temporary fix and note about null feature group mucking up selection of features...

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index cf5a57a..ab1e62d 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -718,9 +718,10 @@ public class AlignmentSorter
                 ||
                 // or ignore based on selection criteria
                 (featureLabels != null && !AlignmentSorter.containsIgnoreCase(sf[f].type, featureLabels))
-                || (groupLabels != null 
-                        && (sf[f].getFeatureGroup() == null 
-                                || !AlignmentSorter.containsIgnoreCase(sf[f].getFeatureGroup(), groupLabels))))
+                || (groupLabels != null
+                        // problem here: we cannot eliminate null feature group features
+                        && (sf[f].getFeatureGroup() != null 
+                                && !AlignmentSorter.containsIgnoreCase(sf[f].getFeatureGroup(), groupLabels))))
         {
           // forget about this feature
           sf[f] = null;