From 9390152fd31fd0d9c52833f1e5c63d222cb38d82 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 16 Dec 2016 09:45:09 +0000
Subject: [PATCH] JAL-1705 JAL-98 use SortedMap as more accurate type than Map

---
 src/jalview/analysis/AlignmentUtils.java |    5 +++--
 src/jalview/analysis/Conservation.java   |    3 ++-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 34fe221..ea96b3b 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -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
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 7b9da46..5e5f716 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -33,6 +33,7 @@ import java.awt.Color;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
+import java.util.SortedMap;
 import java.util.TreeMap;
 import java.util.Vector;
 
@@ -243,7 +244,7 @@ public class Conservation
        * or not conserved (-1)
        * Using TreeMap means properties are displayed in alphabetical order
        */
-      Map<String, Integer> resultHash = new TreeMap<String, Integer>();
+      SortedMap<String, Integer> resultHash = new TreeMap<String, Integer>();
       SymbolCounts symbolCounts = values.getSymbolCounts();
       char[] symbols = symbolCounts.symbols;
       int[] counts = symbolCounts.values;
-- 
1.7.10.2