/**
  * Checks if selected or selected refs feature is the feature set at current pos, so an exon as
  * well as a transcript will have an outline color
  */
 public Color getOutlineColor() {
   SeqFeatureI selected = null;
   if (baseEditor instanceof BaseEditorPanel) {
     selected = ((BaseEditorPanel) baseEditor).getSelectedFeature();
   }
   FeatureSetI featureSet = baseEditor.getFeatureSetAtPosition(pos, tier);
   if (featSetContainsFeat(featureSet, selected)) return Color.magenta;
   else return null;
 }
  /**
   * Get component to be rendered, if pos outside of current range getFeatureAtPosition and reset
   * currentRange, if feature is non null and not an instance of FeatureSetI then its an exon, and
   * set isExon flag
   */
  public Component getBaseRendererComponent(char base, int pos, int tier, SequenceI seq) {
    init(base, pos, tier, seq);

    hatchColor = null;
    if (((BaseEditorPanel) baseEditor).getShowHitZones()) {
      Vector hitZones = ((BaseEditorPanel) baseEditor).hitZones;

      for (int hitIndex = 0; hitIndex < hitZones.size(); hitIndex++) {
        int[] hitZone = (int[]) hitZones.elementAt(hitIndex);

        if (pos >= hitZone[0] && pos < hitZone[1]) {
          hatchColor = Color.yellow;
          break;
        }
      }
    }

    currentFeature = baseEditor.getFeatureAtPosition(pos, tier);
    double[] range = establishRange(currentFeature, pos, tier, false);

    if (range[1] != currentRange[1] || range[0] != currentRange[0]) {
      currentRange[0] = range[0];
      currentRange[1] = range[1];

      currentFeatureSet = baseEditor.getFeatureSetAtPosition(pos, tier);
      range = establishRange(currentFeatureSet, pos, tier, true);
      transcriptRange[0] = range[0];
      transcriptRange[1] = range[1];

      if (currentFeature != null) {
        // This decides the index into the color array, transcripts
        // can have different colors for their features
        transcriptColorIndex =
            (baseEditor.getRangeIndex(tier, (int) currentRange[0], (int) currentRange[1]))
                % transcriptColorList.length;
        exonColorIndex =
            (baseEditor.getExonRangeIndex(tier, (int) currentRange[0], (int) currentRange[1]))
                % transcriptColorList[transcriptColorIndex].length;
      }
      if (currentFeature == null) {
        isExon = false;
        isIntron = false;
        // } else if (currentFeature.canHaveChildren()) {
      } else if (currentFeature.hasKids()) { // 1 level annots can but dont
        isExon = false;
        isIntron = true;
      } else {
        isExon = true;
        isIntron = false;
      }
    }
    return this;
  }