bio 1.2.1 → 1.3.0

data/test/runner.rb

@@ -6,9 +6,25 @@ require 'pathname'
 bioruby_libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'], 'lib')).cleanpath.to_s
 $:.unshift(bioruby_libpath) unless $:.include?(bioruby_libpath)
 
-if RUBY_VERSION > "1.8.2"
+if !defined?(Test::Unit::AutoRunner) then
+  # Ruby 1.9.1 does not have Test::Unit::AutoRunner
+  Test::Unit.setup_argv do |files|
+    [ File.dirname($0) ]
+  end
+  # tests called when exiting the program
+
+elsif defined?(Test::Unit::Color) then
+  # workaround for test-unit-2.0.x
+  r = Test::Unit::AutoRunner.new(true)
+  r.to_run.push File.dirname($0)
+  r.process_args(ARGV)
+  exit r.run
+
+elsif RUBY_VERSION > "1.8.2"
+  # current Test::Unit -- Ruby 1.8.3 or later
   exit Test::Unit::AutoRunner.run(true, File.dirname($0))
 else
+  # old Test::Unit -- Ruby 1.8.2 or older
   exit Test::Unit::AutoRunner.run(false, File.dirname($0))
 end
 

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

@@ -0,0 +1,112 @@
+#
+# = test/unit/bio/appl/blast/test_ncbioptions.rb - Unit test for Bio::Blast::NCBIOptions
+#
+# Copyright::  Copyright (C) 2008 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/appl/blast/ncbioptions'
+
+module Bio
+
+  class TestBlastNCBIOptions < Test::Unit::TestCase
+
+    def setup
+      @str = '-p blastn -m0 -m 1 -m2 -m 3 -F T -m 4 m5 -pblastx -m 6 -m 7'
+      @options = %w( -p blastn -m0 -m 1 -m2 -m 3 -F T -m 4 m5
+                     -pblastx -m 6 -m 7 )
+      @normalized_options = %w( -F T m5 -p blastx -m 7 )
+      @obj = Bio::Blast::NCBIOptions.parse(@str)
+    end
+
+    def test_parse
+      str = '-p tblastx -d cdna_human -i est001.fst -o test.blastn -e 0.1'
+      options = %w( -p tblastx -d cdna_human -i est001.fst
+                    -o test.blastn -e 0.1 )
+      obj = Bio::Blast::NCBIOptions.parse(str)
+      assert_equal(options, obj.options)
+    end
+
+    def test_normalize!
+      assert_nothing_raised { @obj.normalize! }
+      assert_equal(@normalized_options, @obj.options)
+    end
+
+    def test_get
+      assert_equal('blastx', @obj.get('-p'))
+      assert_equal('blastx', @obj.get('p'))
+
+      assert_equal('7', @obj.get('-m'))
+      assert_equal('7', @obj.get('m'))
+
+      assert_equal('T', @obj.get('-F'))
+      assert_equal('T', @obj.get('F'))
+
+      assert_nil(@obj.get('-X'))
+    end
+
+    def test_delete
+      assert_equal('blastx', @obj.delete('-p'))
+      assert_nil(@obj.delete('p'))
+
+      assert_equal('7', @obj.delete('-m'))
+      assert_nil(@obj.delete('m'))
+
+      assert_equal('T', @obj.delete('F'))
+      assert_nil(@obj.delete('-F'))
+
+      assert_nil(@obj.delete('-X'))
+    end
+
+    def test_set
+      assert_equal('blastx', @obj.set('-p', 'blastp'))
+      assert_equal('blastp', @obj.set('p', 'tblastx'))
+      assert_equal('tblastx',@obj.get('p'))
+      
+      assert_equal('7', @obj.set('m', '8'))
+      assert_equal('8', @obj.set('-m', '0'))
+      assert_equal('0', @obj.get('m'))
+      
+      assert_equal('T', @obj.set('-F', 'F'))
+      assert_equal('F', @obj.get('F'))
+
+      assert_nil(@obj.set('-d', 'nr'))
+      assert_equal('nr', @obj.get('d'))
+
+      assert_nil(@obj.set('i', 'test.fst'))
+      assert_equal('test.fst', @obj.get('-i'))
+    end
+
+    def test_equal_equal
+      obj1 = Bio::Blast::NCBIOptions.parse(@str)
+      assert_equal(true, @obj == obj1)
+
+      obj2 = Bio::Blast::NCBIOptions.parse('-F F')
+      assert_equal(false, @obj == obj2)
+
+      assert_equal(false, @obj == 12345)
+    end
+
+    def test_add_options
+      opts = %w( -p tblastx -m 8 -d cdna -i est.fst -o test.blast -e 0.01 )
+      result_opts = %w( -F T m5 ) + opts
+      assert_nothing_raised { @obj.add_options(opts) }
+      assert_equal(result_opts, @obj.options)
+    end
+
+    def test_make_command_line_options
+      opts = %w( -p tblastx -d cdna -i est.fst -o test.blast -e 0.01 )
+      result_opts = opts + %w( -m 0 -m 1 -m 2 -m 3 -F T -m 4 m5 -m 6 -m 7 )
+      assert_equal(result_opts, @obj.make_command_line_options(opts))
+    end
+
+  end #class TestBlastNCBIOptions
+
+end #module Bio

