/* 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;
}
/**
* 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;
}
/**
* 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;
}
public Color getBackgroundBoxColor() {
if (pos == targetNucleotide && tier == targetTier) return targetColor;
int lowSeqSelect;
int highSeqSelect;
if (baseEditor instanceof BaseEditorPanel) {
lowSeqSelect = ((BaseEditorPanel) baseEditor).selectLowPos();
highSeqSelect = ((BaseEditorPanel) baseEditor).selectHighPos();
} else {
lowSeqSelect = -1;
highSeqSelect = -1;
}
if (lowSeqSelect != -1 && highSeqSelect != -1 && pos >= lowSeqSelect && pos <= highSeqSelect) {
return seqSelectColor;
}
int basePos = baseEditor.posToBasePair(pos);
if (((BaseEditorPanel) baseEditor).isSequencingErrorPosition(basePos)) return shiftColor;
if (isExon) {
ExonI exon = null;
if (currentFeature instanceof ExonI) exon = (ExonI) currentFeature;
else if (currentFeature instanceof DrawableSeqFeature)
exon = (ExonI) ((DrawableSeqFeature) currentFeature).getFeature();
if (exon != null && exon.getTranscript() != null) {
Transcript transcript = exon.getTranscript();
int tss = (int) exon.getTranscript().getTranslationStart();
if (basePos == tss
|| basePos == (tss + exon.getStrand())
|| basePos == (tss + (2 * exon.getStrand())))
return DrawableUtil.getStartCodonColor(transcript);
else {
int tes = (int) transcript.getTranslationEnd();
if (basePos == tes
|| basePos == (tes + exon.getStrand())
|| basePos == (tes + (2 * exon.getStrand()))) return Color.red;
else {
int shift_pos = (int) transcript.plus1FrameShiftPosition();
if (basePos == shift_pos) return shiftColor;
else {
shift_pos = (int) transcript.minus1FrameShiftPosition();
if (basePos == shift_pos) return shiftColor;
else {
int stop_pos = (int) transcript.readThroughStopPosition();
if (basePos == stop_pos
|| basePos == (stop_pos + exon.getStrand())
|| basePos == (stop_pos + (2 * exon.getStrand()))) return Color.pink;
}
}
}
}
}
return transcriptColorList[transcriptColorIndex][exonColorIndex];
}
return null;
}