X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fevoruby%2Flib%2Fevo%2Ftool%2Fmsa_processor.rb;h=1d92b60a00a217921affcd67c9d766b9eac05d3b;hb=592097c9d8ed6ed0a74bca26ee12454d774cd345;hp=1bcaeb30f7013876b29103a11452dfca96ccecbc;hpb=e32f4ddeda628ec89e93834f4ec00b0e0bd70e0b;p=jalview.git

diff --git a/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb b/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb
index 1bcaeb3..1d92b60 100644
--- a/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb
@@ -377,7 +377,7 @@ module Evoruby
         end
 
         if @window
-          msas = msa.sliding_extraction( @step, @size )
+          msas = msa.sliding_extraction( @step, @size, '_Q' )
           begin
             io = MsaIO.new()
             w = MsaWriter