From 15d61556bb004b6f5707523942a1ef5d93ec416d Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 26 May 2016 10:52:38 +0100
Subject: [PATCH] JAL-1797 non-case-sensitive counting of residues / gaps

---
 src/jalview/analysis/Conservation.java |   22 ++++++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index d4ae57d..7b3ce25 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -235,10 +235,7 @@ public class Conservation
               c = '-';
             }
 
-            if (!canonicaliseAa && 'a' <= c && c <= 'z')
-            {
-              c -= (32); // 32 = 'a' - 'A'
-            }
+            c = toUpperCase(c);
           }
           values[c]++;
         }
@@ -326,6 +323,7 @@ public class Conservation
       }
       else
       {
+        c = toUpperCase(c);
         nres++;
 
         if (nres == 1)
@@ -347,6 +345,22 @@ public class Conservation
   }
 
   /**
+   * Returns the upper-cased character if between 'a' and 'z', else the
+   * unchanged value
+   * 
+   * @param c
+   * @return
+   */
+  char toUpperCase(char c)
+  {
+    if ('a' <= c && c <= 'z')
+    {
+      c -= (32); // 32 = 'a' - 'A'
+    }
+    return c;
+  }
+
+  /**
    * Calculates the conservation sequence
    * 
    * @param consflag
-- 
1.7.10.2