Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

[jalview.git] / src / jalview / analysis / AlignmentUtils.java

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 34fe221..232cb5d 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -42,6 +42,7 @@ import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
+import jalview.util.RangeComparator;
 import jalview.util.StringUtils;
 
 import java.io.UnsupportedEncodingException;
@@ -60,6 +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;
 
 /**
@@ -2264,14 +2266,7 @@ public class AlignmentUtils
      * ranges are assembled in order. Other cases should not use this method,
      * but instead construct an explicit mapping for CDS (e.g. EMBL parsing).
      */
-    Collections.sort(result, new Comparator<int[]>()
-    {
-      @Override
-      public int compare(int[] o1, int[] o2)
-      {
-        return Integer.compare(o1[0], o2[0]);
-      }
-    });
+    Collections.sort(result, new RangeComparator(true));
     return result;
   }
 
@@ -2840,7 +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)
   {
     /*
@@ -2848,7 +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