import jalview.schemes.TCoffeeColourScheme;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.schemes.TCoffeeColourScheme;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.DBRefFetcher;
import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
import jalview.ws.jws1.Discoverer;
import jalview.ws.DBRefFetcher;
import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
import jalview.ws.jws1.Discoverer;
avc = new jalview.controller.AlignViewController(this, viewport,
alignPanel);
if (viewport.getAlignmentConservationAnnotation() == null)
avc = new jalview.controller.AlignViewController(this, viewport,
alignPanel);
if (viewport.getAlignmentConservationAnnotation() == null)
- alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
- alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
+ alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
+ .getStartRes();
+ alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
+ .getStartSeq();
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- - viewport.endSeq + viewport.startSeq);
+ alignPanel.setScrollValues(vpRanges.getStartRes(),
+ 2 * vpRanges.getStartSeq() - vpRanges.getEndSeq());
{
trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
column, viewport.getAlignment());
{
trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
column, viewport.getAlignment());
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
// edit.alColumnChanges=shifts.getInverse();
// if (viewport.hasHiddenColumns)
// viewport.getColumnSelection().compensateForEdits(shifts);
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
// edit.alColumnChanges=shifts.getInverse();
// if (viewport.hasHiddenColumns)
// viewport.getColumnSelection().compensateForEdits(shifts);
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
viewport.getAlignment()));
addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
viewport.getAlignment()));