paintFlag removed

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

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