bio 1.0.0 → 1.1.0

data/test/unit/bio/db/test_prosite.rb

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/db/test_prosite.rb - Unit test for Bio::PROSITE
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::  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_prosite.rb,v 1.3 2005/12/18 18:21:58 k Exp $
+#  $Id: test_prosite.rb,v 1.6 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'
@@ -1438,12 +1425,12 @@ module Bio
 
     def test_pa2re
       pa = '[AC]-x-V-x(4)-{ED}.'
-      assert_equal(/[AC].V.{4}[^ED]/, @obj.pa2re(pa))
+      assert_equal(/[AC].V.{4}[^ED]/i, @obj.pa2re(pa))
     end
 
     def test_self_pa2re
       pa = '[AC]-x-V-x(4)-{ED}.'
-      assert_equal(/[AC].V.{4}[^ED]/, Bio::PROSITE.pa2re(pa))
+      assert_equal(/[AC].V.{4}[^ED]/i, Bio::PROSITE.pa2re(pa))
     end
 
   end # class TestPROSITE

data/test/unit/bio/db/test_rebase.rb

@@ -1,30 +1,11 @@
 #
 # test/unit/bio/db/test_rebase.rb - Unit test for Bio::REBASE
 #
-# Copyright::  Copyright (C) 2005 Trevor Wennblom <trevor@corevx.com>
-# License::    LGPL
-#
-#  $Id: test_rebase.rb,v 1.2 2006/01/20 09:53:24 k Exp $
-#
-#
-#--
-#
-#  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
-#
-#++
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+# License::   The Ruby License
 #
+#  $Id: test_rebase.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'
@@ -34,8 +15,8 @@ $:.unshift(libpath) unless $:.include?(libpath)
 require 'test/unit'
 require 'bio/db/rebase'
 
-module Bio
-  class TestREBASE < Test::Unit::TestCase
+module Bio #:nodoc:
+  class TestREBASE < Test::Unit::TestCase #:nodoc:
     
     def setup
       enzyme_data = <<END
@@ -108,6 +89,11 @@ END
 
       assert_equal(a['AatI'].supplier_names, ['Toyobo Biochemicals'])
       assert_equal(a['AatI'].suppliers, ['O'])
+      
+      assert_equal(a.enzyme_name?('aasi'), true)
+      assert_equal(a.enzyme_name?('AarI'), true)
+      assert_equal(a.enzyme_name?('Aari'), true)
+      assert_equal(a.enzyme_name?('AbrI'), false)
     end
 
