From 3d51113401b585dc2fc813cbe67f8250e2bcfd43 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 28 Nov 2012 18:08:46 +0000
Subject: [PATCH] fixing up backtrack code

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2008 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/remove_primers                       | 2 ++
 code_ruby/lib/maasha/seq.rb                 | 1 -
 code_ruby/lib/maasha/seq/backtrack.rb       | 5 ++++-
 code_ruby/test/maasha/seq/test_backtrack.rb | 2 ++
 4 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/bp_bin/remove_primers b/bp_bin/remove_primers
index 720d943..5f26eb6 100755
--- a/bp_bin/remove_primers
+++ b/bp_bin/remove_primers
@@ -33,6 +33,8 @@ require 'pp'
 require 'maasha/biopieces'
 require 'maasha/seq'
 
+include BackTrack
+
 casts = []
 casts << {:long=>'forward',    :short=>'f', :type=>'string', :mandatory=>true,  :default=>nil, :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'reverse',    :short=>'r', :type=>'string', :mandatory=>true,  :default=>nil, :allowed=>nil, :disallowed=>nil}
diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index a864601..57d70b2 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -78,7 +78,6 @@ class SeqError < StandardError; end
 class Seq
   #include Patscan
   include PatternMatcher
-  include BackTrack
   include Digest
   include Trim
 
diff --git a/code_ruby/lib/maasha/seq/backtrack.rb b/code_ruby/lib/maasha/seq/backtrack.rb
index 0bb5789..714cb22 100644
--- a/code_ruby/lib/maasha/seq/backtrack.rb
+++ b/code_ruby/lib/maasha/seq/backtrack.rb
@@ -65,13 +65,16 @@ module BackTrack
     matches = []
 
     while result = track_C(self.seq, self.length, pattern, offset, max_mismatches, max_insertions, max_deletions)
-      match = Match.new(result[0], result[1], result[2], result[3], result[4], self.seq[result[0] ... result[0] + result[1]])
+      pos, length, mis, ins, del = result
+
+      match = Match.new(pos, length, mis, ins, del, self.seq[pos ... pos + length])
 
       if block_given?
         yield match
       else
         matches << match
       end
+
       offset = match.pos + 1
     end
 
diff --git a/code_ruby/test/maasha/seq/test_backtrack.rb b/code_ruby/test/maasha/seq/test_backtrack.rb
index 43af1de..02260e8 100644
--- a/code_ruby/test/maasha/seq/test_backtrack.rb
+++ b/code_ruby/test/maasha/seq/test_backtrack.rb
@@ -28,6 +28,8 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib')
 require 'test/unit'
 require 'maasha/seq'
 
+include BackTrack
+
 class BackTrackTest < Test::Unit::TestCase
   def setup
     #                       0         1
-- 
2.39.5