Takes strings, not seqs

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 9e0aef6..d35d84c 100755 (executable)
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -116,21 +116,19 @@ public class Comparison
    * @param s2 SequenceI\r
    * @return float\r
    */\r
-  public final static float PID(SequenceI seq1, SequenceI seq2)\r
+  public final static float PID(String seq1, String seq2)\r
   {\r
-    return PID(seq1, seq2, 0, seq1.getLength());\r
+    return PID(seq1, seq2, 0, seq1.length());\r
   }\r
 \r
   static final int caseShift = 'a' - 'A';\r
 \r
   // Another pid with region specification\r
-  public final static  float PID(SequenceI seq1, SequenceI seq2, int start, int end)\r
+  public final static  float PID(String seq1, String seq2, int start, int end)\r
   {\r
-    String s1 = seq1.getSequence();//.toUpperCase();\r
-    String s2 = seq2.getSequence();//.toUpperCase();\r
-    int s1len = s1.length();\r
-    int s2len = s2.length();\r
 \r
+    int s1len = seq1.length();\r
+    int s2len = seq2.length();\r
 \r
     int len = Math.min(s1len, s2len);\r
 \r
@@ -152,9 +150,9 @@ public class Comparison
 \r
     for (int i = start; i < len; i++)\r
     {\r
-      chr1 =  s1.charAt(i) ;\r
+      chr1 =  seq1.charAt(i) ;\r
 \r
-      chr2 =  s2.charAt(i) ;\r
+      chr2 =  seq2.charAt(i) ;\r
 \r
       if ('a' <= chr1 && chr1 <= 'z')\r
       {\r