bio 1.4.3.0001 → 1.5.0

data/setup.rb

@@ -104,7 +104,7 @@ class ConfigTable
   def remove(name)
     item = lookup(name)
     @items.delete_if {|i| i.name == name }
-    @table.delete_if {|name, i| i.name == name }
+    @table.delete_if {|na, i| i.name == na }
     item
   end
 
@@ -189,7 +189,7 @@ class ConfigTable
       path.sub(/\A#{Regexp.quote(c['prefix'])}/, '$prefix')
     }
 
-    if arg = c['configure_args'].split.detect {|arg| /--with-make-prog=/ =~ arg }
+    if arg = c['configure_args'].split.detect {|a| /--with-make-prog=/ =~ a }
       makeprog = arg.sub(/'/, '').split(/=/, 2)[1]
     else
       makeprog = 'make'
@@ -281,7 +281,6 @@ class ConfigTable
     'site-ruby-common' => 'siteruby',     # For backward compatibility
     'site-ruby'        => 'siterubyver',  # For backward compatibility
     'bin-dir'          => 'bindir',
-    'bin-dir'          => 'bindir',
     'rb-dir'           => 'rbdir',
     'so-dir'           => 'sodir',
     'data-dir'         => 'datadir',
@@ -779,14 +778,14 @@ class ToplevelInstaller
   end
 
   def ToplevelInstaller.load_rbconfig
-    if arg = ARGV.detect {|arg| /\A--rbconfig=/ =~ arg }
+    if arg = ARGV.detect {|a| /\A--rbconfig=/ =~ a }
       ARGV.delete(arg)
       load File.expand_path(arg.split(/=/, 2)[1])
       $".push 'rbconfig.rb'
     else
       require 'rbconfig'
     end
-    ::Config::CONFIG
+    ::RbConfig::CONFIG
   end
 
   def initialize(ardir_root, config)
@@ -920,8 +919,8 @@ class ToplevelInstaller
       end
       set.push name
     end
-    evalopt.each do |name, value|
-      @config.lookup(name).evaluate value, @config
+    evalopt.each do |na, va|
+      @config.lookup(na).evaluate va, @config
     end
     # Check if configuration is valid
     set.each do |n|