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

@@ -1,10 +1,12 @@
 #
 # test/unit/bio/appl/blast/test_report.rb - Unit test for Bio::Blast::Report
 #
-# Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2005, 2008
+#              Mitsuteru Nakao <n@bioruby.org>,
+#              Naohisa Goto <ng@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_report.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -16,32 +18,54 @@ require 'bio/appl/blast/report'
 
 
 module Bio
-  class TestBlastReportData
+
+  module TestBlastReportHelper
     bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
     TestDataBlast = Pathname.new(File.join(bioruby_root, 'test', 'data', 'blast')).cleanpath.to_s
 
-    def self.input
-      File.open(File.join(TestDataBlast, 'b0002.faa')).read
+    private
+
+    def get_input_data(basename = 'b0002.faa')
+      File.open(File.join(TestDataBlast, basename)).read
     end
 
-    def self.output(format = 7)
-      case format
-      when 0
-        File.open(File.join(TestDataBlast, 'b0002.faa.m0')).read 
-      when 7
-        File.open(File.join(TestDataBlast, 'b0002.faa.m7')).read 
-      when 8
-        File.open(File.join(TestDataBlast, 'b0002.faa.m8')).read 
+    def get_output_data(basename = 'b0002.faa', format = 7)
+      fn = basename + ".m#{format.to_i}"
+
+      # available filenames:
+      # 'b0002.faa.m0'
+      # 'b0002.faa.m7'
+      # 'b0002.faa.m8'
+
+      File.open(File.join(TestDataBlast, fn)).read
+    end
+
+    def create_report_object(basename = 'b0002.faa')
+      case self.class.name.to_s
+      when /XMLParser/i
+        text = get_output_data(basename, 7)
+        Bio::Blast::Report.new(text, :xmlparser)
+      when /REXML/i
+        text = get_output_data(basename, 7)
+        Bio::Blast::Report.new(text, :rexml)
+      when /Default/i
+        text = get_output_data(basename, 0)
+        Bio::Blast::Default::Report.new(text)
+      when /Tab/i
+        text = get_output_data(basename, 8)
+        Bio::Blast::Report.new(text)
+      else
+        text = get_output_data(basename, 7)
+        Bio::Blast::Report.new(text)
       end
     end
-  end
+  end #module TestBlastReportHelper
 
-    
   class TestBlastReport < Test::Unit::TestCase
-    require 'bio/appl/blast/report'
+    include TestBlastReportHelper
 
     def setup
-      @report = Bio::Blast::Report.new(Bio::TestBlastReportData.output)
+      @report = create_report_object
     end
     
     def test_iterations
@@ -96,15 +120,15 @@ module Bio
     end
 
     def test_inclusion
-      assert(@report.inclusion)
+      assert_nothing_raised { @report.inclusion }
     end
 
     def test_sc_match
-      assert(@report.sc_match)
+      assert_nothing_raised { @report.sc_match }
     end
 
     def test_sc_mismatch
-      assert(@report.sc_mismatch)
+      assert_nothing_raised { @report.sc_mismatch }
     end
 
     def test_gap_open
@@ -123,16 +147,20 @@ module Bio
       assert_equal(nil, @report.pattern)
     end
 