   end

data/test/unit/bio/db/test_soft.rb

@@ -0,0 +1,138 @@
+#
+# test/unit/bio/db/test_rebase.rb - Unit test for Bio::REBASE
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+# License::   The Ruby License
+#
+#  $Id: test_soft.rb,v 1.3 2007/04/05 23:35:43 trevor Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/db/soft'
+
+module Bio #:nodoc:
+  class TestSOFT < Test::Unit::TestCase #:nodoc:
+    
+    def setup
+      bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4)).cleanpath.to_s
+      test_data_path = Pathname.new(File.join(bioruby_root, 'test', 'data', 'soft')).cleanpath.to_s
+      series_filename = File.join(test_data_path, 'GSE3457_family_partial.soft')
+      dataset_filename = File.join(test_data_path, 'GDS100_partial.soft')
+
+      @obj_series = Bio::SOFT.new( IO.readlines(series_filename))
+      @obj_dataset = Bio::SOFT.new( IO.readlines(dataset_filename))
+    end
+
+    def test_series
+      assert_equal( @obj_series.platform[:geo_accession], 'GPL2092')
+      assert_equal( @obj_series.platform[:organism], 'Populus')
+      assert_equal( @obj_series.platform[:contributor], ["Jingyi,,Li", "Olga,,Shevchenko", "Steve,H,Strauss", "Amy,M,Brunner"])
+      assert_equal( @obj_series.platform[:data_row_count], '240')
+      assert_equal( @obj_series.platform.keys.sort {|a,b| a.to_s <=> b.to_s}[0..2], [:contact_address, :contact_city, :contact_country])
+      assert_equal( @obj_series.platform[:"contact_zip/postal_code"], '97331')
+      assert_equal( @obj_series.platform[:table].header, ["ID", "GB_ACC", "SPOT_ID", "Function/Family", "ORGANISM", "SEQUENCE"])             
+      assert_equal( @obj_series.platform[:table].header_description, {"ORGANISM"=>"sequence sources",
+       "SEQUENCE"=>"oligo sequence used",
+       "Function/Family"=>"gene functions and family",
+       "ID"=>"",
+       "SPOT_ID"=>"",
+       "GB_ACC"=>"Gene bank accession number"}) 
+      assert_equal( @obj_series.platform[:table].rows.size, 240)          
+      assert_equal( @obj_series.platform[:table].rows[5], ["A039P68U",
+       "AI163321",
+       "",
+       "TF, flowering protein CONSTANS",
+       "P. tremula x P. tremuloides",
+       "AGAAAATTCGATATACTGTCCGTAAAGAGGTAGCACTTAGAATGCAACGGAATAAAGGGCAGTTCACCTC"])            
+      assert_equal( @obj_series.platform[:table].rows[5][4], 'P. tremula x P. tremuloides')         
+      assert_equal( @obj_series.platform[:table].rows[5][:organism], 'P. tremula x P. tremuloides') 
+      assert_equal( @obj_series.platform[:table].rows[5]['ORGANISM'], 'P. tremula x P. tremuloides')
+      
+      assert_equal( @obj_series.series[:geo_accession], 'GSE3457')           
+      assert_equal( @obj_series.series[:contributor], ["Jingyi,,Li",
+       "Olga,,Shevchenko",
+       "Ove,,Nilsson",
+       "Steve,H,Strauss",
+       "Amy,M,Brunner"])             
+      assert_equal( @obj_series.series[:platform_id], 'GPL2092')             
+      assert_equal( @obj_series.series[:sample_id].size, 74)          
+      assert_equal( @obj_series.series[:sample_id][0..4], ["GSM77557", "GSM77558", "GSM77559", "GSM77560", "GSM77561"])         
+                                                                 
+      assert_equal( @obj_series.database[:name], 'Gene Expression Omnibus (GEO)')                  
+      assert_equal( @obj_series.database[:ref], 'Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D562-6')                   