data/test/data/clustalw/example1-seqnos.aln

@@ -0,0 +1,58 @@
+CLUSTAL 2.0.9 multiple sequence alignment
+
+
+query                      -MKNTLLKLGVCVSLLGITPFVSTISSVQAERTVEHKVIKNETGTISISQ 49
+gi|115023|sp|P10425|       MKKNTLLKVGLCVSLLGTTQFVSTISSVQASQKVEQIVIKNETGTISISQ 50
+gi|115030|sp|P25910|       -MKTVFILISMLFPVAVMAQKSVKIS-----------------DDISITQ 32
+gi|2984094                 MGGFLFFFLLVLFSFSSEYPKHVKET------------------LRKITD 32
+gi|282554|pir||S25844      -------------------------------------------MTVEVRE 7
+                                                                         .: :
+
+query                      LNKNVWVHTELGYFSG-EAVPSNGLVLNTSKGLVLVDSSWDDKLTKELIE 98
+gi|115023|sp|P10425|       LNKNVWVHTELGYFNG-EAVPSNGLVLNTSKGLVLVDSSWDNKLTKELIE 99
+gi|115030|sp|P25910|       LSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVN 82
+gi|2984094                 RIYGVFGVYEQVSYEN-RGFISNAYFYVADDGVLVVDALSTYKLGKELIE 81
+gi|282554|pir||S25844      VAEGVYAYEQAP---G-GWCVSNAGIVVGGDGALVVDTLSTIPRARRLAE 53
+                               *:   .     .     **. .   ..   ::*:       . * :
+
+query                      MVEKKFKKRVTDVIITHAHADRIGGMKTLKERGIKAHSTALTAELAKKNG 148
+gi|115023|sp|P10425|       MVEKKFQKRVTDVIITHAHADRIGGITALKERGIKAHSTALTAELAKKSG 149
+gi|115030|sp|P25910|       WVTDSLHAKVTTFIPNHWHGDCIGGLGYLQRKGVQSYANQMTIDLAKEKG 132
+gi|2984094                 SIRSVTNKPIRFLVVTHYHTDHFYGAKAFREVGAEVIAHEWAFDYISQPS 131
+gi|282554|pir||S25844      WVDKLAAGPGRTVVNTHFHGDHAFGNQVFAP-GTRIIAHEDMRSAMVTTG 102
+                            : .        .: .* * *   *   :   * .  :     .     .
+
+query                      --------------------YEEPLGDLQSVTNLKFGN----MKVETFYP 174
+gi|115023|sp|P10425|       --------------------YEEPLGDLQTVTNLKFGN----TKVETFYP 175
+gi|115030|sp|P25910|       --------------------LPVPEHGFTDSLTVSLDG----MPLQCYYL 158
+gi|2984094                 SYNFFLARKKILKEHLEGTELTPPTITLTKNLNVYLQVGKEYKRFEVLHL 181
+gi|282554|pir||S25844      ----LALTGLWPRVDWGEIELRPPNVTFRDRLTLHVGE----RQVELICV 144
+                                                  *   :    .: .        .:    
+
+query                      GKGHTEDNIVVWLPQYQILAGGCLVKSASSKDLGNVADAYVNEWSTSIEN 224
+gi|115023|sp|P10425|       GKGHTEDNIVVWLPQYQILAGGCLVKSAEAKNLGNVADAYVNEWSTSIEN 225
+gi|115030|sp|P25910|       GGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDK 208
+gi|2984094                 CRAHTNGDIVVWIPDEKVLFSGDIVFDGRLPFLG---SGNSRTWLVCLDE 228
+gi|282554|pir||S25844      GPAHTDHDVVVWLPEERVLFAGDVVMSGVTPFAL---FGSVAGTLAALDR 191
+                             .*:  ::***:*  .:* .* :: .           .        ::.
+
+query                      VLKRYGNINLVVPGHGEVGDR-----GLLLHTLDLLK------------- 256
+gi|115023|sp|P10425|       MLKRYRNINLVVPGHGKVGDK-----GLLLHTLDLLK------------- 257
+gi|115030|sp|P25910|       VKAKFPSARYVVPGHGDYGGT-----ELIEHTKQIVNQYIESTSKP---- 249
+gi|2984094                 ILKMKPRILLPGHGEALIGEKKIK--EAVSWTRKYIKDLRETIRKLYEEG 276
+gi|282554|pir||S25844      LAELEPEVVVGGHGPVAGPEVIDANRDYLRWVQRLAADAVDRRLTPLQAA 241
+                           :            *              :  .                  
+
+query                      --------------------------------------------------
+gi|115023|sp|P10425|       --------------------------------------------------
+gi|115030|sp|P25910|       --------------------------------------------------
+gi|2984094                 --CDVECVRERINEELIKIDPSYAQVPVFF-NVNPVNAYYVYFEIENEIL 323
+gi|282554|pir||S25844      RRADLGAFAGLLDAERLVANLHRAHEELLGGHVRDAMEIFAELVAYNGGQ 291
+                                                                             
+
+query                      ------
+gi|115023|sp|P10425|       ------
+gi|115030|sp|P25910|       ------
+gi|2984094                 MGE--- 326
+gi|282554|pir||S25844      LPTCLA 297
+                                 

data/test/network/bio/appl/blast/test_remote.rb

@@ -1,5 +1,5 @@
 #
-# = test/functional/bio/appl/blast/test_remote.rb - Unit test for Bio::Blast::Remote::Genomenet and Bio::Blast::Remote::DDBJ with network connection
+# = test/functional/bio/appl/blast/test_remote.rb - Unit test for Bio::Blast::Remote::Genomenet with network connection
 #
 # Copyright::   Copyright (C) 2011
 #               Naohisa Goto <ng@bioruby.org>
@@ -74,20 +74,6 @@ module FuncTestBlastRemote
     end
   end #class NetTestBlastRemoteGenomeNet
 
-  # This test class only contains tests for meta information.
-  # BLAST execution tests are written in ../test_blast.rb 
-  class NetTestBlastRemoteDDBJ < Test::Unit::TestCase
-
-    include NetTestBlastRemoteCommon
-
-    BLASTN_DBNAME_KEYWORDS = [ /ddbj/i, /nt/i ]
-    BLASTP_DBNAME_KEYWORDS = [ /uniprot/i, /pdb/i ]
-
-    def setup
-      @klass = Bio::Blast::Remote::DDBJ
-    end
-  end #class NetTestBlastRemoteDDBJ
-
 end #module FuncTestBlastRemote
 end #module Bio
 

data/test/network/bio/appl/test_blast.rb

@@ -44,18 +44,6 @@ module FunctTestBlast
     end
   end #class NetTestBlast_GenomeNet
 
