From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Sun, 12 Jul 2009 20:52:48 +0000 (+0000)
Subject: more ruby stuff
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=c7646eddde8b81fe50450d7765568706dad23407;p=biopieces.git

more ruby stuff

git-svn-id: http://biopieces.googlecode.com/svn/trunk@566 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/Maasha/lib/match.rb b/code_ruby/Maasha/lib/match.rb
new file mode 100644
index 0000000..2467b93
--- /dev/null
+++ b/code_ruby/Maasha/lib/match.rb
@@ -0,0 +1,33 @@
+class Match
+	attr_accessor :q_beg, :s_beg, :len
+
+	def initialize( q_beg, s_beg, len )
+		@q_beg = q_beg
+		@s_beg = s_beg
+		@len   = len
+	end
+
+	# Method that expands a match forwards and backwards given two strings.
+	def expand( q_seq, s_seq )
+		self.expand_forward( q_seq, s_seq )
+		self.expand_backward( q_seq, s_seq )
+	end
+
+	# Protected method that expands a match forwards given two strings.
+	def expand_forward( q_seq, s_seq )
+		while @q_beg + @len < q_seq.length and @s_beg + @len < s_seq.length and q_seq[ @q_beg + @len + 1 ] == s_seq[ @s_beg + @len + 1 ]
+			@len += 1
+		end
+	end
+
+	# Protected method that expands a match backwards given two strings.
+	def expand_backward( q_seq, s_seq )
+		while @q_beg > 0 and @s_beg > 0 and q_seq[ @q_beg - 1 ] == s_seq[ @s_beg - 1 ]
+		  @q_beg -= 1
+			@s_beg -= 1
+			@len   += 1
+		end
+	end
+
+	protected :expand_forward, :expand_backward
+end
diff --git a/code_ruby/Maasha/lib/seq.rb b/code_ruby/Maasha/lib/seq.rb
index 26bfee3..99f2124 100644
--- a/code_ruby/Maasha/lib/seq.rb
+++ b/code_ruby/Maasha/lib/seq.rb
@@ -1,5 +1,12 @@
 # Class containing generic sequence methods and nucleic acid and amino acid subclasses.
 class Seq < String
+	attr_accessor :seq, :offset
+
+	def initialize ( seq = "", offset = 0 )
+		super( seq )
+		@offset = offset
+	end
+
 	# Guess the sequence type by analyzing the first 100 residues allowing for ambiguity codes.
 	def guess_type
 		raise ArgumentError, "No sequence." if self.empty?
@@ -43,6 +50,26 @@ class Seq < String
 		self.replace( self.generate( length ) )
 	end
 
+	# Method that returns the next word from a given offset and size.
+	def next_word( size, step = 1 )
+		return nil if @offset + size > self.length
+		word = self[ @offset .. @offset + size - 1 ]
+		@offset += step
+
+		word
+	end
+
+	# Method that creates a list of words from a string.
+	def to_words( size, step = 1 )
+		words = []
+
+		while word = self.next_word( size, step )
+			words << word
+		end
+
+		words
+	end
+
 	# Class containing methods specific for amino acid (AA) sequences.
 	class AA < Seq
 		# Method that returns an array of amino acid residues.
diff --git a/code_ruby/Maasha/test/test_match.rb b/code_ruby/Maasha/test/test_match.rb
new file mode 100755
index 0000000..bec9e4f
--- /dev/null
+++ b/code_ruby/Maasha/test/test_match.rb
@@ -0,0 +1,39 @@
+#!/usr/bin/env ruby
+
+require 'Maasha/lib/match'
+require 'test/unit'
+
+class TestMatch < Test::Unit::TestCase 
+
+	def test_expand_forward
+		match = Match.new( 1, 1, 2 )
+
+		class << match
+			public :expand_forward
+		end
+
+		match.expand_forward( "ATCG", "ATCG" )
+
+		assert_equal( 3, match.len )
+	end
+
+	def test_expand_backward
+		match = Match.new( 1, 1, 2 )
+
+		class << match
+			public :expand_backward
+		end
+
+		match.expand_backward( "ATCG", "ATCG" )
+
+		assert_equal( 3, match.len )
+	end
+
+	def test_expand
+		match = Match.new( 1, 1, 2 )
+
+		match.expand( "ATCG", "ATCG" )
+
+		assert_equal( 4, match.len )
+	end
+end
diff --git a/code_ruby/Maasha/test/test_seq.rb b/code_ruby/Maasha/test/test_seq.rb
index ce6f466..39f4714 100755
--- a/code_ruby/Maasha/test/test_seq.rb
+++ b/code_ruby/Maasha/test/test_seq.rb
@@ -2,6 +2,7 @@
 
 require 'Maasha/lib/seq'
 require 'test/unit'
+require 'pp'
 
 class TestSeq < Test::Unit::TestCase 
 
@@ -183,6 +184,21 @@ class TestSeq < Test::Unit::TestCase
 		assert_equal( 40, s.length )
 	end
 
+	# Testing Seq#next_word
+
+	def test_next_word
+		s = Seq::NA::DNA.new( "ATCG" )
+
+		assert_equal( "AT", s.next_word( 2 ) )
+	end
+
+	# Testing Seq#to_words
+	def test_to_words
+		s = Seq::NA::DNA.new( "ATCG" )
+		
+		assert_equal( "AT", s.to_words( 2 ).first )
+	end
+
 	# Testing Seq::AA#residues
 
 	def test_Seq_AA_residues