From: cmzmasek <chris.zma@outlook.com>
Date: Fri, 9 Jun 2017 20:27:07 +0000 (-0700)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=592097c9d8ed6ed0a74bca26ee12454d774cd345;p=jalview.git

in progress
---

diff --git a/forester/ruby/evoruby/lib/evo/msa/msa.rb b/forester/ruby/evoruby/lib/evo/msa/msa.rb
index 1cdc78d..dede7c7 100644
--- a/forester/ruby/evoruby/lib/evo/msa/msa.rb
+++ b/forester/ruby/evoruby/lib/evo/msa/msa.rb
@@ -423,7 +423,7 @@ module Evoruby
       end
     end
 
-    def extract( first, last )
+    def extract( first, last, suffix )
       if !is_aligned()
         error_msg = "attempt to extract from unaligned msa"
         raise StandardError, error_msg, caller
@@ -442,12 +442,18 @@ module Evoruby
       end
       msa = Msa.new()
       for i in 0 ... get_number_of_seqs
-        msa.add_sequence( get_sequence( i ).get_subsequence( first, last ) )
+        subseq = get_sequence( i ).get_subsequence( first, last )
+        if suffix != nil
+          msa.add( subseq.get_name + suffix, subseq.get_sequence_as_string )
+        else
+          msa.add( subseq.get_name, subseq.get_sequence_as_string )
+        end
       end
+
       msa
     end
 
-    def sliding_extraction( step, size )
+    def sliding_extraction( step, size, suffix = nil )
       counter = 0
       done = false
       msas = Array.new()
@@ -460,7 +466,7 @@ module Evoruby
         end
         unless first >= last
           counter +=1
-          res = extract( first, last)
+          res = extract(first, last, suffix)
           res.set_name(first.to_s + "-" + last.to_s)
           msas << res
         end
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