X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FComparison.java;h=d35d84cf53eff789efa86f539b8b82480bf12bf4;hb=d8c6e303402455460fb1d987b4c18a2d75e6a3c9;hp=9e0aef6ee00024ea568591bd4db4fe194b6441d6;hpb=eae7c51e082c38ead935bf5c28d46120abca86bf;p=jalview.git

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