JAL-3759 exclude hidden columns when processing column selection

[jalview.git] / src / jalview / controller / AlignViewController.java

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 0bb2d03..1fc1946 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -90,7 +90,8 @@ public class AlignViewController implements AlignViewControllerI
         gps = jalview.analysis.Grouping.makeGroupsFromCols(
                 (sg == null) ? viewport.getAlignment().getSequencesArray()
                         : sg.getSequences().toArray(new SequenceI[0]),
-                cs, viewport.getAlignment().getGroups());
+                cs, viewport.getAlignment().getGroups(),
+                viewport.getAlignment().getHiddenColumns());
       }
     }
     if (gps != null)