コード例 #1
0
  /**
   * Adds a collection of results to the list of results (but not to the result panel)
   *
   * @param features a list of results
   * @return the number of results added
   */
  public int addResults(java.util.Collection<SeqFeatureI> features) {
    int count = 0;

    for (SeqFeatureI feature : features) {
      if (!feature.isAnnot() && !getResults().contains(feature)) {
        getResults().add(feature);
        count++;
      }
    }
    return count;
  }
コード例 #2
0
  /**
   * 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();
  }
コード例 #3
0
 public boolean canRender(SeqFeatureI feature) {
   return feature.isAnnot();
 }