-  class NetTestBlast_DDBJ < Test::Unit::TestCase
-    include NetTestBlastCommonProteinQuery
-
-    def setup
-      @blast = Bio::Blast.new('blastp', 'SWISS',
-                              ['-e', '1e-10',
-                              '-v', '10',
-                              '-b', '10' ],
-                              'ddbj')
-    end
-  end #class NetTestBlast_DDBJ
-
 end #module FuncTestBlast
 end #module Bio
 

data/test/network/bio/io/test_pubmed.rb

@@ -108,6 +108,55 @@ module Bio
       assert(str.index(/\<PubmedArticleSet\>/))
     end
 
+    def test_search
+      a = @pm.search('(bioruby OR ruby) AND bioinformatics')
+      assert_kind_of(Array, a)
+      # Maximum number of results of Bio::PubMed#search is limited to 20.
+      assert_equal(20, a.size,
+                   'The failure may be caused by changes of NCBI PubMed.')
+      a.each do |x|
+        assert_kind_of(String, x)
+        assert_equal(x.strip, x.to_i.to_s,
+                     'PMID is not an integer value. This suggests that NCBI have changed the PMID policy.')
+      end
+    end
+
+    def test_query
+      pmid = 20739307
+      str = @pm.query(pmid)
+      assert_kind_of(String, str)
+      check_pubmed_entry(pmid, str)
+    end
+
+    def test_query_single_str
+      pmid = "20739307"
+      str = @pm.query(pmid)
+      assert_kind_of(String, str)
+      check_pubmed_entry(pmid, str)
+    end
+
+    def test_query_multiple
+      arg = [ "16734914", 16381885, "10592173" ]
+      str = @pm.query(*arg)
+      assert_kind_of(String, str)
+      str.split(/\n\n/).each do |s|
+        check_pubmed_entry(arg.shift, s)
+      end
+    end
+
+    def test_pmfetch
+      pmid = 20739307
+      str = @pm.pmfetch(pmid)
+      assert_kind_of(String, str)
+      check_pubmed_entry(pmid, str)
+    end
+
+    def test_pmfetch_str
+      pmid = "20739307"
+      str = @pm.pmfetch(pmid)
+      assert_kind_of(String, str)
+      check_pubmed_entry(pmid, str)
+    end
   end #module FuncTestPubmedCommon
 
   class FuncTestPubmed < Test::Unit::TestCase

data/test/network/bio/io/test_togows.rb

@@ -5,7 +5,6 @@
 #               Naohisa Goto <ng@bioruby.org>
 # License::     The Ruby License
 #
-#  $Id:$
 #
 
 # loading helper routine for testing bioruby

data/test/network/bio/test_command.rb

@@ -1,7 +1,7 @@
 #
 # test/network/bio/test_command.rb - Functional test for network connection methods in Bio::Command
 #
-# Copyright::	Copyright (C) 2008, 2011
+# Copyright::	Copyright (C) 2008, 2011, 2015
 # 		Naohisa Goto <ng@bioruby.org>
 # License::	The Ruby License
 #
@@ -17,19 +17,82 @@ require 'bio/command'
 
 module Bio
   class FuncTestCommandNet < Test::Unit::TestCase
+    def setup
+      @host = "bioruby.open-bio.org"
+      @port = 80 
+      @path = "/"
+      @url = "http://bioruby.open-bio.org:80/"
+    end
+
     def test_read_uri
+      str = nil
       assert_nothing_raised {
-        Bio::Command.read_uri("http://bioruby.open-bio.org/")
+        str = Bio::Command.read_uri(@url)
       }
+      assert(!str.to_s.empty?)
     end
 
     def test_start_http
+      ht = Bio::Command.start_http(@host, @port)
+      assert_kind_of(Net::HTTP, ht)
+      res = ht.get(@path)
+      assert_kind_of(Net::HTTPResponse, res)
+    end
+
+    def test_start_http_with_block
+      res = Bio::Command.start_http(@host, @port) do |ht|
+        assert_kind_of(Net::HTTP, ht)
+        ht.get(@path)
+      end
+      assert_kind_of(Net::HTTPResponse, res)
+    end
+
+    def test_start_http_default_port
+      ht = Bio::Command.start_http(@host)
+      assert_kind_of(Net::HTTP, ht)
+      res = ht.get(@path)
+      assert_kind_of(Net::HTTPResponse, res)
     end
 