-    def test_extrez_query
+    def test_entrez_query
       assert_equal(nil, @report.entrez_query)
     end
 
     def test_each_iteration
-      @report.each_iteration { |itr| }
+      assert_nothing_raised {
+        @report.each_iteration { |itr| }
+      }
     end
 
     def test_each_hit
-      @report.each_hit { |hit| }
+      assert_nothing_raised {
+        @report.each_hit { |hit| }
+      }
     end
 
     def test_hits
@@ -177,9 +205,10 @@ module Bio
   end
   
   class TestBlastReportIteration < Test::Unit::TestCase
+    include TestBlastReportHelper
+
     def setup
-      data = Bio::TestBlastReportData.output
-      report = Bio::Blast::Report.new(data)
+      report = create_report_object
       @itr = report.iterations.first
     end
 
@@ -204,9 +233,10 @@ module Bio
   end
 
   class TestBlastReportHit < Test::Unit::TestCase
+    include TestBlastReportHelper
+
     def setup
-      data = Bio::TestBlastReportData.output
-      report = Bio::Blast::Report.new(data)
+      report = create_report_object
       @hit = report.hits.first
     end
 
@@ -315,9 +345,10 @@ module Bio
   end
 
   class TestBlastReportHsp < Test::Unit::TestCase
+    include TestBlastReportHelper
+
     def setup
-      data = Bio::TestBlastReportData.output
-      report = Bio::Blast::Report.new(data)
+      report = create_report_object
       @hsp = report.hits.first.hsps.first
     end
     
@@ -325,7 +356,7 @@ module Bio
       assert_equal(1, @hsp.num)
     end
 
-    def test_Hsp_hit_score
+    def test_Hsp_bit_score
       assert_equal(1567.75, @hsp.bit_score)
     end
 
@@ -342,7 +373,7 @@ module Bio
     end
 
     def test_Hsp_gaps
-      assert(@hsp.gaps)
+      assert_nothing_raised { @hsp.gaps }
     end
 
     def test_Hsp_positive
@@ -382,11 +413,11 @@ module Bio
     end
 
     def test_Hsp_pattern_from
-      @hsp.pattern_from
+      assert_nothing_raised { @hsp.pattern_from }
     end
 
     def test_Hsp_pattern_to
-      @hsp.pattern_to 
+      assert_nothing_raised { @hsp.pattern_to }
     end
 
