Merge remote-tracking branch 'origin/develop' into bug/JAL-2591

diff --cc src/jalview/appletgui/AnnotationColumnChooser.java
index 2557c8d,22978c3..3a7188e
--- 1/src/jalview/appletgui/AnnotationColumnChooser.java
--- 2/src/jalview/appletgui/AnnotationColumnChooser.java
+++ b/src/jalview/appletgui/AnnotationColumnChooser.java
@@@ -306,10 -307,10 +306,11 @@@ public class AnnotationColumnChooser ex
              av.hideColumns(positions[0], positions[1]);
            }
          }
 +        // TODO not clear why we need to hide all the columns (above) if we are
 +        // going to copy the hidden columns over wholesale anyway
          av.getAlignment().setHiddenColumns(oldHidden);
        }
+       av.sendSelection();
        ap.paintAlignment(true);
      }
  

diff --cc src/jalview/gui/AnnotationColumnChooser.java
index bb475da,f81455e..6fc5fad
--- 1/src/jalview/gui/AnnotationColumnChooser.java
--- 2/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@@ -252,13 -253,12 +252,13 @@@ public class AnnotationColumnChooser ex
              av.hideColumns(positions[0], positions[1]);
            }
          }
 +        // TODO not clear why we need to hide all the columns (above) if we are
 +        // going to copy the hidden columns over wholesale anyway
          av.getAlignment().setHiddenColumns(oldHidden);
        }
+       av.sendSelection();
        ap.paintAlignment(true);
      }
- 
    }
  
    @Override