bio 1.0.0 → 1.1.0

data/test/unit/bio/io/test_soapwsdl.rb

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/io/test_soapwsdl.rb - Unit test for SOAP/WSDL
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copytight::   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::     The Ruby License
 #
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: test_soapwsdl.rb,v 1.1 2005/12/18 17:09:53 nakao Exp $ 
+#  $Id: test_soapwsdl.rb,v 1.3 2007/04/05 23:35:43 trevor Exp $ 
 #
 
 require 'pathname'
@@ -37,7 +24,7 @@ class TestSOAPWSDL < Test::Unit::TestCase
   end
 
   def test_methods
-    methods = ['wsdl', 'wsdl=', 'log', 'log=']
+    methods = ['list_methods','wsdl', 'wsdl=', 'log', 'log=']
     assert_equal(methods.sort, (@obj.instance_methods - Object.methods).sort)
   end
 

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

@@ -3,9 +3,9 @@
 #
 # Copyright::   Copyright (C) 2006 
 #               Mitsuteru C. Nakao <n@bioruby.org>
-# Lisence::     Ruby's
+# License::     The Ruby License
 #
-# $Id: test_aa.rb,v 1.1 2006/02/08 07:20:24 nakao Exp $
+# $Id: test_aa.rb,v 1.4 2007/04/14 05:09:23 k Exp $
 #
 
 require 'pathname'
@@ -67,7 +67,7 @@ module Bio
       re = /RRLEHTFVFLRNFSLMLLRY/
       assert_equal(re, @obj.to_re)
       @obj[1, 1] = 'B'
-      re = /R[DN]LEHTFVFLRNFSLMLLRY/
+      re = /R[DNB]LEHTFVFLRNFSLMLLRY/
       assert_equal(re, @obj.to_re)
     end
 

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

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/sequence/test_common.rb - Unit test for Bio::Sequencce::Common
 #
-#   Copyright (C) 2006 Mitsuteru C. Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2006 Mitsuteru C. Nakao <n@bioruby.org>
+# License::    The Ruby License
 #
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: test_common.rb,v 1.2 2006/02/07 16:53:08 nakao Exp $
+#  $Id: test_common.rb,v 1.4 2007/04/05 23:35:44 trevor Exp $
 #
 
 require 'pathname'

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

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/sequence/test_compat.rb - Unit test for Bio::Sequencce::Compat
 #
-#   Copyright (C) 2006 Mitsuteru C. Nakao <n@bioruby.org>
+# Copyright::   Copyright (C) 2006 Mitsuteru C. Nakao <n@bioruby.org>
+# License::     The Ruby License
 #
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: test_compat.rb,v 1.1 2006/02/05 17:39:27 nakao Exp $
+#  $Id: test_compat.rb,v 1.3 2007/04/05 23:35:44 trevor Exp $
 #
 
 require 'pathname'

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

@@ -3,9 +3,9 @@
 #
 # Copyright::   Copyright (C) 2006 
 #               Mitsuteru C. Nakao <n@bioruby.org>
-# Lisence::     Ruby's
+# License::     The Ruby License
 #
-# $Id: test_na.rb,v 1.1 2006/02/08 07:08:22 nakao Exp $
+# $Id: test_na.rb,v 1.5 2007/04/05 23:35:44 trevor Exp $
 #
 
 require 'pathname'
@@ -98,6 +98,32 @@ module Bio
       assert_equal(45, @obj.gc_percent)
     end
 
