/**
* 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 getBaseComponent(int position, TierI tier, Orientation o) {
transcript = null;
int bp = tier.getBasePair(position);
int oldPos = position;
// We need to change the position if dealing with aa view
if (tier.getType() == SequenceType.AA) {
int offset = getOffset(position, tier);
bp += offset * tier.getStrand().toInt();
position = tier.getPosition(bp);
}
char base = tier.charAt(position);
if (tier.featureExsitsAt(position, TierI.Level.BOTTOM)) {
this.state = State.EXON;
SeqFeatureI feature = tier.featureAt(position, TierI.Level.BOTTOM);
Transcript parentClone = null;
Transcript otherParentClone = null;
if (tier.getType() == SequenceType.AA
&& feature.getParent() != null
&& feature.getParent().isTranscript()) {
FeatureSetI parent = feature.getParent();
int index = parent.getFeatureIndex(feature);
int start = parent.getEnd();
// the transcript start might be different than the lowest exon start
// when in the middle of an edit
if (parent.canHaveChildren()) {
for (int i = 0; i < parent.size(); i++) {
SeqFeatureI sf = parent.getFeatureAt(i);
if ((Strand.valueOf(sf.getStrand()) == Strand.FORWARD && sf.getStart() < start)
|| (Strand.valueOf(sf.getStrand()) == Strand.REVERSE && sf.getStart() > start))
start = sf.getStart();
}
}
int translationStart = parent.getTranslationStart();
int translationEnd = parent.getTranslationEnd();
int translationPos = parent.getFeaturePosition(translationStart);
int oldstart = start;
start += ((translationPos - 1) % 3) * parent.getStrand();
// Tring to avoid all the recalculation...
if (feature.getParent() == currentParent
&& start == currentStart
&& featureStart == feature.getStart()
&& featureEnd == feature.getEnd()) {
parentClone = currentParentClone;
otherParentClone = currentParentClone2;
} else {
// need to get a full translation so that we can get the amino acids
// in the UTR region
parentClone = (Transcript) feature.getParent().clone();
otherParentClone = (Transcript) feature.getParent().clone();
if (!parentClone.setTranslationStart(start)) {
start = oldstart;
TranslationI cds = otherParentClone.getTranslation();
cds.calcTranslationStartForLongestPeptide();
translationStart = otherParentClone.getTranslationStart();
translationPos = otherParentClone.getFeaturePosition(translationStart);
start += ((translationPos - 1) % 3) * otherParentClone.getStrand();
parentClone.setTranslationStart(start);
}
parentClone.setTranslationEnd(parentClone.getEnd());
parentClone.setPeptideSequence(null);
String translation = parentClone.translate();
SequenceI sequence = parentClone.getPeptideSequence();
currentParent = (Transcript) feature.getParent();
currentParentClone = parentClone;
currentParentClone2 = otherParentClone;
currentStart = start;
featureStart = feature.getStart();
featureEnd = feature.getEnd();
if (otherParentClone.getFeatureContaining(translationEnd) == null) {
TranslationI cds = otherParentClone.getTranslation();
cds.setTranslationEndFromStart();
}
}
SeqFeatureI sf = parentClone.getFeatureAt(index);
if (bp >= sf.getLow() && bp <= sf.getHigh()) {
base = getPeptide(bp, sf);
} else {
base = '\0';
}
if (otherParentClone != null) {
feature = otherParentClone.getFeatureAt(index);
}
} else if (tier.getType() == SequenceType.AA
&& feature.getParent() != null
&& !feature.getParent().isTranscript()) {
base = '\0';
}
if (isUTR(bp, feature, tier)) {
this.state = State.UTR;
}
if (isTranslationStart(bp, feature)) {
this.state = State.TRANSLATION_START;
}
if (isTranslationEnd(bp, feature)) {
this.state = State.TRANSLATION_END;
}
// Can have an error or a shift on a position but not both
if (isSequencingErrorPosition(bp, feature, tier.getType())) {
this.state = State.ERROR;
// set base to the base of the new sequence?
