X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=ea96b3b29efeca02a5e236062ffc93a10e9daad7;hb=45e015aabe8f35a4a13be26e7630641ef8c94fbb;hp=ba3cd6008723ca88bffda1261706cfad4b4838f6;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index ba3cd60..ea96b3b 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -60,6 +60,7 @@ 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;
 
 /**
@@ -2840,7 +2841,7 @@ 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)
   {
     /*
@@ -2848,7 +2849,7 @@ 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