+    def test_gc_content
+      assert_in_delta(0.4, @obj.gc_content, Float::EPSILON)
+      @obj[0, 1] = 'g'
+      assert_in_delta(0.45, @obj.gc_content, Float::EPSILON)
+    end
+
+    def test_at_content
+      assert_in_delta(0.6, @obj.at_content, Float::EPSILON)
+      @obj[0, 1] = 'g'
+      assert_in_delta(0.55, @obj.at_content, Float::EPSILON)
+    end
+
+    def test_gc_skew
+      assert_in_delta(0.0, @obj.gc_skew, Float::EPSILON)
+      @obj[0, 1] = 'g'
+      assert_in_delta(1.0/9.0, @obj.gc_skew, Float::EPSILON)
+      @obj.gsub!(/a/, 'c')
+      assert_in_delta(-3.0/8.0, @obj.gc_skew, Float::EPSILON)
+    end
+
+    def test_at_skew
+      assert_in_delta(1.0/3.0, @obj.at_skew, Float::EPSILON)
+      @obj[0, 1] = 'g'
+      assert_in_delta(3.0/11.0, @obj.at_skew, Float::EPSILON)
+    end
+
     def test_iliegal_bases
       @obj[0, 1] = 'n'
       @obj[1, 1] = 'y'
@@ -115,7 +141,7 @@ module Bio
       @obj[3,1] = 's'
       @obj[4,1] = 'y'
       @obj[5,1] = 'w'
-      assert_equal(/a[atgc][ag][gc][tc][at]gcatgcatgcaaaa/, @obj.to_re)
+      assert_equal(/a[atgcyrwskmbdhvn][agr][gcw][tcy][atw]gcatgcatgcaaaa/, @obj.to_re)
     end
 
     def test_names

data/test/unit/bio/shell/plugin/test_seq.rb

@@ -3,9 +3,9 @@
 #
 # Copyright::   Copyright (C) 2005 
 #               Mitsuteru Nakao <n@bioruby.org>
-# License::     Ruby's
+# License::     The Ruby License
 #
-# $Id: test_seq.rb,v 1.7 2006/02/27 09:40:13 nakao Exp $
+# $Id: test_seq.rb,v 1.9 2007/04/05 23:35:44 trevor Exp $
 #
 
 require 'pathname'
@@ -40,17 +40,17 @@ END
 
     def test_naseq
       str = 'ACGT'
-      assert_equal(Bio::Sequence::NA, seq(str).class)
-      assert_equal(Bio::Sequence::NA.new(str), seq(str))
-      assert_equal('acgt', seq(str))
+      assert_equal(Bio::Sequence, getseq(str).class)
+      assert_equal(Bio::Sequence::NA, getseq(str).moltype)
+      assert_equal('acgt', getseq(str).seq)
     end
 
 
     def test_aaseq
       str = 'WD'
-      assert_equal(Bio::Sequence::AA, seq(str).class)
-      assert_equal(Bio::Sequence::AA.new('WD'), seq(str))
-      assert_equal('WD', seq(str))
+      assert_equal(Bio::Sequence, getseq(str).class)
+      assert_equal(Bio::Sequence::AA, getseq(str).moltype)
+      assert_equal('WD', getseq(str).seq)
     end
 
 

data/test/unit/bio/test_alignment.rb

@@ -1,24 +1,12 @@
 #
 # test/unit/bio/test_alignment.rb - Unit test for Bio::Alignment
 #
-#   Copyright (C) 2004 Moses Hohman <mmhohman@northwestern.edu>
-#                 2005 Naohisa Goto <ng@bioruby.org>
+# Copyright::  Copyright (C) 2004
+#              Moses Hohman <mmhohman@northwestern.edu>
+#              2005 Naohisa Goto <ng@bioruby.org>
+# License::    The Ruby License
 #
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: test_alignment.rb,v 1.7 2006/01/24 14:11:34 ngoto Exp $
+#  $Id: test_alignment.rb,v 1.11 2007/04/05 23:35:42 trevor Exp $
 #
 
 require 'pathname'
@@ -544,34 +532,35 @@ module Bio
     end
   end #class TestAlignmentEnumerableExtension
 
-  class TestAlignmentClustalWFormatter < Test::Unit::TestCase
+  class TestAlignmentOutput < Test::Unit::TestCase
     def setup
       @obj = Object.new
-      @obj.extend(Alignment::ClustalWFormatter)
+      @obj.extend(Alignment::Output)
     end
 