}
if (isShiftPosition(bp, feature, tier.getType())) {
this.state = State.SHIFT;
}
} else if (tier.featureExsitsAt(position, TierI.Level.TOP)) {
SeqFeatureI feature = tier.featureAt(position, Level.TOP);
this.state = State.INTRON;
if (tier.getType() == SequenceType.AA) {
base = '\0';
}
int start = feature.getEnd();
int end = feature.getStart();
if (feature.canHaveChildren()) {
for (int i = 0; i < feature.size(); i++) {
SeqFeatureI sf = feature.getFeatureAt(i);
if ((Strand.valueOf(sf.getStrand()) == Strand.FORWARD && sf.getStart() < start)
|| (Strand.valueOf(sf.getStrand()) == Strand.REVERSE && sf.getStart() > start))
start = sf.getStart();
if ((Strand.valueOf(sf.getStrand()) == Strand.FORWARD && sf.getEnd() > end)
|| (Strand.valueOf(sf.getStrand()) == Strand.REVERSE && sf.getEnd() < end))
end = sf.getEnd();
}
}
if (bp <= Math.min(start, end) || bp >= Math.max(start, end)) {
this.state = State.OUT;
base = '\0';
}
} else {
this.state = State.OUT;
base = '\0';
}
if (!(state == State.SHIFT || state == State.ERROR)
&& getRegionLow() <= position
&& position <= getRegionHigh()) {
this.state = State.SELECTED;
base = tier.charAt(oldPos);
}
init(base);
return this;
}
/**
* If right mouse deselect base If end of feature drag notify AnnotationEditor (endRangeChange)
* and recalc translation end from start
*/
public void mouseReleased(MouseEvent e) {
// RIGHT MOUSE CLICK
if (MouseButtonEvent.isRightMouseClick(e)) {
BaseRenderer rend = baseEditorPanel.getRendererAt(tier);
if (rend instanceof SelectableDNARenderer) {
((SelectableDNARenderer) rend).setTargetPos(-1, -1);
baseEditorPanel.repaint();
}
}
// SEQ SELECT DRAG
if (dragType == baseEditorPanel.SEQ_SELECT_DRAG) {
SequenceI seq = baseEditorPanel.getSequenceForTier(startDragTier);
int lowBP = baseEditorPanel.posToResidue(baseEditorPanel.selectLowPos());
int highBP = baseEditorPanel.posToResidue(baseEditorPanel.selectHighPos());
String sequence = seq.getResidues(lowBP, highBP);
String header = " Arbitrary selection (" + seq.getName() + ": " + lowBP + "," + highBP + ")";
// controllingWindow.copySeqToClipboard(new Sequence (header, sequence));
ClipboardUtil.copySeqToClipboard(new Sequence(header, sequence));
resetDragState();
baseEditorPanel.repaint();
return;
}
// NOT SEQ SELECT DRAG
else {
// NOT DRAGGING - RETURN
if (!MouseButtonEvent.isLeftMouseClick(e) || !dragging || dragFeature == null) {
resetDragState();
return;
}
// DRAGGING ANNOT ENDS
if (dragging && dragFeature != null && dragFeature.isAnnot()) {
// NOTIFY ANNOTATION EDITOR (generates transaction)
int oldStart = (preDragStartBasePair == -1) ? dragFeature.getStart() : preDragStartBasePair;
int oldEnd = (preDragEndBasePair == -1) ? dragFeature.getEnd() : preDragEndBasePair;
AnnotationEditor ae = baseEditorPanel.getAnnotationEditor();
ae.setAnnotTerminus(
dragFeature.getAnnotatedFeature(),
oldStart,
oldEnd,
dragFeature.getStart(),
dragFeature.getEnd());
// RECALC CDS (if exon/transcript - not for 1 level annots)
if (dragFeature.isExon()
&& dragFeature.getRefFeature() != null
&& (dragFeature.getRefFeature().isTranscript())) {
// ExonI exon = (ExonI)dragFeature;
// Transcript t = (Transcript)exon.getRefFeature();
SeqFeatureI transcript = dragFeature.getRefFeature();
TranslationI cds = transcript.getTranslation();
int transStart = transcript.getStart();
int cdsStart = cds.getTranslationStart();
boolean isForward = transcript.isForwardStrand();
if (cds.isMissing5prime()
&& ((isForward && transStart < cdsStart) || (!isForward && transStart > cdsStart))) {
cds.calcTranslationStartForLongestPeptide(); // missing start
} else {
cds.setTranslationEndFromStart(); // got start - set end
}
}
baseEditorPanel.repaint();
}
}
resetDragState();
baseEditorPanel.getCurationState().getSZAP().repaint();
}