bio 1.3.0 → 1.3.1

data/lib/bio/sequence/compat.rb

@@ -37,7 +37,11 @@ class Sequence
 
 module Common
 
-  # *DEPRECIATED* Do not use! Use Bio::Sequence#output instead. 
+  # <b>Bio::Sequence#to_fasta is DEPRECIATED</b>
+  # Do not use Bio::Sequence#to_fasta ! Use Bio::Sequence#output instead. 
+  # Note that Bio::Sequence::NA#to_fasta, Bio::Sequence::AA#to_fasata,
+  # and Bio::Sequence::Generic#to_fasta <b>can still be used</b>,
+  # because there are no alternative methods.
   # 
   # Output the FASTA format string of the sequence.  The 1st argument is
   # used as the comment string.  If the 2nd option is given, the output

data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb

@@ -5,7 +5,7 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: calculated_cuts.rb,v 1.7 2007/07/16 19:28:48 k Exp $
+#  $Id:$
 #
 
 require 'bio/util/restriction_enzyme'
@@ -44,9 +44,11 @@ class CalculatedCuts
 
   # Set to +true+ if the fragment CalculatedCuts is working on is circular
   attr_accessor :circular
-  
-  # An +Array+ with the primary strand with vertical cuts, the horizontal cuts, and the complementary strand with vertical cuts.
-  attr_reader :strands_for_display
+
+  #--
+  ## An +Array+ with the primary strand with vertical cuts, the horizontal cuts, and the complementary strand with vertical cuts.
+  #attr_reader :strands_for_display
+  #++
   
   # If +false+ the strands_for_display method needs to be called to update the contents
   # of @strands_for_display.  Becomes out of date whenever add_cuts_from_cut_ranges is called.

data/lib/bio/version.rb

@@ -10,7 +10,7 @@
 module Bio
 
   # BioRuby version (Array containing Integer)
-  BIORUBY_VERSION = [1, 3, 0].extend(Comparable).freeze
+  BIORUBY_VERSION = [1, 3, 1].extend(Comparable).freeze
 
   # Extra version specifier (String or nil).
   # Existance of the value indicates pre-release version or modified version.