-    def test_have_same_name_true
+    def test_clustal_have_same_name_true
       assert_equal([ 0, 1 ], @obj.instance_eval {
-                     have_same_name?([ 'ATP ATG', 'ATP ATA', 'BBB' ]) })
+               __clustal_have_same_name?([ 'ATP ATG', 'ATP ATA', 'BBB' ]) })
     end
 
     def test_have_same_name_false
       assert_equal(false, @obj.instance_eval {
-               have_same_name?([ 'GTP ATG', 'ATP ATA', 'BBB' ]) })
+               __clustal_have_same_name?([ 'GTP ATG', 'ATP ATA', 'BBB' ]) })
     end
 
     def test_avoid_same_name
       assert_equal([ 'ATP_ATG', 'ATP_ATA', 'BBB' ],
-                   @obj.instance_eval {
-                     avoid_same_name([ 'ATP ATG', 'ATP ATA', 'BBB' ]) })
+               @obj.instance_eval {
+                 __clustal_avoid_same_name([ 'ATP ATG', 'ATP ATA', 'BBB' ]) })
     end
+
     def test_avoid_same_name_numbering
       assert_equal([ '0_ATP', '1_ATP', '2_BBB' ],
-                   @obj.instance_eval {
-                     avoid_same_name([ 'ATP', 'ATP', 'BBB' ]) })
+               @obj.instance_eval {
+                 __clustal_avoid_same_name([ 'ATP', 'ATP', 'BBB' ]) })
     end
 
-  end #class TestAlignmentClustalWFormatter
+  end #class TestAlignmentOutput
 
 
   class TestAlignment < Test::Unit::TestCase

data/test/unit/bio/test_command.rb

@@ -1,23 +1,12 @@
 #
 # test/unit/bio/test_command.rb - Unit test for external command execution methods
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::	Copyright (C) 2005-2006
+#               Mitsuteru Nakao <n@bioruby.org>,
+# 		Naohisa Goto <ng@bioruby.org>
+# License::	The Ruby License
 #
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: test_command.rb,v 1.1 2005/10/27 15:11:51 nakao Exp $
+#  $Id: test_command.rb,v 1.5 2007/04/05 23:35:42 trevor Exp $
 #
 
 require 'pathname'
@@ -29,42 +18,270 @@ require 'test/unit'
 require 'bio/command'
 
 module Bio
-  class TestCommandTools < Test::Unit::TestCase
+  class TestCommand < Test::Unit::TestCase
     
-    def test_command_tools_constants
-      Bio::Command::Tools::UNSAFE_CHARS_UNIX
-      Bio::Command::Tools::QUOTE_CHARS_WINDOWS
-      Bio::Command::Tools::UNESCAPABLE_CHARS
+    def test_command_constants
+      Bio::Command::UNSAFE_CHARS_UNIX
+      Bio::Command::QUOTE_CHARS_WINDOWS
+      Bio::Command::UNESCAPABLE_CHARS
     end
 
     def test_escape_shell_windows
+      str = "bio_ruby.123@456:789"
+      assert_equal("bio_ruby.123@456:789",
+                   Bio::Command.escape_shell_windows(str))
+      str = "bio\'\"r u\"b\\y123@456:789"
+      assert_equal("\"bio'\"\"r u\"\"b\\y123@456:789\"",
+                   Bio::Command.escape_shell_windows(str))
     end
 
     def test_escape_shell_unix
+      str = "bio_ruby.123@456:789"
+      assert_equal("bio_ruby.123@456:789",
+                   Bio::Command.escape_shell_unix(str))
+      str = "bio\'\"r u\"b\\y123@456:789"
+      assert_equal("bio\\'\\\"r\\ u\\\"b\\\\y123@456:789",
+                   Bio::Command.escape_shell_unix(str))
     end
 
