JAL-2591 Refactor HiddenColumns to use ArrayList instead of Vector

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index e79e303..fe84012 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();
     }
-    alignmentStartEnd = alignmentToExport
-            .getVisibleStartAndEndIndex(viewport.getAlignment()
-                    .getHiddenColumns()
-                    .getHiddenRegions());
+    alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
+            .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
             omitHidden, alignmentStartEnd, settings);
     return ed;
@@ -1885,9 +1883,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (viewport.hasHiddenColumns())
     {
       hiddenColumns = new ArrayList<>();
-      int hiddenOffset = viewport.getSelectionGroup().getStartRes(),
-              hiddenCutoff = viewport.getSelectionGroup().getEndRes();
-      for (int[] region : viewport.getAlignment().getHiddenColumns())
+      int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+      int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
+      ArrayList<int[]> hiddenRegions = viewport.getAlignment()
+              .getHiddenColumns().getHiddenColumnsCopy();
+      for (int[] region : hiddenRegions)
       {
         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
         {