     def test_Hsp_qseq
@@ -405,13 +436,700 @@ module Bio
     end
 
     def test_Hsp_percent_identity
-      @hsp.percent_identity
+      assert_nothing_raised { @hsp.percent_identity }
+    end
+
+    def test_Hsp_mismatch_count
+      assert_nothing_raised { @hsp.mismatch_count }
+    end
+
+  end 
+
+  class TestBlastReportREXML < TestBlastReport
+  end
+
+  class TestBlastReportIterationREXML < TestBlastReportIteration
+  end
+
+  class TestBlastReportHitREXML < TestBlastReportHit
+  end
+
+  class TestBlastReportHspREXML < TestBlastReportHsp
+  end
+
+  if defined? XMLParser then
+
+  class TestBlastReportXMLParser < TestBlastReport
+  end
+
+  class TestBlastReportIterationXMLParser < TestBlastReportIteration
+  end
+
+  class TestBlastReportHitXMLParser < TestBlastReportHit
+  end
+
+  class TestBlastReportHspXMLParser < TestBlastReportHsp
+  end
+
+  end #if defined? XMLParser
+
+  class TestBlastReportDefault < TestBlastReport
+    undef test_entrez_query
+    undef test_filter
+    undef test_hsp_len
+    undef test_inclusion
+    undef test_parameters
+    undef test_query_id
+    undef test_statistics
+
+    def test_program
+      assert_equal('BLASTP', @report.program)
+    end
+
+    def test_reference
+      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(text_str, @report.reference)
+    end
+
+    def test_version
+      assert_equal('BLASTP 2.2.10 [Oct-19-2004]', @report.version)
+    end
+
+    def test_kappa
+      assert_equal(0.134, @report.kappa)
+    end
+
+    def test_lambda
+      assert_equal(0.319, @report.lambda)
+    end
+
+    def test_entropy
+      assert_equal(0.383, @report.entropy)
+    end
+
+    def test_gapped_kappa
+      assert_equal(0.0410, @report.gapped_kappa)
+    end
+
+    def test_gapped_lambda
+      assert_equal(0.267, @report.gapped_lambda)
+    end
+
+    def test_gapped_entropy
+      assert_equal(0.140, @report.gapped_entropy)
+    end
+  end
+
+  class TestBlastReportIterationDefault < TestBlastReportIteration
+    undef test_statistics
+  end
+
+  class TestBlastReportHitDefault < TestBlastReportHit
+    undef test_Hit_accession
+    undef test_Hit_hit_id
+    undef test_Hit_num
+    undef test_Hit_query_def
+    undef test_Hit_query_id
+    undef test_Hit_query_len
+
+    def setup
+      @filtered_query_sequence = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQxxxxxxxxxxxxxxALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
+      super
+    end
+
+    def test_Hit_bit_score
+      # differs from XML because of truncation in the default format
+      assert_equal(1567.0, @hit.bit_score)
+    end
+
+    def test_Hit_identity
+      # differs from XML because filtered residues are not counted in the
+      # default format
+      assert_equal(806, @hit.identity)
+    end
+
+    def test_Hit_midline
+      # differs from XML because filtered residues are not specified in XML
+      seq = @filtered_query_sequence.gsub(/x/, ' ')
+      assert_equal(seq, @hit.midline)
+    end
+
+    def test_Hit_query_seq
+      # differs from XML because filtered residues are not specified in XML
+      seq = @filtered_query_sequence.gsub(/x/, 'X')
+      assert_equal(seq, @hit.query_seq)
+    end
+  end
+
+  class TestBlastReportHspDefault < TestBlastReportHsp
+    undef test_Hsp_density
+    undef test_Hsp_mismatch_count
+    undef test_Hsp_num
+    undef test_Hsp_pattern_from
+    undef test_Hsp_pattern_to
+
+    def setup
+      @filtered_query_sequence = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQxxxxxxxxxxxxxxALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
+      super
+    end
+
+    def test_Hsp_identity