data/test/data/gcg/pileup-aa.msf

@@ -0,0 +1,67 @@
+!!AA_MULTIPLE_ALIGNMENT 1.0
+PileUp of: @/home/ngoto/.seqlab-localhost/pileup_24.list
+
+ Symbol comparison table: GenRunData:blosum62.cmp  CompCheck: 1102
+
+                   GapWeight: 8
+             GapLengthWeight: 2 
+
+ pileup_24.msf  MSF: 282  Type: P  April 22, 2009 22:31  Check: 5701 ..
+
+ Name: xx_3183087       Len:   282  Check: 6631  Weight:  1.00
+ Name: xx_3183086       Len:   282  Check: 3789  Weight:  1.00
+ Name: xx_192453532     Len:   282  Check: 2081  Weight:  1.00
+ Name: xx_72157730      Len:   282  Check: 5946  Weight:  1.00
+ Name: xx_210090185     Len:   282  Check: 7419  Weight:  1.00
+ Name: xx_45552463      Len:   282  Check: 9835  Weight:  1.00
+
+//
+
+              1                                                   50
+  xx_3183087  ~MAFLGLFSL LVLQSMATGA .TGEDENILF QKEIRHSMGY DSLKNGE.EF 
+  xx_3183086  ~MYFLGLLSL LVLPSKAFKA .AREDENILF LKEIRHSLGF DSLKNGE.EF 
+xx_192453532  MLLLVVLPPL LLLRGCFCQA ISSGEENIIF LQEIRQAVGY SHFREDE.EF 
+ xx_72157730  ~~~~~~~~MA FSKQQDISGQ DERRGTNLFF ATQIADVFRF NQVDQDQLHG 
+xx_210090185  ~~~~~~~~~~ ~~~MRSSTSQ EKDHPENIFF AQQMSRVLRF HKMDASDLHM 
+ xx_45552463  ~~~~~~~~~~ ~~~MADAAGQ KP..GENIVF ATQLDQGLGL ASSDPEQ... 
+
+              51                                                 100
+  xx_3183087  SNYINKWVEN NTRTFSF.TK DDEVQIPMMY QQGEFYYGEF SDGSNEAGGI 
+  xx_3183086  TTHINKWVEN NTRTFSF.TK DDEVQIPMMY QQGEFYYGEF SDGSNEAGGI 
+xx_192453532  SERINSWVLN NTRTFSF.TR DDGVQTLMMY QQGDFYYGEF SDGTTEAGGV 
+ xx_72157730  TKSINDWVSK NTTQETFKVL DERVPVSLMI QKGKYALAV. .DNTNDC... 
+xx_210090185  RQTINSWVEE RTRLGTFHI. SRDVEVPMMH QQGRFKLAY. .DEDLNC... 
+ xx_45552463  .ATINNWVEQ LTRPDTFH.L DGEVQVPMMS LKERFRYAD. .LPALDA... 
+
+              101                                                150
+  xx_3183087  YQVLEIPYEG DEISMMLVLS RQEVPLATLE PLVKAQLVEE WANSVKKQKV 
+  xx_3183086  YQVLEIPYEG DEISMMIVLS RQEVPLVTLE PLVKASLINE WANSVKKQKV 
+xx_192453532  YQVLEMLYEG EDMSMMIVLP RQEVPLASLE PIIKAPLLEE WANNVKRQKV 
+ xx_72157730  .LVLEMPYQG RNLSLLIALP VKDDGLGQLE TKLSADILQS WDAGLKSRQV 
+xx_210090185  .QILEMPYRG KHLSMVVVLP DKMDDLSAIE TSLTPDLLRH WRKSMSEEST 
+ xx_45552463  .MALELPYKD SDLSMLIVLP NTKTGLPALE EKLRLTTLSQ ITQSLYETKV 
+
+              151                                                200
+  xx_3183087  EVYLPRFTVE QEIDLKDVLK ALGITEIFIK D.ANLTG... .LSDNKEIFL 
+  xx_3183086  EVYLPRFTVE QEIDLKDVLK GLGITEVFSR S.ADLTA... .MSDNKELYL 
+xx_192453532  EVYLPRFKVE QKIDLRESLQ QLGIRSIFSK D.ADLSAMTA QMTDGQDLFI 
+ xx_72157730  NVLLPKFKLE AQFQLKEFLQ RMGMSDAFDE DRANFEGISG ...DRE.LHI 
+xx_210090185  MVQIPKFKVE QDFLLKEKLA EMGMTDLFSM ADADLSGITG ...SRD.LHV 
+ xx_45552463  ALKLPRFKAE FQVELSEVFQ KLGMSRMFS. DQAEFGKMLQ ...SPEPLKV 
+
+              201                                                250
+  xx_3183087  SKAIHKSFLE VNEEGSEAAA VSGMIAISRM AVLYP..... QVIVDHPFFF 
+  xx_3183086  AKAFHKAFLE VNEEGSEAAA ASGMIAISRM AVLYP..... QVIVDHPFFF 
+xx_192453532  GKAVQKAYLE VTEEGAEGAA GSGMIALTRT LVLYP..... QVMADHPFFF 
+ xx_72157730  SAVIHKAFVD VNEEGSEAAA ATAVVMMRRC APPREPEKPI LFRADHPFIF 
+xx_210090185  SHVVHKAFVE VNEEGSEAAA ATAVNMMKRS L...DGE... MFFADHPFLF 
+ xx_45552463  SAIIHKAFIE VNEEGTEAAA ATGMVMCYAS MLTFEPQ.PV QFHVQHPFNY 
+
+              251                             282
+  xx_3183087  LIRNRRTGTI LFMGRVMHPE TMNTSGHDFE EL
+  xx_3183086  LVRNRRTGTV LFMGRVMHPE AMNTSGHDFE EL
+xx_192453532  IIRNRKTGSI LFMGRVMNPE LIDPFDNNFD M~
+ xx_72157730  MIRHRPTKSV LFMGRMMDPS ~~~~~~~~~~ ~~
+xx_210090185  LIRDNDSNSV LFLGRLVRPE GHTTKDEL~~ ~~
+ xx_45552463  YIINKDS.TI LFAGRINKF~ ~~~~~~~~~~ ~~
+

