From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 16 Dec 2010 12:17:47 +0000 (+0000)
Subject: speedup fix of max_homopol
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=13f4ed32debae50e9212343ef65a4cf42fa8b39c;p=biopieces.git

speedup fix of max_homopol

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1190 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/Maasha/lib/seq.rb b/code_ruby/Maasha/lib/seq.rb
index a6f071d..23e6965 100644
--- a/code_ruby/Maasha/lib/seq.rb
+++ b/code_ruby/Maasha/lib/seq.rb
@@ -165,12 +165,12 @@ class Seq
   # Method that returns the length of the longest homopolymeric stretch
   # found in a sequence.
   def homopol_max
-    max = 0
+    max = 1
 
-    if self.seq
-      self.seq.upcase.scan(/[A]+|[T]+|[G]+|[C]+|[N]+/) do |match|
-        max = [match.size, max].max
-      end
+    return 0 if self.seq.nil? or self.seq.empty?
+
+    self.seq.upcase.scan(/A{#{max},}|T{#{max},}|G{#{max},}|C{#{max},}|N{#{max},}/) do |match|
+      max = [match.size, max].max
     end
 
     max