X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=code_ruby%2Flib%2Fmaasha%2Fseq.rb;h=e4b6bfd7c27d5933d0bd9c6b65210bd9a7b32ea0;hb=b2ea0b5a51a558478af60e9df4c643dd58552086;hp=d8a73d31ba8d660fa08bb6aac9c0c24f91137151;hpb=351549b36ba20cf06daf9cf0e14273d84ae1f83e;p=biopieces.git

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index d8a73d3..e4b6bfd 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -27,8 +27,10 @@ require 'maasha/seq/digest'
 require 'maasha/seq/trim'
 require 'narray'
 
-autoload :BackTrack, 'maasha/seq/backtrack.rb'
-autoload :Dynamic,   'maasha/seq/dynamic.rb'
+autoload :BackTrack,   'maasha/seq/backtrack'
+autoload :Dynamic,     'maasha/seq/dynamic'
+autoload :Homopolymer, 'maasha/seq/homopolymer'
+autoload :Levenshtein, 'maasha/seq/levenshtein'
 
 # Residue alphabets
 DNA     = %w[a t c g]
@@ -67,7 +69,6 @@ TRANS_TAB11 = {
   "GTG" => "V", "GCG" => "A", "GAG" => "E", "GGG" => "G"
 }
 
-
 # Error class for all exceptions to do with Seq.
 class SeqError < StandardError; end
 
@@ -383,8 +384,14 @@ class Seq
 
   # Method to determine the Hamming Distance between
   # two Sequence objects (case insensitive).
-  def hamming_distance(seq)
-    self.seq.upcase.hamming_distance(seq.seq.upcase)
+  def hamming_distance(entry)
+    self.seq.upcase.hamming_distance(entry.seq.upcase)
+  end
+
+  # Method to determine the Edit Distance between
+  # two Sequence objects (case insensitive).
+  def edit_distance(entry)
+    Levenshtein.distance(self.seq, entry.seq)
   end
 
   # Method that generates a random sequence of a given length and type.
@@ -515,23 +522,6 @@ class Seq
     comp
   end
 
-  # Method that returns the length of the longest homopolymeric stretch
-  # found in a sequence.
-  def homopol_max(min = 1)
-    return 0 if self.seq.nil? or self.seq.empty?
-
-    found = false
-
-    self.seq.upcase.scan(/A{#{min},}|T{#{min},}|G{#{min},}|C{#{min},}|N{#{min},}/) do |match|
-      found = true
-      min   = match.size > min ? match.size : min
-    end
-
-    return 0 unless found
- 
-    min
-  end
-
   # Method that returns the percentage of hard masked residues
   # or N's in a sequence.
   def hard_mask