From: cmzmasek <chris.zma@outlook.com>
Date: Fri, 9 Jun 2017 20:39:20 +0000 (-0700)
Subject: in progress...
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9fe0c828e4a8e1f61a1acba1e7b8439dd5edc598;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 dede7c7..a61e62a 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, suffix )
+    def extract( first, last, min_non_gap_length, suffix )
       if !is_aligned()
         error_msg = "attempt to extract from unaligned msa"
         raise StandardError, error_msg, caller
@@ -443,17 +443,19 @@ module Evoruby
       msa = Msa.new()
       for i in 0 ... get_number_of_seqs
         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 )
+        unless ( ( subseq.get_length - subseq.get_gap_length ) < min_non_gap_length )
+          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
       end
 
       msa
     end
 
-    def sliding_extraction( step, size, suffix = nil )
+    def sliding_extraction( step, size, min_non_gap_length, suffix = nil )
       counter = 0
       done = false
       msas = Array.new()
@@ -466,7 +468,7 @@ module Evoruby
         end
         unless first >= last
           counter +=1
-          res = extract(first, last, suffix)
+          res = extract(first, last, min_non_gap_length, 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 1d92b60..eebf8f6 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, '_Q' )
+          msas = msa.sliding_extraction( @step, @size, @size / 2, '_Q' )
           begin
             io = MsaIO.new()
             w = MsaWriter