+      assert_equal( @obj_series.database[:institute], 'NCBI NLM NIH')             
+                                                                 
+      assert_equal( @obj_series.samples.size, 2)                     
+      assert_equal( @obj_series.samples[:GSM77557][:series_id], 'GSE3457')   
+      assert_equal( @obj_series.samples['GSM77557'][:series_id], 'GSE3457')  
+      assert_equal( @obj_series.samples[:GSM77557][:platform_id], 'GPL2092') 
+      assert_equal( @obj_series.samples[:GSM77557][:type], 'RNA')        
+      assert_equal( @obj_series.samples[:GSM77557][:title], 'fb6a1')       
+      assert_equal( @obj_series.samples[:GSM77557][:table].header, ["ID_REF", "VALUE"])
+      assert_equal( @obj_series.samples[:GSM77557][:table].header_description, {"ID_REF"=>"", "VALUE"=>"normalized signal intensities"})
+      assert_equal( @obj_series.samples[:GSM77557][:table].rows.size, 217)
+      assert_equal( @obj_series.samples[:GSM77557][:table].rows[5], ["A039P68U", "5.36"])  
+      assert_equal( @obj_series.samples[:GSM77557][:table].rows[5][0], 'A039P68U')        
+      assert_equal( @obj_series.samples[:GSM77557][:table].rows[5][:id_ref], 'A039P68U')  
+      assert_equal( @obj_series.samples[:GSM77557][:table].rows[5]['ID_REF'], 'A039P68U')
+    end
+    
+    def test_dataset
+      assert_equal( @obj_dataset.database[:name], 'Gene Expression Omnibus (GEO)')
+
+      assert_equal( @obj_dataset.database[:ref], 'Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D562-6')
+      assert_equal( @obj_dataset.database[:institute], 'NCBI NLM NIH')
+
+      assert_equal( @obj_dataset.subsets.size, 8)
+      assert_equal( @obj_dataset.subsets.keys, ["GDS100_1",
+       "GDS100_2",
+       "GDS100_3",
+       "GDS100_4",
+       "GDS100_5",
+       "GDS100_6",
+       "GDS100_7",
+       "GDS100_8"])
+      assert_equal( @obj_dataset.subsets[:GDS100_7],  {:sample_id=>"GSM548,GSM543",
+       :dataset_id=>"GDS100",
+       :description=>"60 minute",
+       :type=>"time"})
+      assert_equal( @obj_dataset.subsets['GDS100_7'][:sample_id], 'GSM548,GSM543')
+      assert_equal( @obj_dataset.subsets[:GDS100_7][:sample_id], 'GSM548,GSM543')
+      assert_equal( @obj_dataset.subsets[:GDS100_7][:dataset_id], 'GDS100')
+                                                                 
+      assert_equal( @obj_dataset.dataset[:order], 'none')
+      assert_equal( @obj_dataset.dataset[:sample_organism], 'Escherichia coli')
+      assert_equal( @obj_dataset.dataset[:table].header, ["ID_REF",
+       "IDENTIFIER",
+       "GSM549",
+       "GSM542",
+       "GSM543",
+       "GSM547",
+       "GSM544",
+       "GSM545",
+       "GSM546",
+       "GSM548"])
+      assert_equal( @obj_dataset.dataset[:table].rows.size, 15)
+      assert_equal( @obj_dataset.dataset[:table].rows[5], ["6",
+       "EMPTY",
+       "0.097",
+       "0.217",
+       "0.242",
+       "0.067",
+       "0.104",
+       "0.162",
+       "0.104",
+       "0.154"])
+      assert_equal( @obj_dataset.dataset[:table].rows[5][4], '0.242')
+      assert_equal( @obj_dataset.dataset[:table].rows[5][:gsm549], '0.097')
+      assert_equal( @obj_dataset.dataset[:table].rows[5][:GSM549], '0.097')
+      assert_equal( @obj_dataset.dataset[:table].rows[5]['GSM549'], '0.097')
+    end
+  end
+
+end