     def test_new_http
+      ht = Bio::Command.new_http(@host, @port)
+      assert_kind_of(Net::HTTP, ht)
+      res = ht.get(@path)
+      assert_kind_of(Net::HTTPResponse, res)
+    end
+
+    def test_new_http_default_port
+      ht = Bio::Command.new_http(@host)
+      assert_kind_of(Net::HTTP, ht)
+      res = ht.get(@path)
+      assert_kind_of(Net::HTTPResponse, res)
     end
 
     def test_post_form
+      res = Bio::Command.post_form(@url, { 'test' => 'bioruby' })
+      assert_kind_of(Net::HTTPResponse, res)
     end
+
+    def test_http_post_form
+      ht = Bio::Command.new_http(@host)
+      res = Bio::Command.http_post_form(ht, @path,
+                                        { 'test' => 'bioruby' },
+                                        { 'Content-Language' => 'en' })
+      assert_kind_of(Net::HTTPResponse, res)
+    end
+
+    def test_post
+      res = Bio::Command.post(@url, "this is test\n" * 10)
+      assert_kind_of(Net::HTTPResponse, res)
+    end
+
+    def test_http_post
+      ht = Bio::Command.new_http(@host)
+      res = Bio::Command.http_post(ht, @path,
+                                        "this is test\n" * 10,
+                                        { 'Content-Language' => 'en' })
+      assert_kind_of(Net::HTTPResponse, res)
+    end
+
   end #class FuncTestCommandNet
 end

data/test/unit/bio/appl/bl2seq/test_report.rb

@@ -40,7 +40,6 @@ module Bio
 
   class TestBl2seqReportConstants < Test::Unit::TestCase
     def test_rs
-      rs = nil
       assert_equal(nil, Bio::Blast::Bl2seq::Report::RS)
       assert_equal(nil, Bio::Blast::Bl2seq::Report::DELIMITER)
     end

data/test/unit/bio/appl/blast/test_report.rb

@@ -62,7 +62,7 @@ module Bio
     end
   end #module TestBlastReportHelper
 
-  class TestBlastReport < Test::Unit::TestCase
+  module TemplateTestBlastReport
     include TestBlastReportHelper
 
     def setup
@@ -90,9 +90,7 @@ module Bio
     end
 
     def test_reference
-      xml_quoted_str = "~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~&quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs&quot;,  Nucleic Acids Res. 25:3389-3402."
       text_str = '~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~"Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs",  Nucleic Acids Res. 25:3389-3402.'
-#      assert_equal(xml_quoted_str, @report.reference)
       assert_equal(text_str, @report.reference)
     end
 
@@ -203,9 +201,10 @@ module Bio
     def test_message
       assert_equal(nil, @report.message)
     end
-  end
-  
-  class TestBlastReportIteration < Test::Unit::TestCase
+  end #module TemplateTestBlastReport
+
+
+  module TemplateTestBlastReportIteration
     include TestBlastReportHelper
 
     def setup
@@ -231,9 +230,10 @@ module Bio
     def test_message
       assert_equal(nil, @itr.message)
     end
-  end
+  end #module TemplateTestBlastReportIteration
 
-  class TestBlastReportHit < Test::Unit::TestCase
+
+  module TemplateTestBlastReportHit
     include TestBlastReportHelper
 
     def setup
@@ -343,9 +343,10 @@ module Bio
     def test_Hit_lap_at
       assert_equal([1, 820, 1, 820], @hit.lap_at)
     end
-  end
+  end #module TemplateTestBlastReportHit
 
-  class TestBlastReportHsp < Test::Unit::TestCase
+
+  module TemplateTestBlastReportHsp
     include TestBlastReportHelper
 
     def setup
@@ -444,37 +445,63 @@ module Bio
       assert_nothing_raised { @hsp.mismatch_count }
     end
 
-  end 
+  end #module TestBlastReportHsp
+
+  class TestBlastReport < Test::Unit::TestCase
+    include TemplateTestBlastReport
+  end
+
+  class TestBlastReportIteration < Test::Unit::TestCase
+    include TemplateTestBlastReportIteration
+  end
 
-  class TestBlastReportREXML < TestBlastReport
+  class TestBlastReportHit < Test::Unit::TestCase
+    include TemplateTestBlastReportHit
   end
 
-  class TestBlastReportIterationREXML < TestBlastReportIteration
+  class TestBlastReportHsp < Test::Unit::TestCase
+    include TemplateTestBlastReportHsp
   end
 
-  class TestBlastReportHitREXML < TestBlastReportHit
+  class TestBlastReportREXML < Test::Unit::TestCase
+    include TemplateTestBlastReport
   end
 
