From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 6 Dec 2012 11:15:19 +0000 (+0000)
Subject: fixed unit tests
X-Git-Url: https://git.donarmstrong.com/?p=biopieces.git;a=commitdiff_plain;h=98f798c64a0b795f642bceaa06fb9b951a519ead

fixed unit tests

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2036 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index 913f4d9..6c0f35b 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -27,6 +27,9 @@ require 'maasha/seq/digest'
 require 'maasha/seq/trim'
 require 'narray'
 
+autoload :BackTrack, 'maasha/seq/backtrack.rb'
+autoload :Dynamic,   'maasha/seq/dynamic.rb'
+
 # Residue alphabets
 DNA     = %w[a t c g]
 RNA     = %w[a u c g]
diff --git a/code_ruby/lib/maasha/seq/backtrack.rb b/code_ruby/lib/maasha/seq/backtrack.rb
index ab2c00f..c216ec9 100644
--- a/code_ruby/lib/maasha/seq/backtrack.rb
+++ b/code_ruby/lib/maasha/seq/backtrack.rb
@@ -96,8 +96,8 @@ module BackTrack
     end
 
     raise BackTrackError, "Bad pattern: #{pattern}"                                          unless pattern.downcase =~ OK_PATTERN
-    raise BackTrackError, "start: #{start} out of range (0 .. #{self.length - 1})"           unless (0 .. self.length).include? start
-    raise BackTrackError, "stop: #{stop} out of range (0 .. #{self.length - 1})"             unless (0 .. self.length).include? stop
+    raise BackTrackError, "start: #{start} out of range (0 .. #{self.length - 1})"           unless (0 ... self.length).include? start
+    raise BackTrackError, "stop: #{stop} out of range (0 .. #{self.length - 1})"             unless (0 ... self.length).include? stop
     raise BackTrackError, "max_mismatches: #{max_mismatches} out of range (0 .. #{MAX_MIS})" unless (0 .. MAX_MIS).include? max_mismatches
     raise BackTrackError, "max_insertions: #{max_insertions} out of range (0 .. #{MAX_INS})" unless (0 .. MAX_INS).include? max_insertions
     raise BackTrackError, "max_deletions: #{max_deletions} out of range (0 .. #{MAX_DEL})"   unless (0 .. MAX_DEL).include? max_deletions
diff --git a/code_ruby/test/maasha/seq/test_backtrack.rb b/code_ruby/test/maasha/seq/test_backtrack.rb
index 1af799e..6765b17 100644
--- a/code_ruby/test/maasha/seq/test_backtrack.rb
+++ b/code_ruby/test/maasha/seq/test_backtrack.rb
@@ -27,17 +27,13 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib')
 
 require 'test/unit'
 require 'maasha/seq'
-require 'maasha/seq/backtrack'
-
-class Seq
-  include BackTrack
-end
 
 class BackTrackTest < Test::Unit::TestCase
   def setup
     #                       0         1
     #                       01234567890123456789
     @seq = Seq.new("test", "tacgatgctagcatgcacgg")
+    @seq.extend(BackTrack)
   end
 
   def test_BackTrack_patscan_with_bad_pattern_raises
diff --git a/code_ruby/test/maasha/seq/test_dynamic.rb b/code_ruby/test/maasha/seq/test_dynamic.rb
index 8e1121e..b87bacf 100755
--- a/code_ruby/test/maasha/seq/test_dynamic.rb
+++ b/code_ruby/test/maasha/seq/test_dynamic.rb
@@ -26,17 +26,13 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib')
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 require 'maasha/seq'
-require 'maasha/seq/dynamic'
 require 'test/unit'
 require 'pp'
 
-class Seq
-  include Dynamic
-end
-
 class TestDynamic < Test::Unit::TestCase
   def setup
     @p = Seq.new("test", "atcg")
+    @p.extend(Dynamic)
   end
 
   def test_Dynamic_no_match_returns_nil
@@ -125,11 +121,13 @@ class TestDynamic < Test::Unit::TestCase
 
   def test_Dynamic_patscan_locates_three_patterns_ok
     p = Seq.new("test", "ataacgagctagctagctagctgactac")
+    p.extend(Dynamic)
     assert_equal(3, p.patscan("tag").count)
   end
 
   def test_Dynamic_patscan_with_pos_locates_two_patterns_ok
     p = Seq.new("test", "ataacgagctagctagctagctgactac")
+    p.extend(Dynamic)
     assert_equal(2, p.patscan("tag", 10).count)
   end
 end