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

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/io/test_ddbjxml.rb - Unit test for DDBJ XML.
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright:: 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_ddbjxml.rb,v 1.1 2005/12/11 14:59:25 nakao Exp $ 
+#  $Id: test_ddbjxml.rb,v 1.4 2007/04/05 23:35:43 trevor Exp $ 
 #
 
 require 'pathname'
@@ -33,7 +20,8 @@ module Bio
 class TestDDBJXMLConstants < Test::Unit::TestCase
 
   def test_constants
-    constants = ["DDBJ", "TxSearch", "ClustalW", "PML", "Gib", "Fasta", "BASE_URI", "SRS", "Gtop", "GetEntry", "Blast"].sort
+    constants = ["DDBJ", "TxSearch", "ClustalW", "PML", "Gib", "Fasta", 
+                 "BASE_URI", "SRS", "SERVER_URI", "Gtop", "GetEntry", "Blast"].sort
     assert_equal(constants, Bio::DDBJ::XML.constants.sort)
   end
 

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

@@ -0,0 +1,109 @@
+#
+# = test/unit/bio/io/test_ensembl.rb - Unit test for Bio::Ensembl.
+#
+# Copyright::   Copyright (C) 2006, 2007
+#               Mitsuteru C. Nakao <n@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: test_ensembl.rb,v 1.6 2007/04/05 23:35:43 trevor Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/io/ensembl'
+
+# tests for ensembl.rb,v 1.4
+class TestEnsembl_v14 < Test::Unit::TestCase
+  def test_ensembl_url
+    assert_equal('http://www.ensembl.org', Bio::Ensembl::ENSEMBL_URL)
+  end
+  
+  def test_server
+    obj = Bio::Ensembl.new('Homo_sapiens')
+    assert_equal('http://www.ensembl.org', obj.server)
+  end
+
+  def test_organism
+    organism = 'Homo_sapiens'
+    obj = Bio::Ensembl.new(organism)
+    assert_equal(organism, obj.organism)
+  end
+  
+  def test_self_human
+    organism = 'Homo_sapiens'    
+    obj = Bio::Ensembl.human
+    assert_equal(organism, obj.organism)
+  end
+
+  def test_self_mouse
+    organism = 'Mus_musculus'
+    obj = Bio::Ensembl.mouse
+    assert_equal(organism, obj.organism)
+  end
+
+  def test_new_with_2_args
+    organism = 'Oryza_sativa'
+    server_url = 'http://www.gramene.org'
+    obj = Bio::Ensembl.new(organism, server_url)
+    assert_equal(organism, obj.organism)
+    assert_equal(server_url, obj.server)
+  end
+end
+
+
+class TestEnsembl < Test::Unit::TestCase
+  def test_server_name
+    assert_equal('http://www.ensembl.org', Bio::Ensembl::EBIServerURI)
+  end
+
+  def test_server_uri
+    assert_equal('http://www.ensembl.org', Bio::Ensembl.server_uri)
+  end
+  
+  def test_set_server_uri
+    host = 'http://localhost'
+    Bio::Ensembl.server_uri(host)
+    assert_equal(host, Bio::Ensembl.server_uri)
+  end
+end
+
+
+class TestEnsemblBase < Test::Unit::TestCase
+  def test_exportview
+    
+  end
+end
+
+class TestEnsemblBaseClient < Test::Unit::TestCase
+  def test_class
+
+  end
+end
+
+
+class TestEnsemblHuman < Test::Unit::TestCase
+  def test_organism
+    assert_equal("Homo_sapiens", Bio::Ensembl::Human::Organism)
+  end
+end
+
+class TestEnsemblMouse < Test::Unit::TestCase
+  def test_organism
+    assert_equal("Mus_musculus", Bio::Ensembl::Mouse::Organism)
+  end
+end
+
+
+class TestEnsemblOldStyleClient < Test::Unit::TestCase
+  class Rice < Bio::Ensembl::Base
+    Organism = 'Oryza_sativa'
+  end
+
+  def test_organism
+    assert_equal('Oryza_sativa', Rice::Organism)
+  end
+end
+  

