Select all cutandpaste

[jalview.git] / src / jalview / util / Comparison.java

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