-  class TestBlastReportHspREXML < TestBlastReportHsp
+  class TestBlastReportIterationREXML < Test::Unit::TestCase
+    include TemplateTestBlastReportIteration
+  end
+
+  class TestBlastReportHitREXML < Test::Unit::TestCase
+    include TemplateTestBlastReportHit
+  end
+
+  class TestBlastReportHspREXML < Test::Unit::TestCase
+    include TemplateTestBlastReportHsp
   end
 
   if defined? XMLParser then
 
-  class TestBlastReportXMLParser < TestBlastReport
+  class TestBlastReportXMLParser < Test::Unit::TestCase
+    include TemplateTestBlastReport
   end
 
-  class TestBlastReportIterationXMLParser < TestBlastReportIteration
+  class TestBlastReportIterationXMLParser < Test::Unit::TestCase
+    include TemplateTestBlastReportIteration
   end
 
-  class TestBlastReportHitXMLParser < TestBlastReportHit
+  class TestBlastReportHitXMLParser < Test::Unit::TestCase
+    include TemplateTestBlastReportHit
   end
 
-  class TestBlastReportHspXMLParser < TestBlastReportHsp
+  class TestBlastReportHspXMLParser < Test::Unit::TestCase
+    include TemplateTestBlastReportHsp
   end
 
   end #if defined? XMLParser
 
-  class TestBlastReportDefault < TestBlastReport
+  class TestBlastReportDefault < Test::Unit::TestCase
+    include TemplateTestBlastReport
+
     undef test_entrez_query
     undef test_filter
     undef test_hsp_len
@@ -519,13 +546,16 @@ module Bio
     def test_gapped_entropy
       assert_equal(0.140, @report.gapped_entropy)
     end
-  end
+  end #class TestBlastReportDefault
 
-  class TestBlastReportIterationDefault < TestBlastReportIteration
+  class TestBlastReportIterationDefault < Test::Unit::TestCase
+    include TemplateTestBlastReportIteration
     undef test_statistics
   end
 
-  class TestBlastReportHitDefault < TestBlastReportHit
+  class TestBlastReportHitDefault < Test::Unit::TestCase
+    include TemplateTestBlastReportHit
+
     undef test_Hit_accession
     undef test_Hit_hit_id
     undef test_Hit_num
@@ -560,9 +590,11 @@ module Bio
       seq = @filtered_query_sequence.gsub(/x/, 'X')
       assert_equal(seq, @hit.query_seq)
     end
-  end
+  end #class TestBlastReportHitDefault
+
+  class TestBlastReportHspDefault < Test::Unit::TestCase
+    include TemplateTestBlastReportHsp
 
-  class TestBlastReportHspDefault < TestBlastReportHsp
     undef test_Hsp_density
     undef test_Hsp_mismatch_count
     undef test_Hsp_num
@@ -612,7 +644,8 @@ module Bio
       # differs from XML because not available in the default BLASTP format
       assert_equal(nil, @hsp.query_frame)
     end
-  end
+  end #class TestBlastReportHspDefault
+
 
   module TestBlastReportTabularHelper
     def def_test_assert_nil(test_method)
@@ -634,10 +667,11 @@ module Bio
         assert_nil(instance_variable_get(instance).__send__(method))
       end
     end
-  end #module 
+  end #module TestBlastReportTabularHelper
 
-  class TestBlastReportTabular < TestBlastReport
+  class TestBlastReportTabular < Test::Unit::TestCase
     extend TestBlastReportTabularHelper
+    include TemplateTestBlastReport
 
     def_test_assert_nil :test_db
     def_test_assert_nil :test_db_len
@@ -678,7 +712,8 @@ module Bio
     end
   end #class TestBlastReportTabular
 
-  class TestBlastReportIterationTabular < TestBlastReportIteration
+  class TestBlastReportIterationTabular < Test::Unit::TestCase
+    include TemplateTestBlastReportIteration
 
     # No statistics information available in the "-m 8" format
     def test_statistics
@@ -686,8 +721,9 @@ module Bio
     end
   end #class TestBlastReportIterationTabular
 
-  class TestBlastReportHitTabular < TestBlastReportHit
+  class TestBlastReportHitTabular < Test::Unit::TestCase
     extend TestBlastReportTabularHelper
+    include TemplateTestBlastReportHit
 
     def_test_assert_nil :test_Hit_hit_id
     def_test_assert_nil :test_Hit_identity
@@ -714,8 +750,9 @@ module Bio
     end
   end #class TestBlastReportHitTabular
 