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

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/io/test_fastacmd.rb - Unit test for Bio::Blast::Fastacmd.
 #
-#   Copyright (C) 2006 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2006 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_fastacmd.rb,v 1.1 2006/01/28 08:05:52 nakao Exp $
+#  $Id: test_fastacmd.rb,v 1.3 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'

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

@@ -0,0 +1,237 @@
+#
+# = test/unit/bio/io/test_flatfile.rb - unit test for Bio::FlatFile
+#
+#   Copyright (C) 2006 Naohisa Goto <ng@bioruby.org>
+#
+# License:: The Ruby License
+#
+#  $Id: test_flatfile.rb,v 1.2 2007/04/05 23:35:43 trevor Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio'
+require 'stringio'
+
+
+module Bio
+    
+module TestFlatFile
+
+  bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4)).cleanpath.to_s
+  TestDataPath = Pathname.new(File.join(bioruby_root, 'test', 'data')).cleanpath.to_s
+  TestDataFastaFormat01 = File.join(TestDataPath, 'fasta', 'example1.txt')
+
+  class TestBufferedInputStreamClassMethod < Test::Unit::TestCase
+    def test_self_for_io
+      io = File.open(TestDataFastaFormat01)
+      obj = Bio::FlatFile::BufferedInputStream.for_io(io)
+      assert_instance_of(Bio::FlatFile::BufferedInputStream, obj)
+      assert_equal(TestDataFastaFormat01, obj.path)
+    end
+
+    def test_self_open_file
+      obj = Bio::FlatFile::BufferedInputStream.open_file(TestDataFastaFormat01)
+      assert_instance_of(Bio::FlatFile::BufferedInputStream, obj)
+      assert_equal(TestDataFastaFormat01, obj.path)
+    end
+
+    def test_self_open_file_with_block
+      obj2 = nil
+      Bio::FlatFile::BufferedInputStream.open_file(TestDataFastaFormat01) do |obj|
+        assert_instance_of(Bio::FlatFile::BufferedInputStream, obj)
+        assert_equal(TestDataFastaFormat01, obj.path)
+        obj2 = obj
+      end
+      assert_raise(IOError) { obj2.close }
+    end
+  end #class TestBufferedInputStreamClassMethod
+
+  class TestBufferedInputStream < Test::Unit::TestCase
+    def setup
+      io = File.open(TestDataFastaFormat01)
+      path = TestDataFastaFormat01
+      @obj = Bio::FlatFile::BufferedInputStream.new(io, path)
+    end
+
+    def test_to_io
+      assert_kind_of(IO, @obj.to_io)
+    end
+
+    def test_close
+      assert_nil(@obj.close)
+    end
+
+    def test_rewind
+      @obj.prefetch_gets
+      @obj.rewind
+      assert_equal('', @obj.prefetch_buffer)
+    end
+
+    def test_pos
+      @obj.gets
+      @obj.gets
+      @obj.prefetch_gets
+      assert_equal(117, @obj.pos) #the number depends on original data
+    end
+
+    def test_pos=()
+      str = @obj.gets
+      assert_equal(0, @obj.pos = 0)
+    end
+      
+    def test_eof_false_first
+      assert_equal(false, @obj.eof?)
+    end
+
+    def test_eof_false_after_prefetch
+      while @obj.prefetch_gets; nil; end
+      assert_equal(false, @obj.eof?)
+    end
+
+    def test_eof_true
+      while @obj.gets; nil; end
+      assert_equal(true, @obj.eof?)
+    end
+
+    def test_gets
+      @obj.gets
+      @obj.gets
+      assert_equal("gagcaaatcgaaaaggagagatttctgcatatcaagagaaaattcgagctgagatacattccaagtgtggctactc", @obj.gets.chomp)
+    end
+
+    def test_gets_equal_prefetch_gets
+      @obj.prefetch_gets
+      str = @obj.prefetch_gets
+      @obj.prefetch_gets
+      @obj.gets
+      assert_equal(@obj.gets, str)
+    end
+
+    def test_ungets
+      @obj.gets
+      @obj.gets
+      str1 = @obj.gets
+      str2 = @obj.gets
+      assert_nil(@obj.ungets(str2))
+      assert_nil(@obj.ungets(str1))
+      assert_equal(str1, @obj.gets)
+      assert_equal(str2, @obj.gets)
+    end
+
+    def test_getc
+      assert_equal(?>, @obj.getc)
+    end
+
+    def test_getc_after_prefetch
+      @obj.prefetch_gets
+      assert_equal(?>, @obj.getc)
+    end
+
+    def test_ungetc
+      c = @obj.getc
+      assert_nil(@obj.ungetc(c))
+      assert_equal(c, @obj.getc)
+    end
+
+    def test_ungetc_after_prefetch
+      str = @obj.prefetch_gets
+      c = @obj.getc
+      assert_nil(@obj.ungetc(c))
+      assert_equal(str, @obj.gets)
+    end
+
+    def test_prefetch_buffer
+      str = @obj.prefetch_gets
+      str += @obj.prefetch_gets
+      assert_equal(str, @obj.prefetch_buffer)
+    end
+
+    def test_prefetch_gets
+      @obj.prefetch_gets
+      @obj.prefetch_gets
+      @obj.gets
+      str = @obj.prefetch_gets
+      @obj.gets
+      assert_equal(str, @obj.gets)
+    end
+
+    def test_prefetch_gets_with_arg
+      # test @obj.gets
+      str = @obj.prefetch_gets("\n>")
+      assert_equal(str, @obj.gets("\n>"))
+      # test using IO object
+      io = @obj.to_io
+      io.rewind
+      assert_equal(str, io.gets("\n>"))
+    end
+
+    def test_skip_spaces
+      @obj.gets('CDS')
+      assert_nil(@obj.skip_spaces)
+      assert_equal(?a, @obj.getc)
+    end
+                   
+  end #class TestBufferedInputStream
+
+  class TestFlatFileWithCustomClass < Test::Unit::TestCase
+
+    # very simple parser for tab-separated data
+    class SimpleFormat
+      # delimiter needed for flatfile
+      DELIMITER = RS = nil # nil means no delimiter and reading entire file
+      def initialize(str)
+        @data = str.split(/\n/).collect { |x| x.to_s.split(/\t/) }
+      end
+      attr_reader :data
+    end
+
+    def test_simpleformat
+      testdata = "AAA\tBBB\tCCCCC\tDDDD\n123\t456\n"
+      testio = StringIO.new(testdata)
+      Bio::FlatFile.open(SimpleFormat, testio) do |ff|
+        ff.each do |entry|
+          assert_equal([ [ 'AAA', 'BBB', 'CCCCC', 'DDDD' ],
+                         [ '123', '456' ] ], entry.data)
+        end
+      end
+    end
+
+    # very simple parser for "//"-separated entries
+    class SimpleFormat2
+      # delimiter needed for flatfile
+      DELIMITER = RS = "//\n" # the end of each entry is "//\n"
+      def initialize(str)
+        # very simple parser only to store a text data
+        @data = str
+      end
+      attr_reader :data
+    end
+
+    def test_simpleformat2
+      testdata = <<__END_OF_TESTDATA__
+test01
+This is a test.
+//
+test02
+This is an example.
+//
+__END_OF_TESTDATA__
+      a = testdata.split(/(\/\/\n)/)
+      results = [ a[0]+a[1], a[2]+a[3] ]
+      testio = StringIO.new(testdata)
+      Bio::FlatFile.open(SimpleFormat2, testio) do |ff|
+        ff.each do |entry|
+          assert_equal(results.shift, entry.data)
+        end
+      end
+    end
+
+  end #class TestFlatFileWithCustomClass
+
+end #module TestFlatFile
+
+end #module Bio