From: James Procter <j.procter@dundee.ac.uk>
Date: Tue, 17 Oct 2023 09:53:13 +0000 (+0100)
Subject: JAL-4089 selected columns are reported in absolute column numbers, not visible columns
X-Git-Tag: Release_2_11_4_0~136^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=55895fe0142a04bd24d3166314a48b3282314a34;p=jalview.git

JAL-4089 selected columns are reported in absolute column numbers, not visible columns
---

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 4a38ec0..b427739 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -340,10 +340,12 @@ public class ColumnSelection
 
   /**
    * Returns a read-only view of the (possibly empty) list of selected columns
+   * (base 1)
    * <p>
-   * The list contains no duplicates but is not necessarily ordered. It also may
-   * include columns hidden from the current view. To modify (for example sort)
-   * the list, you should first make a copy.
+   * The list contains no duplicates but is not necessarily ordered. Columns are
+   * reported in alignment coordinates (base 1), so may also include columns
+   * hidden from the current view. To modify (for example sort) the list, you
+   * should first make a copy.
    * <p>
    * The list is not thread-safe: iterating over it could result in
    * ConcurrentModificationException if it is modified by another thread.
diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 4b11494..dcedafa 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -884,14 +884,7 @@ public abstract class AAStructureBindingModel
       {
         for (int s : cs.getSelected())
         {
-          if (hiddenCols == null)
-          {
             matched.set(s);
-          }
-          else
-          {
-            matched.set(hiddenCols.visibleToAbsoluteColumn(s));
-          }
         }
       }
       else