polished pairwise alignment code

[biopieces.git] / code_ruby / lib / maasha / align / pair.rb

diff --git a/code_ruby/lib/maasha/align/pair.rb b/code_ruby/lib/maasha/align/pair.rb
index 2c8c523d7e85822fe4a7c10a411bb036d835e265..8bcbf25bddad3a8143e44d43a6c3a20c1e6790af 100644 (file)
--- a/code_ruby/lib/maasha/align/pair.rb
+++ b/code_ruby/lib/maasha/align/pair.rb
@@ -22,7 +22,7 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-require 'maasha/align/match'
+require 'maasha/align/matches'
 require 'maasha/math_aux'
 
 FACTOR_SCORE_LENGTH =  1.0
@@ -69,6 +69,7 @@ module PairAlign
 
       while (matches.size == 0 and kmer > 0)
         matches = Matches.find(q_seq, s_seq, space.q_min, space.s_min, space.q_max, space.s_max, kmer)
+        #matches = Mem.find(q_seq, s_seq, kmer, space.q_min, space.s_min, space.q_max, space.s_max)
 
         if @matches.empty?
           matches.sort_by! { |m| m.length }