From ff3943fa5e1978e90b901a181916dbf790c93cb9 Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Mon, 6 Jun 2016 12:55:58 +0100 Subject: [PATCH] JAL-1944 bugfix for wrong alignment numbering when exporting an alignment and export hidden sequences is enabled --- src/jalview/gui/AlignFrame.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index aa07a93..7ab8311 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1325,10 +1325,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, else { alignmentToExport = viewport.getAlignment(); - alignmentStartEnd = viewport.getAlignment() - .getVisibleStartAndEndIndex( - viewport.getColumnSelection().getHiddenColumns()); } + alignmentStartEnd = alignmentToExport + .getVisibleStartAndEndIndex(viewport.getColumnSelection() + .getHiddenColumns()); AlignmentExportData ed = new AlignmentExportData(alignmentToExport, omitHidden, alignmentStartEnd, settings); return ed; -- 1.7.10.2