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 8087210..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)
@@ -315,14 +316,17 @@ public class AlignViewController implements AlignViewControllerI
   }
 
   /**
-   * Sorts the alignment (or current selection) by either average score or
-   * density of the specified feature types, and adds to the command history. If
-   * {@code types} is null, all visible feature types are used for the sort. If
-   * no feature types apply, does nothing.
+   * Sorts the alignment (or current selection) by either average score or density
+   * of the specified feature types, and adds to the command history. If
+   * {@code types} is null, all visible feature types are used for the sort. If no
+   * feature types apply, does nothing.
    * 
    * @param types
    * @param methodText
+   *                     - text shown in Undo/Redo command
    * @param method
+   *                     - passed to
+   *                     jalview.analysis.AlignmentSorter.sortByFeatures()
    */
   protected void sortByFeatures(List<String> types, String methodText,
           final String method)