X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FComparison.java;h=3a831d02e0ebfe8df3e267805e12dd9032edaef1;hb=06fef82a8d6fcdcfadc58d747f9f774297cd639d;hp=d8e599ba174eaccc988ad0e47ad65ec8c835013e;hpb=8116c10ff719ac0b542b33dbabfc9051634bf5ea;p=jalview.git

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index d8e599b..3a831d0 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -13,27 +13,17 @@ public class Comparison {
      String si   = ii.getSequence();
      String sj   = jj.getSequence();
 
-     int ilen = end-start+1;
-     int jlen = end-start+1;
+     int ilen = si.length()-1;
+     int jlen = sj.length()-1;
 
-     if ( jalview.util.Comparison.isGap( si.charAt(start+ilen)) )
-      {
+     while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))
+     {
        ilen--;
-
-       while (jalview.util.Comparison.isGap( si.charAt(start+ilen)))
-       {
-         ilen--;
-       }
      }
 
-     if ( jalview.util.Comparison.isGap( sj.charAt(start+jlen)) )
+     while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))
      {
        jlen--;
-
-       while (jalview.util.Comparison.isGap( sj.charAt(start+jlen)))
-       {
-         jlen--;
-       }
      }
 
      int   count = 0;
@@ -63,7 +53,7 @@ public class Comparison {
   }
 
   /**    */
-  public static float PID(Sequence s1 , Sequence s2)
+  public static float PID(SequenceI s1 , SequenceI s2)
   {
     int len;