From 1aa28ef25eda19a0ac70e4fc099790fbd5e04ef4 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 16 Aug 2010 10:13:53 +0000
Subject: [PATCH] updateing seq.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1058 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_ruby/Maasha/lib/seq.rb | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/code_ruby/Maasha/lib/seq.rb b/code_ruby/Maasha/lib/seq.rb
index ff5bd44..4ce1e01 100644
--- a/code_ruby/Maasha/lib/seq.rb
+++ b/code_ruby/Maasha/lib/seq.rb
@@ -4,41 +4,41 @@ class Seq < String
 	def guess_type
 		raise ArgumentError, "No sequence." if self.empty?
 
-		seq_beg = self[ 0, 100 ].upcase
+		seq_beg = self[0, 100].upcase
 
 		if seq_beg.count( "FLPQIE" ) > 0
-			Seq::AA.new( self )
-		elsif seq_beg.count( "U" ) > 0
-			Seq::NA::RNA.new( self )
+			Seq::AA.new(self)
+		elsif seq_beg.count("U") > 0
+			Seq::NA::RNA.new(self)
 		else
-			Seq::NA::DNA.new( self )
+			Seq::NA::DNA.new(self)
 		end
 	end
 
 	# Method to wrap a sequence to a given width using a given delimiter.
-	def wrap( width = 80, delimit = "\n" )
-		raise ArgumentError, "Cannot wrap sequence to negative width: #{ width }." if width <= 0
+	def wrap(width = 80, delimit = $/)
+		raise ArgumentError, "Cannot wrap sequence to negative width: #{width}." if width <= 0
 
-		self.delete!( " \t\n\r" )
-		self.gsub( /.{#{ width }}(?!$)/, "\\0#{ delimit }" )
+		self.delete!(" \t\n\r")
+		self.gsub(/.{#{width}}(?!$)/, "\\0#{delimit}")
 	end
 
 	# Method to wrap and replace a sequence to a given width using a given delimiter.
-	def wrap!( width = 80, delimit = "\n" )
-		self.replace( self.wrap( width, delimit ) )
+	def wrap!(width = 80, delimit = $/)
+		self.replace(self.wrap(width, delimit))
 	end
 
 	# Method that generates a random sequence of a given length.
-	def generate( length )
-		raise ArgumentError, "Cannot generate negative sequence length: #{ length }." if length <= 0
+	def generate(length)
+		raise ArgumentError, "Cannot generate negative sequence length: #{length}." if length <= 0
 
 		alph = self.residues
-		Array.new( length ) { alph[ rand( alph.size ) ] }.join( "" )
+		Array.new(length) { alph[rand(alph.size)] }.join("")
 	end
 
 	# Method that replaces sequence with a randomly generated sequence of a given length.
-	def generate!( length )
-		self.replace( self.generate( length ) )
+	def generate!(length)
+		self.replace(self.generate(length))
 	end
 
 	# Class containing methods specific for amino acid (AA) sequences.
-- 
2.39.5