revamped find_homopolymers

[biopieces.git] / code_ruby / lib / maasha / seq.rb

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index 91e79295039e7f8e572efa0ceaf231e8e91c1bd4..2788e5dcc02d78cdb9e3fd38ef83749bad158b79 100644 (file)
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -27,8 +27,9 @@ 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.rb'
+autoload :Dynamic,     'maasha/seq/dynamic.rb'
+autoload :Homopolymer, 'maasha/seq/homopolymer.rb'
 
 # Residue alphabets
 DNA     = %w[a t c g]
@@ -416,6 +417,15 @@ class Seq
     self
   end
 
+  # Method to add two Seq objects.
+  def +(entry)
+    new_entry = Seq.new()
+    new_entry.seq  = self.seq  + entry.seq
+    new_entry.type = self.type              if self.type == entry.type
+    new_entry.qual = self.qual + entry.qual if self.qual and entry.qual
+    new_entry
+  end
+
   # Method to concatenate sequence entries.
   def <<(entry)
     raise SeqError, "sequences of different types" unless self.type == entry.type
@@ -506,23 +516,6 @@ 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