     def test_escape_shell
+      str = "bio_ruby.123@456:789"
+      assert_equal("bio_ruby.123@456:789",
+                   Bio::Command.escape_shell(str))
+      str = "bio\'\"r u\"b\\y123@456:789"
+      case RUBY_PLATFORM
+      when /mswin32|bccwin32/
+        assert_equal("\"bio'\"\"r u\"\"b\\y123@456:789\"",
+                     Bio::Command.escape_shell(str))
+      else
+        assert_equal("bio\\'\\\"r\\ u\\\"b\\\\y123@456:789",
+                     Bio::Command.escape_shell(str))
+      end
     end
 
     def test_make_command_line
+      ary = [ "ruby", 
+        "test.rb", "atgcatgc", "bio\'\"r u\"b\\y123@456:789" ]
+      case RUBY_PLATFORM
+      when /mswin32|bccwin32/
+        assert_equal("ruby" + 
+                       " test.rb atgcatgc" + 
+                       " \"bio'\"\"r u\"\"b\\y123@456:789\"",
+                     Bio::Command.make_command_line(ary))
+      else
+        assert_equal("ruby" + 
+                       " test.rb atgcatgc" + 
+                       " bio\\'\\\"r\\ u\\\"b\\\\y123@456:789",
+                     Bio::Command.make_command_line(ary))
+      end
     end
 
     def test_make_command_line_windows
+      ary = [ "C:\\Program Files\\Ruby\\bin\\ruby.exe", 
+        "test.rb", "atgcatgc", "bio\'\"r u\"b\\y123@456:789" ]
+      assert_equal("\"C:\\Program Files\\Ruby\\bin\\ruby.exe\"" + 
+                     " test.rb atgcatgc" + 
+                     " \"bio'\"\"r u\"\"b\\y123@456:789\"",
+                   Bio::Command.make_command_line_windows(ary))
     end
 
     def test_make_command_line_unix
+      ary = [ "/usr/local/bin/ruby", 
+        "test.rb", "atgcatgc", "bio\'\"r u\"b\\y123@456:789" ]
+      assert_equal("/usr/local/bin/ruby" + 
+                     " test.rb atgcatgc" +
+                     " bio\\'\\\"r\\ u\\\"b\\\\y123@456:789",
+                   Bio::Command.make_command_line_unix(ary))
+    end
+
+    def test_call_command
+    end
+
+    def test_call_command_popen
+    end
+
+    def test_call_command_fork
+    end
+
+    def test_call_command_open3
+    end
+
+    def test_query_command
+    end
+
+    def test_query_command_popen
+    end
+
+    def test_query_command_fork
+    end
+
+    def test_query_command_open3
+    end
+
+    def test_read_uri
+    end
+
+    def test_start_http
+    end
+
+    def test_new_http
+    end
+
+    def test_post_form
+    end
+
+    def test_make_cgi_params_by_hash_in_symbol
+      ary = [
+             "type1=bp",
+             "type2=bp",
+             "downstream=",
+             "upstream=",
+             "format=fasta",
+             "options=similarity",
+             "options=gene",
+             "action=export",
+             "_format=Text",
+             "output=txt",
+             "submit=Continue%20%3E%3E",
+            ]
+      hash = {
+        :type1 => 'bp',
+        :type2 => 'bp',
+        :downstream => '',
+        :upstream => '',
+        :format => 'fasta',
+        :options => ['similarity', 'gene'],
+        :action => 'export',
+        :_format => 'Text',
+        :output => 'txt',
+        :submit => 'Continue >>',
+      }
+      result = Bio::Command.make_cgi_params(hash)
+      ary.each do |str|
+        assert_match(str, result)
+      end
+    end
+
+    def test_make_cgi_params_by_hash_in_string
+      ary = [
+             "type1=bp",
+             "type2=bp",
+             "downstream=",
+             "upstream=",
+             "format=fasta",
+             "options=similarity",
+             "options=gene",
+             "action=export",
+             "_format=Text",
+             "output=txt",
+             "submit=Continue%20%3E%3E",
+            ]
+      hash = {
+        "type1" => 'bp',
+        "type2" => 'bp',
+        "downstream" => '',
+        "upstream" => '',
+        "format" => 'fasta',
+        "options" => ['similarity', 'gene'],
+        "action" => 'export',
+        "_format" => 'Text',
+        "output" => 'txt',
+        "submit" => 'Continue >>',
+      }
+      result = Bio::Command.make_cgi_params(hash)
+      ary.each do |str|
+        assert_match(str, result)
+      end
     end
 