+      # differs from XML because filtered residues are not counted in the
+      # default format
+      assert_equal(806, @hsp.identity)
+    end
+
+    def test_Hsp_positive
+      # differs from XML because filtered residues are not counted in the
+      # default format
+      assert_equal(806, @hsp.positive)
+    end
+
+    def test_Hsp_midline
+      # differs from XML because filtered residues are not specified in XML
+      seq = @filtered_query_sequence.gsub(/x/, ' ')
+      assert_equal(seq, @hsp.midline)
+    end
+
+    def test_Hsp_qseq
+      # differs from XML because filtered residues are not specified in XML
+      seq = @filtered_query_sequence.gsub(/x/, 'X')
+      assert_equal(seq, @hsp.qseq)
+    end
+    
+    def test_Hsp_bit_score
+      # differs from XML because of truncation in the default format
+      assert_equal(1567.0, @hsp.bit_score)
+    end
+
+    def test_Hsp_hit_frame
+      # differs from XML because not available in the default BLASTP format
+      assert_equal(nil, @hsp.hit_frame)
+    end
+
+    def test_Hsp_query_frame
+      # differs from XML because not available in the default BLASTP format
+      assert_equal(nil, @hsp.query_frame)
+    end
+  end
+
+  ########################################################################
+  # Tests for new BLAST XML format (blastall 2.2.14 or later)
+  # with the result of multiple query sequences
+  ########################################################################
+
+  class TestBlastReportMulti < Test::Unit::TestCase
+    include TestBlastReportHelper
+
+    def setup
+      @report = create_report_object('blastp-multi')
+      @overall = [ @report ] + @report.reports
+    end
+
+    def test_reports
+      assert_equal(5, @report.reports.size)
+    end
+
+    def test_iterations
+      assert_equal(1, @report.iterations.size)
+      assert_equal([ 1, 1, 1, 1, 1],
+                   @report.reports.collect { |x| x.iterations.size })
+    end
+
+    def test_parameters
+      @overall.each do |r|
+        assert_equal('BLOSUM62', r.parameters['matrix'])
+        assert_equal(0.001,      r.parameters['expect'])
+        assert_equal(11,         r.parameters['gap-open'])
+        assert_equal(1,          r.parameters['gap-extend'])
+        assert_equal('F',        r.parameters['filter'])
+      end
+    end
+
+    def test_program
+      @overall.each do |r|
+        assert_equal('blastp', r.program)
+      end
+    end
+
+    def test_version
+      @overall.each do |r|
+        assert_equal('blastp 2.2.18 [Mar-02-2008]', r.version)
+      end
+    end
+
+    def test_reference
+      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.'
+
+      @overall.each do |r|
+        assert_equal(text_str, r.reference)
+      end
+    end
+
+    def test_db
+      @overall.each do |r|
+        assert_equal('BA000007.faa', r.db)
+      end
+    end
+
+    def test_query_id
+      qids = [ 'lcl|1_0', 'lcl|2_0', 'lcl|3_0', nil, 'lcl|5_0' ]
+      assert_equal(qids[0], @report.query_id)
+      assert_equal(qids,
+                   @report.reports.collect { |r| r.query_id })
+    end
+
+    def test_query_def
+      qdefs =
+        [ 'gi|1790845|gb|AAC77338.1| predicted DNA-binding transcriptional regulator [Escherichia coli str. K-12 substr. MG1655]',
+          'gi|1790846|gb|AAC77339.1| lipoate-protein ligase A [Escherichia coli str. K-12',
+          'gi|1790847|gb|AAC77340.1| conserved protein [Escherichia coli str. K-12 substr. MG1655]',
+          nil,
+          'gi|1790849|gb|AAC77341.1| 3-phosphoserine phosphatase [Escherichia coli str. K-12 substr. MG1655]'
+        ]
+      assert_equal(qdefs[0], @report.query_def)
+      assert_equal(qdefs,