data/test/data/sim4/complement-A4.sim4

@@ -0,0 +1,43 @@
+
+seq1 = sample41-1c.fst, 284 bp
+seq2 = sample40-2.fst (genome4), 770 bp
+
+>mrna4c
+>genome4
+
+(complement)
+
+1-72  (351-424)   89% ->
+73-142  (563-630)   95% ==
+213-284  (700-770)   95%
+
+      0     .    :    .    :    .    :    .    :    .    :
+      1 TTTTAGCCGGCACGAGATTG AGCGTATGATCACGCGCGCGGCCTCCT C
+        ||||||||||||||||||||-||||-||||||||||||||||||||||-|
+    351 TTTTAGCCGGCACGAGATTGCAGCG ATGATCACGCGCGCGGCCTCCTAC
+
+     50     .    :    .    :    .    :    .    :    .    :
+     49 AGAGTGATGCATGATACAACTT AT          ATATGTACTTAGCTG
+        -|||| ||||||||||||||||- |->>>...>>>|||||||||||||-|
+    400  GAGTCATGCATGATACAACTTCTTGGTT...GATATATGTACTTAGC G
+
+    100     .    :    .    :    .    :    .    :    .    :
+     88 GCAACCGAGATTTACTTTCGAAGCACTGTGATGAACCCGCGGCCCTTTGA
+        ||||||||||||||||||||||| |||||||||||||||||-||||||||
+    577 GCAACCGAGATTTACTTTCGAAGGACTGTGATGAACCCGCG CCCTTTGA
+
+    150     .
+    138 GCGCT
+        |||||
+    626 GCGCT
+
+      0     .    :    .    :    .    :    .    :    .    :
+    213 TATATATGTACTTAGCGG ACACCGAGATTTACTTTCGAAGGACTGTGGA
+        ||||||||||||||||||-|-|||||||||||||||||||||||||||-|
+    700 TATATATGTACTTAGCGGCA ACCGAGATTTACTTTCGAAGGACTGTG A
+
+     50     .    :    .    :
+    262 TGAACCCGCGCCCTTTGAGCGCT
+        |||||||||||||||||||||||
+    748 TGAACCCGCGCCCTTTGAGCGCT
+

data/test/data/sim4/simple-A4.sim4

@@ -0,0 +1,25 @@
+
+seq1 = sample10-1.fst, 94 bp
+seq2 = sample10-2.fst (genome1), 599 bp
+
+>mrna1
+>genome1
+
+1-40  (145-184)   100% <-
+41-94  (404-457)   94%
+
+      0     .    :    .    :    .    :    .    :    .    :
+      1 TTGTTTCCGTCGCTGGTTATTGTCTAGAACGCAAAAATAG         T
+        ||||||||||||||||||||||||||||||||||||||||<<<...<<<|
+    145 TTGTTTCCGTCGCTGGTTATTGTCTAGAACGCAAAAATAGCTG...TACT
+
+     50     .    :    .    :    .    :    .    :    .    :
+     42 CTACACATCACTAGCGTGGGTGGGCGGAAAGAGCAGCTCGCCACT CAAG
+        ||||||||||||||| |||||||||||||-|||||||||||||||-||||
+    405 CTACACATCACTAGCCTGGGTGGGCGGAA GAGCAGCTCGCCACTTCAAG
+
+    100 
+     91 CTAA
+        ||||
+    454 CTAA
+

data/test/data/sim4/simple2-A4.sim4

@@ -0,0 +1,25 @@
+
+seq1 = sample10-1.fst, 96 bp
+seq2 = sample10-2.fst (genome1), 599 bp
+
+>mrna1
+>genome1
+
+1-42  (143-184)   100% <-
+43-96  (404-457)   94%
+
+      0     .    :    .    :    .    :    .    :    .    :
+      1 AGTTGTTTCCGTCGCTGGTTATTGTCTAGAACGCAAAAATAG        
+        ||||||||||||||||||||||||||||||||||||||||||<<<...<<
+    143 AGTTGTTTCCGTCGCTGGTTATTGTCTAGAACGCAAAAATAGCTG...TA
+
+     50     .    :    .    :    .    :    .    :    .    :
+     43  TCTACACATCACTAGCGTGGGTGGGCGGAAAGAGCAGCTCGCCACT CA
+        <|||||||||||||||| |||||||||||||-|||||||||||||||-||
+    403 CTCTACACATCACTAGCCTGGGTGGGCGGAA GAGCAGCTCGCCACTTCA
+
+    100     .
+     91 AGCTAA
+        ||||||
+    452 AGCTAA
+

