removed amatch dependency in ruby code

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1307 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/Maasha/lib/digest.rb b/code_ruby/Maasha/lib/digest.rb
index 3268a9d10638adc69cac19d19a724098108f8d1d..727e51c6905b9f452b536224f18bb6bc8b700e58 100644 (file)
--- a/code_ruby/Maasha/lib/digest.rb
+++ b/code_ruby/Maasha/lib/digest.rb
@@ -22,8 +22,6 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-require 'seq'
-
 # Error class for all exceptions to do with Digest.
 class DigestError < StandardError; end
 

diff --git a/code_ruby/Maasha/lib/seq.rb b/code_ruby/Maasha/lib/seq.rb
index 30b4c59aa4940cea44a528b28aa99b15e95da55b..18a09586bb9cb915d2e8c974efc0bfae87f1d17a 100644 (file)
--- a/code_ruby/Maasha/lib/seq.rb
+++ b/code_ruby/Maasha/lib/seq.rb
@@ -22,7 +22,6 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-require 'amatch'
 require 'digest'
 require 'patternmatcher'
 
@@ -40,7 +39,6 @@ SCORE_ILLUMINA = 64
 class SeqError < StandardError; end
 
 class Seq
-  include Amatch
   include PatternMatcher
 
   attr_accessor :seq_name, :seq, :type, :qual
@@ -325,8 +323,6 @@ class Seq
       len          = self.length - pos
       subseq       = self.seq[pos ... pos + len].upcase
       subadaptor   = adaptor[0 ... len].upcase
-      m            = Hamming.new(subseq)
-      hamming_dist = m.match(subadaptor)
       hamming_max  = (len * hd_percent * 0.01).round
       return pos if hamming_dist <= hamming_max
 
@@ -349,8 +345,6 @@ class Seq
       len          = pos
       subseq       = self.seq[0 ... len].upcase
       subadaptor   = adaptor[adaptor.length - len ... adaptor.length].upcase
-      m            = Hamming.new(subseq)
-      hamming_dist = m.match(subadaptor)
       hamming_max  = (len * hd_percent * 0.01).round
 
       pos -= 1