bio 1.1.0 → 1.2.0

data/test/unit/bio/sequence/test_aa.rb

@@ -5,7 +5,7 @@
 #               Mitsuteru C. Nakao <n@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: test_aa.rb,v 1.4 2007/04/14 05:09:23 k Exp $
+# $Id: test_aa.rb,v 1.5 2007/12/03 06:19:12 nakao Exp $
 #
 
 require 'pathname'
@@ -19,8 +19,8 @@ require 'bio/sequence/aa'
 
 module Bio
 
-
   class TestSequenceAANew < Test::Unit::TestCase
+
     def test_new
       str = "RRLEHTFVFL RNFSLMLLRY"
       assert(Bio::Sequence::AA.new(str))
@@ -86,6 +86,7 @@ module Bio
              "leucine", "leucine", "arginine", "tyrosine"]
       assert_equal(ary, @obj.names)
     end
+
   end
 
 

data/test/unit/bio/sequence/test_common.rb

@@ -4,7 +4,7 @@
 # Copyright::  Copyright (C) 2006 Mitsuteru C. Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_common.rb,v 1.4 2007/04/05 23:35:44 trevor Exp $
+#  $Id: test_common.rb,v 1.5 2007/12/03 06:19:12 nakao Exp $
 #
 
 require 'pathname'
@@ -31,18 +31,27 @@ module Bio
       assert_equal('atgcatgcatgcatgcaaaa', @obj.to_s)
     end
 
+    def test_to_str
+      assert_equal('atgcatgcatgcatgcaaaa', @obj.to_str)
+    end
+
     def test_seq
       str = "atgcatgcatgcatgcaaaa"
       assert_equal(str, @obj.seq)
     end
 
-
     # <<(*arg)
     def test_push
       str = "atgcatgcatgcatgcaaaaA"
       assert_equal(str, @obj << "A")
     end
 
+    # concat(*arg)
+    def test_concat
+      str = "atgcatgcatgcatgcaaaaA"
+      assert_equal(str, @obj.concat("A"))
+    end
+
     # +(*arg)
     def test_sum 
       str = "atgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaa"

data/test/unit/bio/sequence/test_na.rb

@@ -5,7 +5,7 @@
 #               Mitsuteru C. Nakao <n@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: test_na.rb,v 1.5 2007/04/05 23:35:44 trevor Exp $
+# $Id: test_na.rb,v 1.6 2007/12/03 06:19:12 nakao Exp $
 #
 
 require 'pathname'
@@ -175,6 +175,68 @@ module Bio
 
   end
 
+  class TestSequenceCommon < Test::Unit::TestCase
+
+    def setup
+      @obj  = Bio::Sequence::NA.new('atgcatgcatgcatgcaaaa')
+    end
+
+    def test_to_s
+      assert_equal('atgcatgcatgcatgcaaaa', @obj.to_s)
+    end
+
+    def test_to_str
+      assert_equal('atgcatgcatgcatgcaaaa', @obj.to_str)
+    end
+
+    def test_seq
+      str = "atgcatgcatgcatgcaaaa"
+      assert_equal(str, @obj.seq)
+    end
+
+    # <<(*arg)
+    def test_push
+      str = "atgcatgcatgcatgcaaaaa"
+      assert_equal(str, @obj << "A")
+    end
+
+    # concat(*arg)
+    def test_concat
+      str = "atgcatgcatgcatgcaaaaa"
+      assert_equal(str, @obj.concat("A"))
+    end
+
+    # +(*arg)
+    def test_sum 
+      str = "atgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaa"
+      assert_equal(str, @obj + @obj)
+    end
+
+    # window_search(window_size, step_size = 1)
+    def test_window_search
+      @obj.window_search(4) do |subseq|
+        assert_equal(20, @obj.size)
+      end
+    end
+
+    #total(hash)
+    def test_total
+      hash = {'a' => 1, 'c' => 2, 'g' => 4, 't' => 3}
+      assert_equal(44.0, @obj.total(hash))
+    end
+
+    def test_composition
+      composition = {"a"=>8, "c"=>4, "g"=>4, "t"=>4}
+      assert_equal(composition, @obj.composition)
+    end
+    
+    def test_splicing
+      #(position)
+      assert_equal("atgcatgc", @obj.splicing("join(1..4, 13..16)"))
+    end
+  end
+
+
   class TestSequenceNATranslation < Test::Unit::TestCase
     def setup
 

metadata

@@ -1,10 +1,10 @@
 --- !ruby/object:Gem::Specification 
-rubygems_version: 0.9.2
+rubygems_version: 0.9.4
 specification_version: 1
 name: bio
 version: !ruby/object:Gem::Version 
-  version: 1.1.0
-date: 2007-07-19 00:00:00 +09:00
+  version: 1.2.0
+date: 2007-12-15 00:00:00 +09:00
 summary: Bioinformatics library
 require_paths: 
 - lib
@@ -220,7 +220,6 @@ files:
 - lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_modules.rhtml
 - lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_variables.rhtml
 - lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-bg.gif
-- lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-console.png
 - lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-gem.png
 - lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-link.gif
 - lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.css
@@ -230,6 +229,7 @@ files:
 - lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/commands.rhtml
 - lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/history.rhtml
 - lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/index.rhtml
+- lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/spinner.gif
 - lib/bio/shell/script.rb
 - lib/bio/shell/setup.rb
 - lib/bio/shell/web.rb