/* Establish the currentRange of bases covered by the
currentFeature of this renderer
*/
public double[] establishRange(SeqFeatureI sf, int pos, int tier, boolean use_set) {
double range[];
if (sf == null || (!use_set && (sf.canHaveChildren()))) {
range = baseEditor.getRangeAtPosition(tier, pos);
} else {
range = new double[2];
range[0] = (double) baseEditor.basePairToPos(sf.getLow());
range[1] = (double) baseEditor.basePairToPos(sf.getHigh());
}
return range;
}
/** True if feat or feats refFeat is fs */
private boolean featSetContainsFeat(FeatureSetI fs, SeqFeatureI feat) {
if (fs == null || feat == null) return false;
if (fs == feat) return true;
if (fs == feat.getRefFeature()) return true;
// This should probably be generalized(recursive) for whole ancestor tree and added to
// FeatureSetI - for now only need to do feat and ref feat
// could use FeatureSet.find i guess - is that what thats intended for?
return false;
}
/**
* 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;
}
public boolean canRender(SeqFeatureI feature) {
return feature.isAnnot();
}