-  class TestBlastReportHspTabular < TestBlastReportHsp
+  class TestBlastReportHspTabular < Test::Unit::TestCase
     extend TestBlastReportTabularHelper
+    include TemplateTestBlastReportHsp
 
     def_test_assert_nil :test_Hsp_density
     def_test_assert_nil :test_Hsp_hit_frame
@@ -738,7 +775,7 @@ module Bio
   # with the result of multiple query sequences
   ########################################################################
 
-  class TestBlastReportMulti < Test::Unit::TestCase
+  module TemplateTestBlastReportMulti
     include TestBlastReportHelper
 
     def setup
@@ -955,9 +992,9 @@ module Bio
         assert_equal(nil, r.message)
       end
     end
-  end
-  
-  class TestBlastReportIterationMulti < Test::Unit::TestCase
+  end #module TemplateTestBlastReportMulti
+
+  module TemplateTestBlastReportIterationMulti
     include TestBlastReportHelper
 
     def setup
@@ -1005,9 +1042,9 @@ module Bio
     def test_message
       assert_equal(nil, @itr.message)
     end
-  end
+  end #module TemplateTestBlastReportIterationMulti
 
-  class TestBlastReportHitMulti < Test::Unit::TestCase
+  module TemplateTestBlastReportHitMulti
     include TestBlastReportHelper
 
     def setup
@@ -1119,9 +1156,9 @@ module Bio
     def test_Hit_lap_at
       assert_equal([190, 311, 569, 668], @hit.lap_at)
     end
-  end
+  end #module TemplateTestBlastReportHitMulti
 
-  class TestBlastReportHspMulti < Test::Unit::TestCase
+  module TemplateTestBlastReportHspMulti
     include TestBlastReportHelper
 
     def setup
@@ -1220,34 +1257,59 @@ module Bio
       assert_nothing_raised { @hsp.mismatch_count }
     end
 
-  end 
+  end #module TemplateTestBlastReportHspMulti
+
+
+  class TestBlastReportMulti < Test::Unit::TestCase
+    include TemplateTestBlastReportMulti
+  end
+
+  class TestBlastReportIterationMulti < Test::Unit::TestCase
+    include TemplateTestBlastReportIterationMulti
+  end
+
+  class TestBlastReportHitMulti < Test::Unit::TestCase
+    include TemplateTestBlastReportHitMulti
+  end
+
+  class TestBlastReportHspMulti < Test::Unit::TestCase
+    include TemplateTestBlastReportHspMulti
+  end
 
   # Tests for REXML version
-  class TestBlastReportMultiREXML < TestBlastReportMulti
+  class TestBlastReportMultiREXML < Test::Unit::TestCase
+    include TemplateTestBlastReportMulti
   end
 
-  class TestBlastReportIterationMultiREXML < TestBlastReportIterationMulti
+  class TestBlastReportIterationMultiREXML < Test::Unit::TestCase
+    include TemplateTestBlastReportIterationMulti
   end
 
-  class TestBlastReportHitMultiREXML < TestBlastReportHitMulti
+  class TestBlastReportHitMultiREXML < Test::Unit::TestCase
+    include TemplateTestBlastReportHitMulti
   end
 
-  class TestBlastReportHspMultiREXML < TestBlastReportHspMulti
+  class TestBlastReportHspMultiREXML < Test::Unit::TestCase
+    include TemplateTestBlastReportHspMulti
   end
 
   # Tests for XMLParser version
   if defined? XMLParser then
 
-  class TestBlastReportMultiXMLParser < TestBlastReportMulti
+  class TestBlastReportMultiXMLParser < Test::Unit::TestCase
+    include TemplateTestBlastReportMulti
   end
 
-  class TestBlastReportIterationMultiXMLParser < TestBlastReportIterationMulti
+  class TestBlastReportIterationMultiXMLParser < Test::Unit::TestCase
+    include TemplateTestBlastReportIterationMulti
   end
 
-  class TestBlastReportHitMultiXMLParser < TestBlastReportHitMulti
+  class TestBlastReportHitMultiXMLParser < Test::Unit::TestCase
+    include TemplateTestBlastReportHitMulti
   end
 
-  class TestBlastReportHspMultiXMLParser < TestBlastReportHspMulti
+  class TestBlastReportHspMultiXMLParser < Test::Unit::TestCase
+    include TemplateTestBlastReportHspMulti
   end
 
   end #if defined? XMLParser