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JAL-2591 More refactoring (incomplete)
[jalview.git]
/
src
/
jalview
/
gui
/
AlignFrame.java
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
e79e303
..
ae2e44a
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-1320,10
+1320,8
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
alignmentToExport = viewport.getAlignment();
}
{
alignmentToExport = viewport.getAlignment();
}
- alignmentStartEnd = alignmentToExport
- .getVisibleStartAndEndIndex(viewport.getAlignment()
- .getHiddenColumns()
- .getHiddenRegions());
+ alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
+ .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
omitHidden, alignmentStartEnd, settings);
return ed;
AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
omitHidden, alignmentStartEnd, settings);
return ed;
@@
-1885,8
+1883,8
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (viewport.hasHiddenColumns())
{
hiddenColumns = new ArrayList<>();
if (viewport.hasHiddenColumns())
{
hiddenColumns = new ArrayList<>();
- int hiddenOffset = viewport.getSelectionGroup().getStartRes(),
- hiddenCutoff = viewport.getSelectionGroup().getEndRes();
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+ int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
for (int[] region : viewport.getAlignment().getHiddenColumns())
{
if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
for (int[] region : viewport.getAlignment().getHiddenColumns())
{
if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)