X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=b9b68cec25198d3bf1a175cf0efb7e1d09818bff;hb=dced869b5a728ef726f85893b0b0a6a7be75ec48;hp=d814abb4d5ed7d494510d572f6d54d1ad1ea63dd;hpb=3c3dff5249fee03952b293a4d79ea1c792aa0f60;p=jalview.git

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index d814abb..b9b68ce 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -123,8 +123,8 @@ public class Conservation
 
                 for (j = 1; j <= len; j++)
                 {
-                    sqnum[j] = ((Integer) jalview.schemes.ResidueProperties.aaHash.get(new String(
-                                sq.substring(j - 1, j)))).intValue(); // yuk
+                    sqnum[j] = ((Integer) jalview.schemes.ResidueProperties.aaHash.get(String.valueOf(
+                                sq.charAt(j - 1)))).intValue(); // yuk - JBPNote - case taken care of in aaHash
                 }
 
                 seqNums.setElementAt(sqnum, i);
@@ -163,7 +163,7 @@ public class Conservation
 
                     if (sequence.length() > i)
                     {
-                        res = sequence.substring(i, i + 1);
+                        res = String.valueOf(Character.toUpperCase(sequence.charAt(i)));
 
                         if (residueHash.containsKey(res))
                         {
@@ -260,7 +260,7 @@ public class Conservation
                 continue;
             }
 
-            c = ((Sequence) sequences.elementAt(i)).getCharAt(j);
+            c = ((Sequence) sequences.elementAt(i)).getCharAt(j); // gaps do not have upper/lower case
 
             if (jalview.util.Comparison.isGap((c)))
             {