X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=2340283ea2e31f0f538a1b4561f411ca3fb95e6f;hb=f8b17a9e7363b8a9e7cd12d61bc6d611c7c97d7d;hp=a603ccac45d6d9577a076be41a481c2bf253230c;hpb=05d220bbea0e8ce667490219436b96ebdf9826df;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index a603cca..2340283 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -174,11 +174,6 @@ public abstract class AlignFile extends FileParse
     }
     parseCalled = true;
     parse();
-    // sets the index of each sequence in the alignment
-    for (int i = 0, c = seqs.size(); i < c; i++)
-    {
-      seqs.get(i).setIndex(i);
-    }
   }
 
   /**