+                   @report.reports.collect { |r| r.query_def })
+    end
+
+    def test_query_len
+      qlens = [ 443, 346, 214, nil, 322 ]
+      assert_equal(qlens[0], @report.query_len)
+      assert_equal(qlens,
+                   @report.reports.collect { |r| r.query_len })
+    end
+
+    def test_matrix
+      @overall.each do |r|
+        assert_equal('BLOSUM62', r.matrix)
+      end
+    end
+
+    def test_expect
+      @overall.each do |r|
+        assert_equal(0.001, r.expect)
+      end
+    end
+
+    def test_gap_open
+      @overall.each do |r|
+        assert_equal(11, r.gap_open)
+      end
+    end
+
+    def test_gap_extend
+      @overall.each do |r|
+        assert_equal(1, r.gap_extend)
+      end
+    end
+
+    def test_filter
+      @overall.each do |r|
+        assert_equal('F', r.filter)
+      end
+    end
+
+    def test_pattern
+      @overall.each do |r|
+        assert_equal(nil, r.pattern)
+      end
+    end
+
+    def test_each_iteration
+      @overall.each do |r|
+        count = 0
+        assert_nothing_raised {
+          r.each_iteration { |itr| count += 1 }
+        }
+        assert_equal(1, count)
+      end
+    end
+
+    def test_each_hit
+      @overall.each do |r|
+        assert_nothing_raised {
+          r.each_hit { |hit| }
+        }
+      end
+    end
+
+    def test_hits
+      hsizes = [ 0, 1, 1, 0, 2 ]
+      assert_equal(hsizes[0], @report.hits.size)
+      assert_equal(hsizes,
+                   @report.reports.collect { |r| r.hits.size })
+    end
+
+    def test_statistics
+      assert_equal({}, @report.statistics)
+
+      stat = {
+        "kappa" => 0.041, "eff-space" => 0, "db-num" => 5361, 
+        "hsp-len" => 0, "db-len" => 1609188, "lambda" => 0.267, 
+        "entropy" => 0.14
+      }
+      stats = [ {}, stat, stat, {}, stat ]
+      @report.reports.each do |r|
+        assert_equal(stats.shift, r.statistics)
+      end
+    end
+
+    def test_db_num
+      assert_equal(nil, @report.db_num)
+      ary = [ nil, 5361, 5361, nil, 5361 ]
+      @report.reports.each do |r|
+        assert_equal(ary.shift, r.db_num)
+      end
+    end
+
+    def test_db_len
+      assert_equal(nil, @report.db_len)
+      ary = [ nil, 1609188, 1609188, nil, 1609188 ]
+      @report.reports.each do |r|
+        assert_equal(ary.shift, r.db_len)
+      end
+    end
+
+    def test_hsp_len
+      assert_equal(nil, @report.hsp_len)
+      ary = [ nil, 0, 0, nil, 0 ]
+      @report.reports.each do |r|
+        assert_equal(ary.shift, r.hsp_len)
+      end
+    end
+
+    def test_eff_space
+      assert_equal(nil, @report.eff_space)
+      ary = [ nil, 0, 0, nil, 0 ]
+      @report.reports.each do |r|
+        assert_equal(ary.shift, r.eff_space)
+      end
+    end
+
+    def test_kappa
+      assert_equal(nil, @report.kappa)
+      ary = [ nil, 0.041, 0.041, nil, 0.041 ]
+      @report.reports.each do |r|
+        assert_equal(ary.shift, r.kappa)
+      end
+    end
+
+    def test_lambda
+      assert_equal(nil, @report.lambda)
+      ary = [ nil, 0.267, 0.267, nil, 0.267 ]
+      @report.reports.each do |r|
+        assert_equal(ary.shift, r.lambda)
+      end
+    end
+
+    def test_entropy
+      assert_equal(nil, @report.entropy)
+      ary = [ nil, 0.14, 0.14, nil, 0.14 ]
+      @report.reports.each do |r|
+        assert_equal(ary.shift, r.entropy)
+      end
+    end
+
+    def test_message
+      @overall.each do |r|
+        assert_equal(nil, r.message)
+      end
+    end
+  end
+  
+  class TestBlastReportIterationMulti < Test::Unit::TestCase
+    include TestBlastReportHelper
+
+    def setup
+      report = create_report_object('blastp-multi')
