[BioRuby-cvs] bioruby/test/unit/bio/appl/blast test_report.rb, 1.1, 1.2 test_xmlparser.rb, 1.1, 1.2

Tue Nov 22 03:31:49 EST 2005

Update of /home/repository/bioruby/bioruby/test/unit/bio/appl/blast
In directory pub.open-bio.org:/tmp/cvs-serv11824/test/unit/bio/appl/blast

Modified Files:
	test_report.rb test_xmlparser.rb 
Log Message:
* Fixed the order of arguments of assert_equal method.


Index: test_xmlparser.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/blast/test_xmlparser.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** test_xmlparser.rb	28 Oct 2005 02:32:38 -0000	1.1
--- test_xmlparser.rb	22 Nov 2005 08:31:47 -0000	1.2
***************
*** 72,76 ****
  
      def test_db
!       assert_equal(@report.db, "eco:b0002.faa")
      end
  
--- 72,76 ----
  
      def test_db
!       assert_equal("eco:b0002.faa", @report.db)
      end
  
***************
*** 311,315 ****
      
      def test_num
!       assert_equal(@hsp.num, 1)
      end
  
--- 311,315 ----
      
      def test_num
!       assert_equal(1, @hsp.num)
      end
  

Index: test_report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/blast/test_report.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** test_report.rb	28 Oct 2005 02:30:57 -0000	1.1
--- test_report.rb	22 Nov 2005 08:31:47 -0000	1.2
***************
*** 63,79 ****
  
      def test_parameters
!       assert_equal(@report.parameters['matrix'], 'BLOSUM62')
!       assert_equal(@report.parameters['expect'], 10)
!       assert_equal(@report.parameters['gap-open'], 11)
!       assert_equal(@report.parameters['gap-extend'], 1)
!       assert_equal(@report.parameters['filter'], 'S')
      end
  
      def test_program
!       assert_equal(@report.program, 'blastp')
      end
  
      def test_version
!       assert_equal(@report.version, 'blastp 2.2.10 [Oct-19-2004]')
      end
  
--- 63,79 ----
  
      def test_parameters
!       assert_equal('BLOSUM62', @report.parameters['matrix'])
!       assert_equal(10, @report.parameters['expect'])
!       assert_equal(11, @report.parameters['gap-open'])
!       assert_equal(1, @report.parameters['gap-extend'])
!       assert_equal('S', @report.parameters['filter'])
      end
  
      def test_program
!       assert_equal('blastp', @report.program)
      end
  
      def test_version
!       assert_equal('blastp 2.2.10 [Oct-19-2004]', @report.version)
      end
  
***************
*** 81,110 ****
        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(@report.reference, xml_quoted_str)
!       assert_equal(@report.reference, text_str)
      end
  
      def test_db
!       assert_equal(@report.db, 'eco:b0002.faa')
      end
  
      def test_query_id
!       assert_equal(@report.query_id, 'lcl|QUERY')
      end
  
      def test_query_def
!       assert_equal(@report.query_def, 'eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal) [EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928 aspartate kinase (A)')
      end
  
      def test_query_len
!       assert_equal(@report.query_len, 820)
      end
  
      def test_matrix
!       assert_equal(@report.matrix, 'BLOSUM62')
      end
  
      def test_expect
!       assert_equal(@report.expect, 10)
      end
  
--- 81,110 ----
        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
  
      def test_db
!       assert_equal('eco:b0002.faa', @report.db)
      end
  
      def test_query_id
!       assert_equal('lcl|QUERY', @report.query_id)
      end
  
      def test_query_def
!       assert_equal('eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal) [EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928 aspartate kinase (A)', @report.query_def)
      end
  
