X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FComparison.java;h=9a86696a2fdd94dd4220b2b454c31137cac98ba3;hb=3cc7159787bd31859f7bc27916e7ff854b895280;hp=c779bb1e9179df755ff7d27b56316d7d6600d599;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index c779bb1..9a86696 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -138,7 +138,7 @@ public class Comparison
 
             if (i < s1.getSequence().length())
             {
-                chr1 = s1.getSequence().charAt(i);
+                chr1 = Character.toUpperCase(s1.getSequence().charAt(i));
             }
             else
             {
@@ -147,7 +147,7 @@ public class Comparison
 
             if (i < s2.getSequence().length())
             {
-                chr2 = s2.getSequence().charAt(i);
+                chr2 = Character.toUpperCase(s2.getSequence().charAt(i));
             }
             else
             {
@@ -200,7 +200,7 @@ public class Comparison
 
             if (i < s1.getSequence().length())
             {
-                chr1 = s1.getSequence().charAt(i);
+                chr1 = Character.toUpperCase(s1.getSequence().charAt(i));
             }
             else
             {
@@ -209,7 +209,7 @@ public class Comparison
 
             if (i < s2.getSequence().length())
             {
-                chr2 = s2.getSequence().charAt(i);
+                chr2 = Character.toUpperCase(s2.getSequence().charAt(i));
             }
             else
             {
@@ -238,6 +238,6 @@ public class Comparison
      */
     public static boolean isGap(char c)
     {
-        return ((c != '.') && (c != '-') && (c != ' ')) ? false : true;
+        return (  c=='-' || c=='.' || c==' ' ) ? true : false;
     }
 }