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

@@ -0,0 +1,129 @@
+#
+# test/functional/bio/io/test_pubmed.rb - Functional test for Bio::PubMed
+#
+# Copyright::   Copyright (C) 2009
+#               Naohisa Goto <ng@bioruby.org>
+# License::     The Ruby License
+#
+#  $Id:$
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'bio/io/pubmed'
+require 'bio/db/medline'
+require 'test/unit'
+
+module Bio
+
+  module FuncTestPubmedCommon
+
+    def test_esearch
+      a = @pm.esearch('agile bioinformatics')
+      assert_kind_of(Array, a)
+      assert_operator(a.size, :>=, 3,
+                      '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_esearch_count
+      a = @pm.esearch('agile bioinformatics',
+                      { "rettype"=>"count" })
+      assert_kind_of(Integer, a)
+      assert_operator(a, :>=, 3,
+                      'The failure may be caused by changes of NCBI PubMed.')
+    end
+
+    def test_esearch_retmax_retstart
+      a = @pm.esearch('p53', { "retmax" => 10, "retstart" => 20 })
+      assert_equal(10, 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
+
+      a1 = @pm.esearch('p53', { "retmax" => 15, "retstart" => 35 })
+      a2 = @pm.esearch('p53', { "retmax" => 10, "retstart" => 0 })
+      assert_equal(35, (a + a1 + a2).sort.uniq.size,
+                   'The failure may be caused by changes of NCBI PubMed.')
+
+      a3 = @pm.esearch('p53', { "retmax" => 10 })
+      assert_equal(a2.sort, a3.sort,
+                   'The failure may be caused by changes of NCBI PubMed.')
+    end
+
+    def check_pubmed_entry(pmid, str)
+      m = Bio::MEDLINE.new(str)
+      assert_equal(pmid.to_s, m.pmid)
+    end
+    private :check_pubmed_entry
+
+    def do_efetch_single(pmid)
+      a = @pm.efetch(pmid)
+      assert_kind_of(Array, a)
+      assert_equal(1, a.size)
+      check_pubmed_entry(pmid, a[0])
+    end
+    private :do_efetch_single
+
+    def test_efetch
+      do_efetch_single(12368254)
+    end
+
+    def test_efetch_str
+      do_efetch_single("16734914")
+    end
+
+    def test_efetch_multiple
+      arg = [ 12368254, 18689808, 19304878 ]
+      a = @pm.efetch(arg)
+      assert_kind_of(Array, a)
+      assert_equal(3, a.size)
+      a.each do |str|
+        check_pubmed_entry(arg.shift, str)
+      end
+    end
+
+    def test_efetch_single_xml
+      arg = 12368254
+      str = @pm.efetch(arg, { "retmode" => 'xml' })
+      assert_kind_of(String, str)
+      assert(str.index(/\<PubmedArticleSet\>/))
+    end
+
+    def test_efetch_multiple_xml
+      arg = [ "16734914", 16381885, "10592173" ]
+      str = @pm.efetch(arg, { "retmode" => 'xml' })
+      assert_kind_of(String, str)
+      assert(str.index(/\<PubmedArticleSet\>/))
+    end
+
+  end #module FuncTestPubmedCommon
+
+  class FuncTestPubmed < Test::Unit::TestCase
+
+    include FuncTestPubmedCommon
+
+    def setup
+      @pm = Bio::PubMed.new
+    end
+  end #class FuncTestPubmed
+
+  class FuncTestPubmedClassMethod < Test::Unit::TestCase
+
+    include FuncTestPubmedCommon
+
+    def setup
+      @pm = Bio::PubMed
+    end
+  end #class FuncTestPubmedClassMethod
+
+end

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

@@ -6,7 +6,7 @@
 #                Mitsuteru C. Nakao <n@bioruby.org>
 #  License::     The Ruby License
 #
-#  $Id: test_report.rb,v 1.3 2007/04/05 23:35:43 trevor Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -70,11 +70,11 @@ module Bio
                  'db']
       
       methods.each do |x|
-        assert_nil(@empty.methods.include?(x))
+        assert_equal(false, @empty.methods.include?(x), "undefined? : #{x}")
       end
 
       methods.each do |x|
-        assert_nil(@blastp.methods.include?(x))
+        assert_equal(false, @blastp.methods.include?(x), "undefined? : #{x}")
       end
     end
 