      def test_query_len
!       assert_equal(820, @report.query_len)
      end
  
      def test_matrix
!       assert_equal('BLOSUM62', @report.matrix)
      end
  
      def test_expect
!       assert_equal(10, @report.expect)
      end
  
***************
*** 122,134 ****
  
      def test_gap_open
!       assert_equal(@report.gap_open, 11)
      end
  
      def test_gap_extend
!       assert_equal(@report.gap_extend, 1)
      end
  
      def test_filter
!       assert_equal(@report.filter, 'S')
      end
  
--- 122,134 ----
  
      def test_gap_open
!       assert_equal(11, @report.gap_open)
      end
  
      def test_gap_extend
!       assert_equal(1, @report.gap_extend)
      end
  
      def test_filter
!       assert_equal('S', @report.filter)
      end
  
***************
*** 154,186 ****
  
      def test_statistics
!       assert_equal(@report.statistics, {"kappa"=>0.041, "db-num"=>1, "eff-space"=>605284.0, "hsp-len"=>42, "db-len"=>820, "lambda"=>0.267, "entropy"=>0.14})
      end
  
      def test_db_num
!       assert_equal(@report.db_num, 1)
      end
  
      def test_db_len
!       assert_equal(@report.db_len, 820)
      end
  
      def test_hsp_len
!       assert_equal(@report.hsp_len, 42)
      end
  
      def test_eff_space
!       assert_equal(@report.eff_space, 605284)
      end
  
      def test_kappa
!       assert_equal(@report.kappa, 0.041)
      end
  
      def test_lambda
!       assert_equal(@report.lambda, 0.267)
      end
  
      def test_entropy
!       assert_equal(@report.entropy, 0.14)
      end
  
--- 154,186 ----
  
      def test_statistics
!       assert_equal({"kappa"=>0.041, "db-num"=>1, "eff-space"=>605284.0, "hsp-len"=>42, "db-len"=>820, "lambda"=>0.267, "entropy"=>0.14}, @report.statistics)
      end
  
      def test_db_num
!       assert_equal(1, @report.db_num)
      end
  
      def test_db_len
!       assert_equal(820, @report.db_len)
      end
  
      def test_hsp_len
!       assert_equal(42, @report.hsp_len)
      end
  
      def test_eff_space
!       assert_equal(605284, @report.eff_space)
      end
  
      def test_kappa
!       assert_equal(0.041, @report.kappa)
      end
  
      def test_lambda
!       assert_equal(0.267, @report.lambda)
      end
  
      def test_entropy
!       assert_equal(0.14, @report.entropy)
      end
  
***************
*** 192,196 ****
    class TestBlastReportIteration < Test::Unit::TestCase
      def setup
!       data = Bio::TestBlastData.data
        report = Bio::Blast::Report.new(data)
        @itr = report.iterations.first
--- 192,196 ----
    class TestBlastReportIteration < Test::Unit::TestCase
      def setup
!       data = Bio::TestBlastReportData.output
        report = Bio::Blast::Report.new(data)
        @itr = report.iterations.first
***************
*** 206,210 ****
  
      def test_num
!       assert_equal(@itr.num, 1)
      end
  
--- 206,210 ----
  
      def test_num
!       assert_equal(1, @itr.num)
      end
  
***************
*** 216,220 ****
    class TestBlastReportHit < Test::Unit::TestCase
      def setup
!       data = Bio::TestBlastData.data
        report = Bio::Blast::Report.new(data)
        @hit = report.hits.first
--- 216,220 ----
    class TestBlastReportHit < Test::Unit::TestCase
      def setup
!       data = Bio::TestBlastReportData.output
        report = Bio::Blast::Report.new(data)
        @hit = report.hits.first
***************
*** 226,238 ****
  
      def test_Hit_query_id
!       assert_equal(@hit.query_id, 'lcl|QUERY')
      end
  
      def test_Hit_query_def
!       assert_equal(@hit.query_def, 'eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal) [EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928 aspartate kinase (A)')
      end
  