+      @itr = report.reports[4].iterations[0]
+    end
+
+    def test_query_id
+      assert_equal('lcl|5_0', @itr.query_id)
+    end
+
+    def test_query_def
+      assert_equal('gi|1790849|gb|AAC77341.1| 3-phosphoserine phosphatase [Escherichia coli str. K-12 substr. MG1655]', @itr.query_def)
+    end
+
+    def test_query_len
+      assert_equal(322, @itr.query_len)
+    end
+
+    def test_hits
+      assert_equal(2, @itr.hits.size)
+    end
+
+    def test_each
+      count = 0
+      assert_nothing_raised {
+        @itr.each { |hit| count += 1 }
+      }
+      assert_equal(2, count)
+    end
+
+    def test_statistics
+      stat = {
+        "kappa" => 0.041, "eff-space" => 0, "db-num" => 5361, 
+        "hsp-len" => 0, "db-len" => 1609188, "lambda" => 0.267, 
+        "entropy" => 0.14
+      }
+      assert_equal(stat, @itr.statistics)
+    end
+
+    def test_num
+      assert_equal(5, @itr.num)
+    end
+
+    def test_message
+      assert_equal(nil, @itr.message)
+    end
+  end
+
+  class TestBlastReportHitMulti < Test::Unit::TestCase
+    include TestBlastReportHelper
+
+    def setup
+      report = create_report_object('blastp-multi')
+      @hit = report.reports[4].iterations[0].hits[1]
+    end
+
+    def test_Hit_hsps
+      assert_equal(1, @hit.hsps.size)
+    end
+
+    def test_Hit_query_id
+      assert_equal('lcl|5_0', @hit.query_id)
+    end
+
+    def test_Hit_query_def
+      assert_equal('gi|1790849|gb|AAC77341.1| 3-phosphoserine phosphatase [Escherichia coli str. K-12 substr. MG1655]', @hit.query_def)
+    end
+
+    def test_Hit_query_len
+      assert_equal(322, @hit.query_len)
+    end
+
+    def test_Hit_num
+      assert_equal(2, @hit.num)
+    end
+
+    def test_Hit_hit_id
+      assert_equal('gi|13363792|dbj|BAB37741.1|', @hit.hit_id) 
+    end
+
+    def test_Hit_len
+      assert_equal(732, @hit.len)
+    end
+
+    def test_Hit_target_len
+      assert_equal(732, @hit.target_len)
+    end
+
+    def test_Hit_definition
+      assert_equal('zinc-transporting ATPase [Escherichia coli O157:H7 str. Sakai]', @hit.definition)
+    end
+
+    def test_Hit_taeget_def
+      assert_equal('zinc-transporting ATPase [Escherichia coli O157:H7 str. Sakai]', @hit.target_def)
+    end
+
+    def test_Hit_accession
+      assert_equal('BAB37741', @hit.accession)
+    end
+
+    def test_Hit_target_id
+      #assert_equal('gi|13363792|dbj|BAB37741.1|', @hit.target_id)
+      assert_equal('BAB37741', @hit.target_id)
+    end
+    
+    def test_Hit_evalue
+      assert_equal(0.000899657, @hit.evalue)
+    end
+
+    def test_Hit_bit_score
+      assert_equal(38.1206, @hit.bit_score)
+    end
+
+    def test_Hit_identity
+      assert_equal(39, @hit.identity)
+    end
+
+    def test_Hit_overlap
+      # alignment length
+      assert_equal(123, @hit.overlap)
+    end
+
+    def test_Hit_query_seq
+      seq = 'VLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVIGDIVDAQYKAKTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVN-EKAEVTIRHADLMGV'
+      assert_equal(seq, @hit.query_seq)
+    end
+
+    def test_Hit_target_seq
+      seq = 'ISELNALGVKGVILTG----------DNPRAAAAIAGELGL---EFKAGLL-----PEDKVKAVTELNQHA--PLAM---VGDGINDAPAMKAAAIGIAMGSGTDVALETADAALTHNHLRGL'
+      assert_equal(seq, @hit.target_seq)
+    end
+
+    def test_Hit_midline
+      seq = '+ +L  LG K  I +G          D  R  A +A EL +   +F   ++      + K K +T L Q    PLA    +GDG ND P +KAA +GIA  +   V  E A+  + H  L G+'
+      assert_equal(seq, @hit.midline)
+    end
+
+    def test_Hit_query_start
+      assert_equal(190, @hit.query_start)
+#      assert_equal(190, @hit.query_from)
+    end
+
