/** 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();
  }
Beispiel #3
0
 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());
 }