/** Performs the update */
public void actionPerformed(ActionEvent e) {
// TODO check that the basepair is within the bounds of an exon
if (basepair < 0 || feature == null) {
throw new IllegalArgumentException("basepair:" + basepair + " feature:" + feature);
}
annotationEditor.setSelections(null, null, null, null);
annotationEditor.setTranslationStart((ExonI) feature, basepair);
curationState.getSZAP().repaint();
// TODO repaint all msa's
}
/**
* 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();
}
public void actionPerformed(ActionEvent e) {
// System.out.println("Calling editor.addNewAnnot(" + e.getActionCommand() + ")"); // DEL
// getActionCommand returns the type the user selected from the menu
editor.addNewAnnot(e.getActionCommand());
}