+    def test_Hit_query_end
+      assert_equal(311, @hit.query_end)
+#      assert_equal(311, @hit.query_to)
+    end
+
+    def test_Hit_target_start
+      assert_equal(569, @hit.target_start)
+#      assert_equal(569, @hit.hit_from)
+    end
+
+    def test_Hit_target_end
+      assert_equal(668, @hit.target_end)
+#      assert_equal(668, @hit.hit_to)
+    end
+
+    def test_Hit_lap_at
+      assert_equal([190, 311, 569, 668], @hit.lap_at)
+    end
+  end
+
+  class TestBlastReportHspMulti < Test::Unit::TestCase
+    include TestBlastReportHelper
+
+    def setup
+      report = create_report_object('blastp-multi')
+      @hsp = report.reports[4].iterations[0].hits[1].hsps[0]
+    end
+    
+    def test_Hsp_num
+      assert_equal(1, @hsp.num)
+    end
+
+    def test_Hsp_bit_score
+      assert_equal(38.1206, @hsp.bit_score)
+    end
+
+    def test_Hsp_score
+      assert_equal(87, @hsp.score)
+    end
+
+    def test_Hsp_evalue
+      assert_equal(0.000899657, @hsp.evalue)
+    end
+
+    def test_Hsp_identity
+      assert_equal(39, @hsp.identity)
+    end
+
+    def test_Hsp_gaps
+      assert_equal(24, @hsp.gaps)
+    end
+
+    def test_Hsp_positive
+      assert_equal(56, @hsp.positive)
+    end
+
+    def test_Hsp_align_len
+      assert_equal(123, @hsp.align_len)
+    end
+
+    def test_Hsp_density
+      assert_nothing_raised { @hsp.density }
+    end
+
+    def test_Hsp_query_frame
+      assert_equal(1, @hsp.query_frame)
+    end
+
+    def test_Hsp_query_from
+      assert_equal(190, @hsp.query_from)
+    end
+
+    def test_Hsp_query_to
+      assert_equal(311, @hsp.query_to)
+    end
+
+    def test_Hsp_hit_frame
+      assert_equal(1, @hsp.hit_frame)
+    end
+
+    def test_Hsp_hit_from
+      assert_equal(569, @hsp.hit_from)
+    end
+
+    def test_Hsp_hit_to
+      assert_equal(668, @hsp.hit_to)
+    end
+
+    def test_Hsp_pattern_from
+      assert_nothing_raised { @hsp.pattern_from }
+    end
+
+    def test_Hsp_pattern_to
+      assert_nothing_raised { @hsp.pattern_to }
+    end
+
+    def test_Hsp_qseq
+      seq = 'VLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVIGDIVDAQYKAKTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVN-EKAEVTIRHADLMGV'
+      assert_equal(seq, @hsp.qseq)
+    end
+
+    def test_Hsp_midline
+      seq = '+ +L  LG K  I +G          D  R  A +A EL +   +F   ++      + K K +T L Q    PLA    +GDG ND P +KAA +GIA  +   V  E A+  + H  L G+'
+      assert_equal(seq, @hsp.midline)
+    end
+
+    def test_Hsp_hseq
+      seq = 'ISELNALGVKGVILTG----------DNPRAAAAIAGELGL---EFKAGLL-----PEDKVKAVTELNQHA--PLAM---VGDGINDAPAMKAAAIGIAMGSGTDVALETADAALTHNHLRGL'
+      assert_equal(seq, @hsp.hseq)
+    end
+
+    def test_Hsp_percent_identity
+      assert_nothing_raised { @hsp.percent_identity }
     end
 
     def test_Hsp_mismatch_count
-      @hsp.mismatch_count
+      assert_nothing_raised { @hsp.mismatch_count }
     end
 
   end 
 
+  # Tests for REXML version
+  class TestBlastReportMultiREXML < TestBlastReportMulti
+  end
+
+  class TestBlastReportIterationMultiREXML < TestBlastReportIterationMulti
+  end
+
+  class TestBlastReportHitMultiREXML < TestBlastReportHitMulti
+  end
+
+  class TestBlastReportHspMultiREXML < TestBlastReportHspMulti
+  end
+
+  # Tests for XMLParser version
+  if defined? XMLParser then
+
+  class TestBlastReportMultiXMLParser < TestBlastReportMulti
+  end
+
+  class TestBlastReportIterationMultiXMLParser < TestBlastReportIterationMulti
+  end
+
+  class TestBlastReportHitMultiXMLParser < TestBlastReportHitMulti
+  end
+
+  class TestBlastReportHspMultiXMLParser < TestBlastReportHspMulti
+  end
+
+  end #if defined? XMLParser
+
 end # module Bio