/** Middle mouse scrolls to where clicked, left mouse selects Right mouse brings up popup menu */
public void mouseClicked(MouseEvent e) {
setPos(e.getX(), e.getY());
if (MouseButtonEvent.isRightMouseClickNoShift(e)) {
if (tier > 2) baseEditorPanel.displayRightClickMenu(e.getX(), e.getY());
}
if (MouseButtonEvent.isMiddleMouseClickNoShift(e)) {
baseEditorPanel.scrollToPosition(pos);
}
// This is for Windows, which doesn't support middle clicks
else if (MouseButtonEvent.isRightMouseClickWithShift(e)) {
baseEditorPanel.scrollToPosition(pos);
}
if (MouseButtonEvent.isLeftMouseClick(e)) {
baseEditorPanel.selectAnnot(pos, tier);
baseEditorPanel.repaint();
}
}
/**
* Left Mouse dragging drags end of feature if drag type right or left boundary. dragType is
* figured in mousePressed
*/
public void mouseDragged(MouseEvent e) {
if (!MouseButtonEvent.isLeftMouseClick(e)) return;
// dragFeature set in mousePressed
// not needed
if (dragging == false && dragFeature != null) {
// changer = baseEditorPanel.getAnnotationEditor().beginRangeChange(dragFeature);// ??
preDragStartBasePair = dragFeature.getStart();
preDragEndBasePair = dragFeature.getEnd();
}
dragging = true;
// dragType determined in MousePressed
if (dragType == baseEditorPanel.START_BOUNDARY)
baseEditorPanel.setCursor(Cursor.getPredefinedCursor(Cursor.W_RESIZE_CURSOR));
else if (dragType == baseEditorPanel.END_BOUNDARY)
baseEditorPanel.setCursor(Cursor.getPredefinedCursor(Cursor.E_RESIZE_CURSOR));
else if (dragType == baseEditorPanel.SEQ_SELECT_DRAG) {
baseEditorPanel.setCursor(Cursor.getPredefinedCursor(Cursor.TEXT_CURSOR));
}
setPos(e.getX(), e.getY());
startPos = pos;
// going right
// substract the one because during dragging
// the person operating the mouse drags it
// one position beyond where they want the
// drop to occur.
// pos--;
if (dragType == baseEditorPanel.START_BOUNDARY) {
// Is this position okay to use as the new
// low end or will it make the feature too short?
if (baseEditorPanel.notTooSmall(
pos, baseEditorPanel.basePairToPos((int) dragFeature.getEnd())))
// this actually changes the model - do we really need to do that
// with every mouse drag - cant we just change it at the end of the
// drag? No - the EDE relies on the feature being changed - bummer
baseEditorPanel.changeStart(dragFeature, pos - dragStartPos, limit_5prime, limit_3prime);
} else if (dragType == baseEditorPanel.END_BOUNDARY) {
// Is this position okay to use as the new
// high end or will it make the feature too short?
if (baseEditorPanel.notTooSmall(
baseEditorPanel.basePairToPos((int) dragFeature.getStart()), pos))
// This changes the actual exon model! EDE relies on this
baseEditorPanel.changeEnd(dragFeature, pos - dragStartPos, limit_5prime, limit_3prime);
} else if (dragType == baseEditorPanel.SEQ_SELECT_DRAG) {
int redrawLowPos = baseEditorPanel.selectLowPos();
int redrawHighPos = baseEditorPanel.selectHighPos();
if (pos < redrawLowPos) redrawLowPos = pos;
if (pos > redrawHighPos) redrawHighPos = pos;
// selectCurrentPos = pos;
baseEditorPanel.setSelectCurrentPos(pos);
baseEditorPanel.repaint(redrawLowPos, redrawHighPos);
return;
}
// repaint with exon seq feature ends changed
baseEditorPanel.repaint(pos, dragStartPos);
dragStartPos = pos;
}
/**
* Right mouse: highlight base. Left mouse: figure dragType, dragFeature, dragStartPos,
* startDragTier
*/
public void mousePressed(MouseEvent e) {
setPos(e.getX(), e.getY());
// show base at right mouse click highlighted (on release - popup menu)
if (MouseButtonEvent.isRightMouseClickNoShift(e)) {
BaseRenderer rend = baseEditorPanel.getRendererAt(tier);
if (rend instanceof SelectableDNARenderer) {
((SelectableDNARenderer) rend).setTargetPos(pos, tier);
baseEditorPanel.repaint();
return;
}
}
if (!MouseButtonEvent.isLeftMouseClick(e)) return;
if (dragStartPos == -1) {
if (e.isControlDown()) dragType = baseEditorPanel.SEQ_SELECT_DRAG;
else dragType = baseEditorPanel.getBoundaryType(pos, tier);
dragFeature = baseEditorPanel.getFeatureAtPosition(pos, tier);
dragStartPos = pos;
startPos = pos;
startDragTier = tier;
if (dragFeature == null
&& ((dragType != baseEditorPanel.SEQ_SELECT_DRAG)
|| startDragTier > baseEditorPanel.getTierCount()
|| startDragTier < 3)) {
resetDragState();
return;
}
if (dragType == baseEditorPanel.START_BOUNDARY) {
/* the 5 prime edge of the feature (exon) can
be moved within limits. These are no farther
in the 3prime direction than the end of the
feature and no farther in the 5prime direction
than the beginning (5prime) of the preceding
intron */
limit_3prime = (int) dragFeature.getEnd();
int lowBound = baseEditorPanel.basePairToPos(dragFeature.getStart());
// subtract one to move into the preceding intron
double[] lowRange = baseEditorPanel.getRangeAtPosition(tier, lowBound - 1);
if (lowRange[0] < 0) limit_5prime = baseEditorPanel.posToBasePair(0);
else limit_5prime = baseEditorPanel.posToBasePair((int) lowRange[0]);
baseEditorPanel.setCursor(Cursor.getPredefinedCursor(Cursor.W_RESIZE_CURSOR));
} else if (dragType == baseEditorPanel.END_BOUNDARY) {
limit_5prime = (int) dragFeature.getStart();
int highBound = baseEditorPanel.basePairToPos((int) dragFeature.getEnd());
double[] highRange = baseEditorPanel.getRangeAtPosition(tier, highBound + 1);
SequenceI seq = baseEditorPanel.getSequenceForTier(tier);
if (highRange[1] > seq.getLength())
limit_3prime = baseEditorPanel.posToBasePair(seq.getLength());
else limit_3prime = baseEditorPanel.posToBasePair((int) highRange[1]);
baseEditorPanel.setCursor(Cursor.getPredefinedCursor(Cursor.E_RESIZE_CURSOR));
} else if (dragType == baseEditorPanel.SEQ_SELECT_DRAG) {
baseEditorPanel.setCursor(Cursor.getPredefinedCursor(Cursor.TEXT_CURSOR));
baseEditorPanel.setSelectBeginPos(pos);
baseEditorPanel.setSelectCurrentPos(pos);
}
}
}
/**
* 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();
}