      def test_Hit_query_len
!       assert_equal(@hit.query_len, 820)
      end
  
--- 226,238 ----
  
      def test_Hit_query_id
!       assert_equal('lcl|QUERY', @hit.query_id)
      end
  
      def test_Hit_query_def
!       assert_equal('eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal) [EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928 aspartate kinase (A)', @hit.query_def)
      end
  
      def test_Hit_query_len
!       assert_equal(820, @hit.query_len)
      end
  
***************
*** 242,254 ****
  
      def test_Hit_hit_id
!       assert_equal(@hit.hit_id, 'gnl|BL_ORD_ID|0') 
      end
  
      def test_Hit_len
!       assert_equal(@hit.len, 820)
      end
  
      def test_Hit_target_len
!       assert_equal(@hit.target_len, 820)
      end
  
--- 242,254 ----
  
      def test_Hit_hit_id
!       assert_equal('gnl|BL_ORD_ID|0', @hit.hit_id) 
      end
  
      def test_Hit_len
!       assert_equal(820, @hit.len)
      end
  
      def test_Hit_target_len
!       assert_equal(820, @hit.target_len)
      end
  
***************
*** 270,325 ****
      
      def test_Hit_evalue
!       assert_equal(@hit.evalue, 0)
      end
  
      def test_Hit_bit_score
!       assert_equal(@hit.bit_score, 1567.75)
      end
  
      def test_Hit_identity
!       assert_equal(@hit.identity, 820)
      end
  
      def test_Hit_overlap
!       assert_equal(@hit.overlap, 820)
      end
  
      def test_Hit_query_seq
        seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
!       assert_equal(@hit.query_seq, seq)
      end
  
      def test_Hit_target_seq
        seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
!       assert_equal(@hit.target_seq, seq)
      end
  
      def test_Hit_midline
        seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
!       assert_equal(@hit.midline, seq)
      end
  
      def test_Hit_query_start
!       assert_equal(@hit.query_start, 1)
! #      assert_equal(@hit.query_from, 1)
      end
  
      def test_Hit_query_end
!       assert_equal(@hit.query_end, 820)
! #      assert_equal(@hit.query_to, 820)
      end
  
      def test_Hit_target_start
!       assert_equal(@hit.target_start, 1)
! #      assert_equal(@hit.hit_from, 1)
      end
  
      def test_Hit_target_end
!       assert_equal(@hit.target_end,  820)
! #      assert_equal(@hit.hit_to,  820)
      end
  
      def test_Hit_lap_at
!       assert_equal(@hit.lap_at, [1, 820, 1, 820])
      end
    end
--- 270,325 ----
      
      def test_Hit_evalue
!       assert_equal(0, @hit.evalue)
      end
  
      def test_Hit_bit_score
!       assert_equal(1567.75, @hit.bit_score)
      end
  
      def test_Hit_identity
!       assert_equal(820, @hit.identity)
      end
  
      def test_Hit_overlap
!       assert_equal(820, @hit.overlap)
      end
  
      def test_Hit_query_seq
        seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
!       assert_equal(seq, @hit.query_seq)
      end
  
      def test_Hit_target_seq
        seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
!       assert_equal(seq, @hit.target_seq)
      end
  
      def test_Hit_midline
        seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
!       assert_equal(seq, @hit.midline)
      end
  
      def test_Hit_query_start
!       assert_equal(1, @hit.query_start)
! #      assert_equal(1, @hit.query_from)
      end
  
      def test_Hit_query_end
!       assert_equal(820, @hit.query_end)
! #      assert_equal(820, @hit.query_to)
      end
  
      def test_Hit_target_start
!       assert_equal(1, @hit.target_start)
! #      assert_equal(1, @hit.hit_from)
      end
  
      def test_Hit_target_end
!       assert_equal(820, @hit.target_end)
! #      assert_equal(820, @hit.hit_to)
      end
  