@@ -91,7 +91,7 @@ module Bio
     end
 
 #    TestIteration < Test::Unit::TestCase
-    def test_undefed_methods
+    def test_undefed_methods_for_iteration
       methods = ['message',
                  'pattern_in_database',
                  'pattern',
@@ -103,7 +103,7 @@ module Bio
                  'converged?']
 
       methods.each do |x|
-        assert_equal(false, @empty.iterations.first.methods.include?(x), "undifined? : #{x}")
+        assert_equal(false, @empty.iterations.first.methods.include?(x), "undefined? : #{x}")
       end
 
       methods.each do |x|

data/test/unit/bio/appl/gcg/test_msf.rb

@@ -0,0 +1,154 @@
+#
+# = test/unit/bio/appl/gcg/test_msf.rb - Unit test for Bio::GCG::Msf
+#
+# Copyright::  Copyright (C) 2009 Naohisa Goto <ng@bioruby.org>
+# License::    The Ruby License
+#
+#  $Id:$
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib'))).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/sequence'
+require 'bio/alignment'
+require 'bio/appl/gcg/seq'
+require 'bio/appl/gcg/msf'
+
+module Bio
+
+  module TestGCGMsfData
+
+    bioruby_root  = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
+
+    Filename_PileupAA = Pathname.new(File.join(bioruby_root, 'test', 'data', 'gcg', 'pileup-aa.msf')).cleanpath.to_s
+
+    PileupAA = File.read(Filename_PileupAA).freeze
+
+    mfst = <<__END_OF_MFST__
+>xx_3183087
+~MAFLGLFSLLVLQSMATGA.TGEDENILFQKEIRHSMGYDSLKNGE.EF
+SNYINKWVENNTRTFSF.TKDDEVQIPMMYQQGEFYYGEFSDGSNEAGGI
+YQVLEIPYEGDEISMMLVLSRQEVPLATLEPLVKAQLVEEWANSVKKQKV
+EVYLPRFTVEQEIDLKDVLKALGITEIFIKD.ANLTG....LSDNKEIFL
+SKAIHKSFLEVNEEGSEAAAVSGMIAISRMAVLYP.....QVIVDHPFFF
+LIRNRRTGTILFMGRVMHPETMNTSGHDFEEL
+>xx_3183086
+~MYFLGLLSLLVLPSKAFKA.AREDENILFLKEIRHSLGFDSLKNGE.EF
+TTHINKWVENNTRTFSF.TKDDEVQIPMMYQQGEFYYGEFSDGSNEAGGI
+YQVLEIPYEGDEISMMIVLSRQEVPLVTLEPLVKASLINEWANSVKKQKV
+EVYLPRFTVEQEIDLKDVLKGLGITEVFSRS.ADLTA....MSDNKELYL
+AKAFHKAFLEVNEEGSEAAAASGMIAISRMAVLYP.....QVIVDHPFFF
+LVRNRRTGTVLFMGRVMHPEAMNTSGHDFEEL
+>xx_192453532
+MLLLVVLPPLLLLRGCFCQAISSGEENIIFLQEIRQAVGYSHFREDE.EF
+SERINSWVLNNTRTFSF.TRDDGVQTLMMYQQGDFYYGEFSDGTTEAGGV
+YQVLEMLYEGEDMSMMIVLPRQEVPLASLEPIIKAPLLEEWANNVKRQKV
+EVYLPRFKVEQKIDLRESLQQLGIRSIFSKD.ADLSAMTAQMTDGQDLFI
+GKAVQKAYLEVTEEGAEGAAGSGMIALTRTLVLYP.....QVMADHPFFF
+IIRNRKTGSILFMGRVMNPELIDPFDNNFDM~
+>xx_72157730
+~~~~~~~~MAFSKQQDISGQDERRGTNLFFATQIADVFRFNQVDQDQLHG
+TKSINDWVSKNTTQETFKVLDERVPVSLMIQKGKYALAV..DNTNDC...
+.LVLEMPYQGRNLSLLIALPVKDDGLGQLETKLSADILQSWDAGLKSRQV
+NVLLPKFKLEAQFQLKEFLQRMGMSDAFDEDRANFEGISG...DRE.LHI
+SAVIHKAFVDVNEEGSEAAAATAVVMMRRCAPPREPEKPILFRADHPFIF
+MIRHRPTKSVLFMGRMMDPS~~~~~~~~~~~~
+>xx_210090185
+~~~~~~~~~~~~~MRSSTSQEKDHPENIFFAQQMSRVLRFHKMDASDLHM
