/**
* 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;
}
/**
* Gets all the annotations in a particular feature set
*
* @param featureSet
* @return
*/
public static Set<SeqFeatureI> getAnnotations(SeqFeatureI featureSet) {
HashSet<SeqFeatureI> result = new HashSet<SeqFeatureI>();
if (featureSet.isTranscript()) {
if (featureSet.isContainedByRefSeq())
// only add if its fully in range
result.add(featureSet);
} else if (featureSet.isAnnotTop() && !featureSet.hasKids()) {
// only add if its fully in range
if (featureSet.isContainedByRefSeq()) result.add(featureSet);
} else {
for (int i = 0, size = featureSet.getFeatures().size(); i < size; i++) {
SeqFeatureI feature = featureSet.getFeatureAt(i);
if (feature.canHaveChildren()) {
result.addAll(getAnnotations(feature));
}
}
}
return result;
}