      def test_Hit_lap_at
!       assert_equal([1, 820, 1, 820], @hit.lap_at)
      end
    end
***************
*** 327,331 ****
    class TestBlastReportHsp < Test::Unit::TestCase
      def setup
!       data = Bio::TestBlastData.data
        report = Bio::Blast::Report.new(data)
        @hsp = report.hits.first.hsps.first
--- 327,331 ----
    class TestBlastReportHsp < Test::Unit::TestCase
      def setup
!       data = Bio::TestBlastReportData.output
        report = Bio::Blast::Report.new(data)
        @hsp = report.hits.first.hsps.first
***************
*** 333,353 ****
      
      def test_Hsp_num
!       assert_equal(@hsp.num, 1)
      end
  
      def test_Hsp_hit_score
!       assert_equal(@hsp.bit_score, 1567.75)
      end
  
      def test_Hsp_score
!       assert_equal(@hsp.score, 4058)
      end
  
      def test_Hsp_evalue
!       assert_equal(@hsp.evalue, 0)
      end
  
      def test_Hsp_identity
!       assert_equal(@hsp.identity, 820)
      end
  
--- 333,353 ----
      
      def test_Hsp_num
!       assert_equal(1, @hsp.num)
      end
  
      def test_Hsp_hit_score
!       assert_equal(1567.75, @hsp.bit_score)
      end
  
      def test_Hsp_score
!       assert_equal(4058, @hsp.score)
      end
  
      def test_Hsp_evalue
!       assert_equal(0, @hsp.evalue)
      end
  
      def test_Hsp_identity
!       assert_equal(820, @hsp.identity)
      end
  
***************
*** 357,365 ****
  
      def test_Hsp_positive
!       assert_equal(@hsp.positive, 820)
      end
  
      def test_Hsp_align_len
!       assert_equal(@hsp.align_len, 820)
      end
  
--- 357,365 ----
  
      def test_Hsp_positive
!       assert_equal(820, @hsp.positive)
      end
  
      def test_Hsp_align_len
!       assert_equal(820, @hsp.align_len)
      end
  
***************
*** 369,393 ****
  
      def test_Hsp_query_frame
!       assert_equal(@hsp.query_frame, 1)
      end
  
      def test_Hsp_query_from
!       assert_equal(@hsp.query_from, 1)
      end
  
      def test_Hsp_query_to
!       assert_equal(@hsp.query_to, 820)
      end
  
      def test_Hsp_hit_frame
!       assert_equal(@hsp.hit_frame, 1)
      end
  
      def test_Hsp_hit_from
!       assert_equal(@hsp.hit_from, 1)
      end
  
      def test_Hsp_hit_to
!       assert_equal(@hsp.hit_to, 820)
      end
  
--- 369,393 ----
  
      def test_Hsp_query_frame
!       assert_equal(1, @hsp.query_frame)
      end
  
      def test_Hsp_query_from
!       assert_equal(1, @hsp.query_from)
      end
  
      def test_Hsp_query_to
!       assert_equal(820, @hsp.query_to)
      end
  
      def test_Hsp_hit_frame
!       assert_equal(1, @hsp.hit_frame)
      end
  
      def test_Hsp_hit_from
!       assert_equal(1, @hsp.hit_from)
      end
  
      def test_Hsp_hit_to
!       assert_equal(820, @hsp.hit_to)
      end
  
***************
*** 402,416 ****
      def test_Hsp_qseq
        seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
!       assert_equal(@hsp.qseq, seq)
      end
  
      def test_Hsp_midline
        seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
!       assert_equal(@hsp.midline, seq)
      end
  
      def test_Hsp_hseq
        seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
!       assert_equal(@hsp.hseq, seq)
      end
  
--- 402,416 ----
      def test_Hsp_qseq
        seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
!       assert_equal(seq, @hsp.qseq)
      end
  
      def test_Hsp_midline
        seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
!       assert_equal(seq, @hsp.midline)
      end
  
      def test_Hsp_hseq
        seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
!       assert_equal(seq, @hsp.hseq)
      end