+RQTINSWVEERTRLGTFHI.SRDVEVPMMHQQGRFKLAY..DEDLNC...
+.QILEMPYRGKHLSMVVVLPDKMDDLSAIETSLTPDLLRHWRKSMSEEST
+MVQIPKFKVEQDFLLKEKLAEMGMTDLFSMADADLSGITG...SRD.LHV
+SHVVHKAFVEVNEEGSEAAAATAVNMMKRSL...DGE...MFFADHPFLF
+LIRDNDSNSVLFLGRLVRPEGHTTKDEL~~~~
+>xx_45552463
+~~~~~~~~~~~~~MADAAGQKP..GENIVFATQLDQGLGLASSDPEQ...
+.ATINNWVEQLTRPDTFH.LDGEVQVPMMSLKERFRYAD..LPALDA...
+.MALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKV
+ALKLPRFKAEFQVELSEVFQKLGMSRMFS.DQAEFGKMLQ...SPEPLKV
+SAIIHKAFIEVNEEGTEAAAATGMVMCYASMLTFEPQ.PVQFHVQHPFNY
+YIINKDS.TILFAGRINKF~~~~~~~~~~~~~
+__END_OF_MFST__
+
+    seqs = mfst.split(/^\>.*/).collect { |x| x.gsub(/\s+/, '').freeze }
+    seqs.shift # removes the first empty string
+    names = mfst.scan(/^\>.*/).collect { |x| x.sub(/\A\>/, '').freeze }
+
+    PileupAA_seqs = seqs.freeze
+    PileupAA_names = names.freeze
+
+  end #module TestGCGMsfData
+
+  class TestGCGMsf < Test::Unit::TestCase
+
+    def setup
+      @paa = Bio::GCG::Msf.new(TestGCGMsfData::PileupAA)
+    end
+
+    def test_alignment
+      seqs = TestGCGMsfData::PileupAA_seqs.dup
+      names = TestGCGMsfData::PileupAA_names
+ 
+      aln = nil
+      assert_nothing_raised { aln = @paa.alignment }
+      assert_equal(names, aln.keys)
+      aln.each do |s|
+        assert_equal(seqs.shift, s)
+      end
+      assert(seqs.empty?)
+    end
+
+    def test_checksum
+      assert_equal(5701, @paa.checksum)
+    end
+
+    def test_date
+      assert_equal('April 22, 2009 22:31', @paa.date)
+    end
+
+    def test_description
+      assert_equal("PileUp of: @/home/ngoto/.seqlab-localhost/pileup_24.list\n\n Symbol comparison table: GenRunData:blosum62.cmp  CompCheck: 1102\n\n                   GapWeight: 8\n             GapLengthWeight: 2 \n\n", @paa.description)
+    end
+
+    def test_entry_id
+      assert_equal('pileup_24.msf', @paa.entry_id)
+    end
+
+    def test_heading
+      assert_equal('!!AA_MULTIPLE_ALIGNMENT 1.0', @paa.heading)
+    end
+
+    def test_length
+      assert_equal(282, @paa.length)
+    end
+
+    def test_seq_type
+      assert_equal('P', @paa.seq_type)
+    end
+
+    def test_compcheck
+      assert_equal(1102, @paa.compcheck)
+    end
+
+    def test_gap_length_weight
+      assert_equal("2", @paa.gap_length_weight)
+    end
+
+    def test_gap_weight
+      assert_equal("8", @paa.gap_weight)
+    end
+
+    def test_symbol_comparison_table
+      assert_equal('GenRunData:blosum62.cmp', @paa.symbol_comparison_table)
+    end
+
+    def test_validate_checksum
+      assert_equal(true, @paa.validate_checksum)
+    end
+
+  end #class TestGCGMsf_PileupAA
+
+end #module Bio
+