-    def test_call_commandline_local
+    def test_make_cgi_params_by_array_of_array
+      ary = [
+             "type1=bp",
+             "type2=bp",
+             "downstream=",
+             "upstream=",
+             "format=fasta",
+             "options=similarity",
+             "options=gene",
+             "action=export",
+             "_format=Text",
+             "output=txt",
+             "submit=Continue%20%3E%3E",
+            ]
+      array_of_array = [
+        ["type1", 'bp'],
+        ["type2", 'bp'], 
+        ["downstream", ''],
+        ["upstream", ''],
+        ["format", 'fasta'],
+        ["options", ['similarity', 'gene']],
+        ["action", 'export'],
+        ["_format", 'Text'],
+        ["output", 'txt'],
+        ["submit", 'Continue >>'],
+      ]
+      result = Bio::Command.make_cgi_params(array_of_array)
+      ary.each do |str|
+        assert_match(str, result)
+      end
     end
 
-    def test_call_commandline_local_popen
+    def test_make_cgi_params_by_array_of_hash
+      ary = [
+             "type1=bp",
+             "type2=bp",
+             "downstream=",
+             "upstream=",
+             "format=fasta",
+             "options=similarity",
+             "options=gene",
+             "action=export",
+             "_format=Text",
+             "output=txt",
+             "submit=Continue%20%3E%3E",
+            ]
+      array_of_hash = [
+                       {"type1" => 'bp'},
+                       {"type2" => 'bp'},
+                       {"downstream" => ''},
+                       {"upstream" => ''},
+                       {"format" => 'fasta'},
+                       {"options" => ['similarity', 'gene']},
+                       {"action" => 'export'},
+                       {"_format" => 'Text'},
+                       {"output" => 'txt'},
+                       {"submit" => 'Continue >>'},
+                      ]
+      result = Bio::Command.make_cgi_params(array_of_hash)
+      ary.each do |str|
+        assert_match(str, result)
+      end
     end
 
-    def test_call_commandline_local_open3
+    def test_make_cgi_params_by_array_of_string
+      str = "type1=bp&type2=bp&downstream=&upstream=&format=fasta&options=similarity&options=gene&action=export&_format=Text&output=txt&submit=Continue%20%3E%3E"
+      array_of_string = [
+                         "type1=bp",
+                         "type2=bp",
+                         "downstream=",
+                         "upstream=",
+                         "format=fasta",
+                         "options=similarity",
+                         "options=gene",
+                         "action=export",
+                         "_format=Text",
+                         "output=txt",
+                         "submit=Continue >>",
+                        ]
+      result = Bio::Command.make_cgi_params(array_of_string)
+      assert_equal(str, result)
     end
 
-    def test_errorlog
+    def test_make_cgi_params_by_string
+      string = "type1=bp&type2=bp&downstream=&upstream=&format=fasta&options=similarity&options=gene&action=export&_format=Text&output=txt&submit=Continue%20%3E%3E"
+      query = " type1=bp&type2=bp&downstream=&upstream=&format=fasta&options=similarity&options=gene&action=export&_format=Text&output=txt&submit=Continue >> "
+      result = Bio::Command.make_cgi_params(query)
+      assert_equal(string, result)
     end
 
   end