0) {
        drawBorders =
            prefs.getAsBoolean(PreferenceManager.CHART_DRAW_BOTTOM_BORDER)
                && prefs.getAsBoolean(PreferenceManager.CHART_DRAW_TOP_BORDER);
      }

      if (drawBorders && prefs.getAsBoolean(PreferenceManager.CHART_DRAW_TOP_BORDER)) {
        borderGraphics.drawLine(
            adjustedRect.x, adjustedRect.y, adjustedRect.x + adjustedRect.width, adjustedRect.y);
      }

      if (drawBorders && prefs.getAsBoolean(PreferenceManager.CHART_DRAW_BOTTOM_BORDER)) {
        borderGraphics.drawLine(
            adjustedRect.x,
            adjustedRect.y + adjustedRect.height,
            adjustedRect.x + adjustedRect.width,
            adjustedRect.y + adjustedRect.height);
      }
    }
    /*
    (CHART_DRAW_TOP_BORDER));
    prefs.setDrawBottomBorder(getBooleanPreference(CHART_DRAW_BOTTOM_BORDER));
    prefs.setColorBorders(getBooleanPreference(CHART_COLOR_BORDERS));
    prefs.setDrawAxis(getBooleanPreference(CHART_DRAW_Y_AXIS));
    prefs.setDrawTrackName(getBooleanPreference(CHART_DRAW_TRACK_NAME));
    prefs.setColorTrackName(getBooleanPreference(CHART_COLOR_TRACK_NAME));
    prefs.setAutoscale(getBooleanPreference(CHART_AUTOSCALE));
    prefs.setShowDataRange(getBooleanPreference(CHART_SHOW_DATA_RANGE));
     */
  }
예제 #2
0
  /**
   * Method description
   *
   * @param track
   * @param context
   * @param arect
   */
  @Override
  public void renderAxis(Track track, RenderContext context, Rectangle arect) {

    // For now disable axes for all chromosome view
    if (context.getChr().equals(Globals.CHR_ALL)) {
      return;
    }

    super.renderAxis(track, context, arect);

    Rectangle drawingRect = calculateDrawingRect(arect);

    PreferenceManager prefs = PreferenceManager.getInstance();

    Color labelColor =
        prefs.getAsBoolean(PreferenceManager.CHART_COLOR_TRACK_NAME)
            ? track.getColor()
            : Color.black;
    Graphics2D labelGraphics = context.getGraphic2DForColor(labelColor);

    labelGraphics.setFont(FontManager.getFont(8));

    if (prefs.getAsBoolean(PreferenceManager.CHART_DRAW_TRACK_NAME)) {

      // Only attempt if track height is > 25 pixels
      if (arect.getHeight() > 25) {
        Rectangle labelRect = new Rectangle(arect.x, arect.y + 10, arect.width, 10);
        labelGraphics.setFont(FontManager.getFont(10));
        GraphicUtils.drawCenteredText(track.getName(), labelRect, labelGraphics);
      }
    }

    if (prefs.getAsBoolean(PreferenceManager.CHART_DRAW_Y_AXIS)) {

      Rectangle axisRect = new Rectangle(arect.x, arect.y + 1, AXIS_AREA_WIDTH, arect.height);

      DataRange axisDefinition = track.getDataRange();
      float maxValue = axisDefinition.getMaximum();
      float baseValue = axisDefinition.getBaseline();
      float minValue = axisDefinition.getMinimum();

      // Bottom (minimum tick mark)
      int pY = computeYPixelValue(drawingRect, axisDefinition, minValue);

      labelGraphics.drawLine(
          axisRect.x + AXIS_AREA_WIDTH - 10, pY, axisRect.x + AXIS_AREA_WIDTH - 5, pY);
      GraphicUtils.drawRightJustifiedText(
          formatter.format(minValue), axisRect.x + AXIS_AREA_WIDTH - 15, pY, labelGraphics);

      // Top (maximum tick mark)
      int topPY = computeYPixelValue(drawingRect, axisDefinition, maxValue);

      labelGraphics.drawLine(
          axisRect.x + AXIS_AREA_WIDTH - 10, topPY, axisRect.x + AXIS_AREA_WIDTH - 5, topPY);
      GraphicUtils.drawRightJustifiedText(
          formatter.format(maxValue), axisRect.x + AXIS_AREA_WIDTH - 15, topPY + 4, labelGraphics);

      // Connect top and bottom
      labelGraphics.drawLine(
          axisRect.x + AXIS_AREA_WIDTH - 10, topPY, axisRect.x + AXIS_AREA_WIDTH - 10, pY);

      // Middle tick mark.  Draw only if room
      int midPY = computeYPixelValue(drawingRect, axisDefinition, baseValue);

      if ((midPY < pY - 15) && (midPY > topPY + 15)) {
        labelGraphics.drawLine(
            axisRect.x + AXIS_AREA_WIDTH - 10, midPY, axisRect.x + AXIS_AREA_WIDTH - 5, midPY);
        GraphicUtils.drawRightJustifiedText(
            formatter.format(baseValue),
            axisRect.x + AXIS_AREA_WIDTH - 15,
            midPY + 4,
            labelGraphics);
      }

    } else if (track.isShowDataRange() && arect.height > 20) {
      drawScale(track.getDataRange(), context, arect);
    }
  }