X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=232cb5daa653c2ca995045dbcc167bb3a80f998e;hb=9eabd6dffd6d19b2826b887a5def80351b9bceed;hp=fbec4be9aa3e600ada494cdcd8dc8b1bbd819c49;hpb=2cdef87796c1b6f575ad04d8170d7a7513655575;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index fbec4be..232cb5d 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -61,6 +61,7 @@ import java.util.Map;
 import java.util.Map.Entry;
 import java.util.NoSuchElementException;
 import java.util.Set;
+import java.util.SortedMap;
 import java.util.TreeMap;
 
 /**
@@ -2834,7 +2835,7 @@ public class AlignmentUtils
    * @param unmapped
    * @return
    */
-  static Map<Integer, Map<SequenceI, Character>> buildMappedColumnsMap(
+  static SortedMap<Integer, Map<SequenceI, Character>> buildMappedColumnsMap(
           AlignmentI unaligned, AlignmentI aligned, List<SequenceI> unmapped)
   {
     /*
@@ -2842,7 +2843,7 @@ public class AlignmentUtils
      * {unalignedSequence, characterPerSequence} at that position.
      * TreeMap keeps the entries in ascending column order. 
      */
-    Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
+    SortedMap<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
 
     /*
      * record any sequences that have no mapping so can't be realigned