/**
* 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;
}