/**
* 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;
boolean goodUser = true;
if (dragFeature != null)
goodUser =
baseEditorPanel.testUser(((AnnotatedFeatureI) dragFeature.getRefFeature()).getOwner());
if (!goodUser
|| (dragFeature == null
&& ((dragType != baseEditorPanel.SEQ_SELECT_DRAG)
|| startDragTier > baseEditorPanel.getTierCount()
|| startDragTier < 3))) {
resetDragState();
return;
}
if (dragType == baseEditorPanel.LEFT_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.RIGHT_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();
}
