X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;fp=src%2Fjalview%2Fgui%2FAlignFrame.java;h=ab1ac0e1b533b8a208d859c7996dd24fb6e5d7c5;hb=97b26ba418dec7a6e926378205d25470bf098633;hp=75d367782a53784f7a24a6e4e94edb84670e9aa3;hpb=9201765247470c08d366abef2713c1c736adf2cb;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 75d3677..ab1ac0e 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -86,6 +86,7 @@ import jalview.schemes.ResidueProperties; import jalview.schemes.TCoffeeColourScheme; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; import jalview.ws.DBRefFetcher; import jalview.ws.DBRefFetcher.FetchFinishedListenerI; import jalview.ws.jws1.Discoverer; @@ -160,6 +161,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignViewport viewport; + ViewportRanges vpRanges; + public AlignViewControllerI avc; List alignPanels = new ArrayList(); @@ -331,6 +334,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, progressBar = new ProgressBar(this.statusPanel, this.statusBar); } + vpRanges = viewport.getRanges(); avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); if (viewport.getAlignmentConservationAnnotation() == null) @@ -640,9 +644,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new String[] { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { - alignPanel.getSeqPanel().seqCanvas.cursorX = viewport + alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges .getStartRes(); - alignPanel.getSeqPanel().seqCanvas.cursorY = viewport + alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges .getStartSeq(); } alignPanel.getSeqPanel().seqCanvas.repaint(); @@ -681,8 +685,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.setScrollValues(viewport.getStartRes(), - 2 * viewport.getStartSeq() - viewport.getEndSeq()); + alignPanel.setScrollValues(vpRanges.getStartRes(), + 2 * vpRanges.getStartSeq() - vpRanges.getEndSeq()); } break; case KeyEvent.VK_PAGE_DOWN: @@ -692,8 +696,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.setScrollValues(viewport.getStartRes(), - viewport.getEndSeq()); + alignPanel.setScrollValues(vpRanges.getStartRes(), + vpRanges.getEndSeq()); } break; } @@ -2143,7 +2147,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // propagate alignment changed. - viewport.setEndSeq(alignment.getHeight()); + vpRanges.setEndSeq(alignment.getHeight()); if (annotationAdded) { // Duplicate sequence annotation in all views. @@ -2547,7 +2551,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { trimRegion = new TrimRegionCommand("Remove Left", true, seqs, column, viewport.getAlignment()); - viewport.setStartRes(0); + vpRanges.setStartRes(0); } else { @@ -2614,13 +2618,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(viewport.getStartRes()); + int startRes = seq.findPosition(vpRanges.getStartRes()); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); // edit.alColumnChanges=shifts.getInverse(); // if (viewport.hasHiddenColumns) // viewport.getColumnSelection().compensateForEdits(shifts); - viewport.setStartRes(seq.findIndex(startRes) - 1); + vpRanges.setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); @@ -2653,12 +2657,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(viewport.getStartRes()); + int startRes = seq.findPosition(vpRanges.getStartRes()); addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, viewport.getAlignment())); - viewport.setStartRes(seq.findIndex(startRes) - 1); + vpRanges.setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences());