bio 1.3.0 → 1.3.1

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

@@ -4,7 +4,7 @@
 # Copyright::  Copyright (C) 2006 Mitsuteru 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'
@@ -41,7 +41,7 @@ module Bio
       assert_equal(Array, ary.class)
     end
 
-    def test_reports_ary
+    def test_reports_ary_contents
       Bio::HMMER.reports(Bio::TestHMMERReportData.output).each do |report|
         assert_equal(Bio::HMMER::Report, report.class)
       end

data/test/unit/bio/appl/sim4/test_report.rb

@@ -0,0 +1,869 @@
+#
+# test/unit/bio/appl/sim4/test_report.rb - Unit test for Bio::Sim4
+#
+# Copyright::  Copyright (C) 2009
+#              Naohisa Goto <ng@bioruby.org>
+# License::    The Ruby License
+#
+#  $Id:$
+#
+
+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/appl/sim4/report'
+
+module Bio
+
+  class TestDataForSim4Report
+    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
+    DataPath = Pathname.new(File.join(bioruby_root, 'test', 'data', 'sim4')).cleanpath.to_s
+
+    def initialize(filename)
+      @filename = filename
+    end
+
+    def read
+      File.read(File.join(DataPath,@filename))
+    end
+
+    def report
+      Bio::Sim4::Report.new(self.read)
+    end
+
+    def self.report(filename)
+      self.new(filename).report
+    end
+
+    def self.report1
+      filename = "simple-A4.sim4"
+      self.new(filename).report
+    end
+
+    def self.report2
+      filename = "simple2-A4.sim4"
+      self.new(filename).report
+    end
+
+    def self.report4
+      filename = "complement-A4.sim4"
+      self.new(filename).report
+    end
+
+  end #class TestDataForSim4Report
+
+
+  class TestSim4Report < Test::Unit::TestCase
+
+    def setup
+      @sim4 = TestDataForSim4Report.report1
+    end
+
+    def test_hits
+      assert_kind_of(Array, @sim4.hits)
+      assert_equal(1, @sim4.hits.size)
+      assert_instance_of(Bio::Sim4::Report::Hit, @sim4.hits[0])
+    end
+
+    def test_all_hits
+      assert_kind_of(Array, @sim4.all_hits)
+      assert_equal(1, @sim4.all_hits.size)
+      assert_instance_of(Bio::Sim4::Report::Hit, @sim4.all_hits[0])
+    end
+
+    def exec_test_seq1_len(sd)
+      assert_equal(94, sd.len)
+    end
+    private :exec_test_seq1_len
+
+    def test_seq1
+      sd = @sim4.seq1
+      assert_instance_of(Bio::Sim4::Report::SeqDesc, sd)
+      assert_equal('mrna1', sd.entry_id)
+      assert_equal('mrna1', sd.definition)
+      assert_equal('sample10-1.fst', sd.filename)
+      exec_test_seq1_len(sd)
+    end
+
+    def exec_test_each(meth)
+      count = 0
+      assert_nothing_raised {
+        @sim4.__send__(meth) do |x|
+          count += 1
+        end
+      }
+      assert_equal(1, count)
+      @sim4.__send__(meth) do |x|
+        assert_instance_of(Bio::Sim4::Report::Hit, x)
+      end
+    end
+    private :exec_test_each
+
+    def test_each
+      exec_test_each(:each)
+    end
+
+    def test_each_hit
+      exec_test_each(:each_hit)
+    end
+
+    def test_num_hits
+      assert_equal(1, @sim4.num_hits)
+    end
+
+    def test_query_def
+      assert_equal('mrna1', @sim4.query_def)
+    end
+
+    def test_query_id
+      assert_equal('mrna1', @sim4.query_id)
+    end
+
+    def test_query_len
+      assert_equal(94, @sim4.query_len)
+    end
+
+  end #class TestSim4Report
+
+  class TestSim4ReportHit < Test::Unit::TestCase
+
+    def setup
+      @hit = TestDataForSim4Report.report1.hits.first
+    end
+
+    def test_align
+      a = [
+           [ "TTGTTTCCGTCGCTGGTTATTGTCTAGAACGCAAAAATAG",
+             "||||||||||||||||||||||||||||||||||||||||",
+             "TTGTTTCCGTCGCTGGTTATTGTCTAGAACGCAAAAATAG" ],
+           [ "         ",
+             "<<<...<<<",
+             "CTG...TAC" ],
+           [ "TCTACACATCACTAGCGTGGGTGGGCGGAAAGAGCAGCTCGCCACT CAAGCTAA",
+             "|||||||||||||||| |||||||||||||-|||||||||||||||-||||||||",
+             "TCTACACATCACTAGCCTGGGTGGGCGGAA GAGCAGCTCGCCACTTCAAGCTAA" ]
+          ]
+      assert_equal(a, @hit.align)
+    end
+
+    def test_complement?
+      assert_equal(nil, @hit.complement?)
+    end
+
+    def test_definition
+      assert_equal('genome1', @hit.definition)
+    end
+
+    def test_each
+      count = 0
+      assert_nothing_raised {
+        @hit.each do |x|
+          count += 1
+        end
+      }
+      assert_equal(2, count)
+      @hit.each do |x|
+        assert_instance_of(Bio::Sim4::Report::SegmentPair, x)
+      end
+    end
+
+    def exec_test_exons(meth)
+      assert_kind_of(Array, @hit.__send__(meth))
+      assert_equal(2, @hit.__send__(meth).size)
+      @hit.__send__(meth).each do |x|
+        assert_instance_of(Bio::Sim4::Report::SegmentPair, x)
+      end
+    end
+    private :exec_test_exons
+
+    def test_exons
+      exec_test_exons(:exons)
+    end
+
+    def test_hit_id
+      assert_equal('genome1', @hit.hit_id)
+    end
+
+    def test_hsps
+      exec_test_exons(:hsps)
+    end
+
+    def test_introns
+      assert_kind_of(Array, @hit.introns)
+      assert_equal(1, @hit.introns.size)
+      @hit.introns.each do |x|
+        assert_instance_of(Bio::Sim4::Report::SegmentPair, x)
+      end
+    end
+
+    def test_len
+      assert_equal(599, @hit.len)
+    end
+
+    def test_query_def
+      assert_equal('mrna1', @hit.query_def)
+    end
+
+    def test_query_id
+      assert_equal('mrna1', @hit.query_id)
+    end
+
+    def test_query_len
+      assert_equal(94, @hit.query_len)
+    end
+
+    def test_segmentpairs
+      assert_kind_of(Array, @hit.segmentpairs)
+      assert_equal(3, @hit.segmentpairs.size)
+      @hit.segmentpairs.each do |x|
+        assert_instance_of(Bio::Sim4::Report::SegmentPair, x)
+      end
+    end
+
+    def exec_test_seq1_len(sd)
+      assert_equal(94, sd.len)
+    end
+    private :exec_test_seq1_len
+
+    def test_seq1
+      sd = @hit.seq1
+      assert_instance_of(Bio::Sim4::Report::SeqDesc, sd)
+      assert_equal('mrna1', sd.entry_id)
+      assert_equal('mrna1', sd.definition)
+      assert_equal('sample10-1.fst', sd.filename)
+      exec_test_seq1_len(sd)
+    end
+
+    def test_seq2
+      sd = @hit.seq2
+      assert_instance_of(Bio::Sim4::Report::SeqDesc, sd)
+      assert_equal('genome1', sd.entry_id)
+      assert_equal('genome1', sd.definition)
+      assert_equal(599, sd.len)
+      #assert_equal('sample10-2.fst', sd.filename)
+      assert_equal('sample10-2.fst (genome1)', sd.filename)
+    end
+
+    def test_target_def
+      assert_equal('genome1', @hit.target_def)
+    end
+
+    def test_target_id
+      assert_equal('genome1', @hit.target_id)
+    end
+
+    def test_target_len
+      assert_equal(599, @hit.target_len)
+    end
+  end #class TestSim4ReportHit
+
+  class TestSim4ReportSegmentPair_exon < Test::Unit::TestCase
+    def setup
+      @exon = TestDataForSim4Report.report1.hits[0].exons[1]
+    end
+
+    def test_align_len
+      assert_equal(55, @exon.align_len)
+    end
+
+    def test_direction
+      assert_equal("", @exon.direction)
+    end
+
+    def test_hit_from
+      assert_equal(404, @exon.hit_from)
+    end
+
+    def test_hit_to
+      assert_equal(457, @exon.hit_to)
+    end
+
+    def test_hseq
+      hseq = "TCTACACATCACTAGCCTGGGTGGGCGGAA GAGCAGCTCGCCACTTCAAGCTAA"
+      assert_equal(hseq, @exon.hseq)
+    end
+
+    def test_midline
+      midline = "|||||||||||||||| |||||||||||||-|||||||||||||||-||||||||"
+      assert_equal(midline, @exon.midline)
+    end
+
+    def test_percent_identity
+      #assert_equal(94, @exon.percent_identity)
+      assert_equal("94", @exon.percent_identity)
+    end
+
+    def test_qseq
+      qseq = "TCTACACATCACTAGCGTGGGTGGGCGGAAAGAGCAGCTCGCCACT CAAGCTAA"
+      assert_equal(qseq, @exon.qseq)
+    end
+
+    def test_query_from
+      assert_equal(41, @exon.query_from)
+    end
+
+    def test_query_to
+      assert_equal(94, @exon.query_to)
+    end
+
+    def exec_test_seq1_from_to(seg)
+      assert_equal(41, seg.from)
+      assert_equal(94, seg.to)
+    end
+    private :exec_test_seq1_from_to
+
+    def test_seq1
+      assert_instance_of(Bio::Sim4::Report::Segment, @exon.seq1)
+      assert_equal("TCTACACATCACTAGCGTGGGTGGGCGGAAAGAGCAGCTCGCCACT CAAGCTAA",
+                   @exon.seq1.seq)
+      exec_test_seq1_from_to(@exon.seq1)
+    end
+
+    def test_seq2
+      assert_instance_of(Bio::Sim4::Report::Segment, @exon.seq2)
+      assert_equal(404, @exon.seq2.from)
+      assert_equal(457, @exon.seq2.to)
+      assert_equal("TCTACACATCACTAGCCTGGGTGGGCGGAA GAGCAGCTCGCCACTTCAAGCTAA",
+                   @exon.seq2.seq)
+    end
+  end #class TestSim4ReportSegmentPair_exon
+
+  class TestSim4ReportSegmentPair_intron < Test::Unit::TestCase
+    def setup
+      @intron = TestDataForSim4Report.report1.hits[0].introns[0]
+    end
+
+    def test_align_len
+      assert_equal(9, @intron.align_len)
+    end
+
+    def test_direction
+      assert_equal(nil, @intron.direction)
+    end
+
+    def test_hit_from
+      assert_equal(185, @intron.hit_from)
+    end
+
+    def test_hit_to
+      assert_equal(403, @intron.hit_to)
+    end
+
+    def test_hseq
+      hseq = "CTG...TAC"
+      assert_equal(hseq, @intron.hseq)
+    end
+
+    def test_midline
+      midline = "<<<...<<<"
+      assert_equal(midline, @intron.midline)
+    end
+
+    def test_percent_identity
+      assert_equal(nil, @intron.percent_identity)
+    end
+
+    def test_qseq
+      qseq = "         "
+      assert_equal(qseq, @intron.qseq)
+    end
+
+    def test_query_from
+      assert_equal(0, @intron.query_from)
+    end
+
+    def test_query_to
+      assert_equal(0, @intron.query_to)
+    end
+
+    def test_seq1
+      assert_instance_of(Bio::Sim4::Report::Segment, @intron.seq1)
+      assert_equal(0, @intron.seq1.from)
+      assert_equal(0, @intron.seq1.to)
+      assert_equal("         ", @intron.seq1.seq)
+    end
+
+    def test_seq2
+      assert_instance_of(Bio::Sim4::Report::Segment, @intron.seq2)
+      assert_equal(185, @intron.seq2.from)
+      assert_equal(403, @intron.seq2.to)
+      assert_equal("CTG...TAC", @intron.seq2.seq)
+    end
+  end #class TestSim4ReportSegmentPair_intron
+
+
+  class TestSim4Report2 < TestSim4Report
+    def setup
+      @sim4 = TestDataForSim4Report.report2
+    end
+
+    def test_query_len
+      assert_equal(96, @sim4.query_len)
+    end
+
+    def exec_test_seq1_len(sd)
+      assert_equal(96, sd.len)
+    end
+    private :exec_test_seq1_len
+  end #class TestSim4Report2
+
+  class TestSim4ReportHit2 < TestSim4ReportHit
+    def setup
+      @hit = TestDataForSim4Report.report2.hits.first
+    end
+
+    def test_align
+      a = [
+           [ "AGTTGTTTCCGTCGCTGGTTATTGTCTAGAACGCAAAAATAG",
+             "||||||||||||||||||||||||||||||||||||||||||",
+             "AGTTGTTTCCGTCGCTGGTTATTGTCTAGAACGCAAAAATAG" ],
+           [ "         ",
+             "<<<...<<<",
+             "CTG...TAC" ],
+           [ "TCTACACATCACTAGCGTGGGTGGGCGGAAAGAGCAGCTCGCCACT CAAGCTAA",
+             "|||||||||||||||| |||||||||||||-|||||||||||||||-||||||||",
+             "TCTACACATCACTAGCCTGGGTGGGCGGAA GAGCAGCTCGCCACTTCAAGCTAA" ]
+          ]
+      assert_equal(a, @hit.align)
+    end
+
+    def test_query_len
+      assert_equal(96, @hit.query_len)
+    end
+
+    def exec_test_seq1_len(sd)
+      assert_equal(96, sd.len)
+    end
+    private :exec_test_seq1_len
+  end #class TestSim4ReportHit2
+
+
+  class TestSim4ReportSegmentPair2_exon < TestSim4ReportSegmentPair_exon
+    def setup
+      @exon = TestDataForSim4Report.report2.hits[0].exons[1]
+    end
+
+    def test_query_from
+      assert_equal(43, @exon.query_from)
+    end
+
+    def test_query_to
+      assert_equal(96, @exon.query_to)
+    end
+
+    def exec_test_seq1_from_to(seg)
+      assert_equal(43, seg.from)
+      assert_equal(96, seg.to)
+    end
+    private :exec_test_seq1_from_to
+
+  end #class TestSim4ReportSegmentPair2_exon
+
+
+  class TestSim4ReportSegmentPair2_intron < TestSim4ReportSegmentPair_intron
+    def setup
+      @intron = TestDataForSim4Report.report2.hits[0].introns[0]
+    end
+  end #class TestSim4ReportSegmentPair2_intron
+
+
+  class TestSim4Report4 < TestSim4Report
+
+    def setup
+      @sim4 = TestDataForSim4Report.report4
+    end
+
+    def exec_test_seq1_len(sd)
+      assert_equal(284, sd.len)
+    end
+    private :exec_test_seq1_len
+
+    def test_seq1
+      sd = @sim4.seq1
+      assert_instance_of(Bio::Sim4::Report::SeqDesc, sd)
+      assert_equal('mrna4c', sd.entry_id)
+      assert_equal('mrna4c', sd.definition)
+      assert_equal('sample41-1c.fst', sd.filename)
+      exec_test_seq1_len(sd)
+    end
+
+    def test_query_def
+      assert_equal('mrna4c', @sim4.query_def)
+    end
+
+    def test_query_id
+      assert_equal('mrna4c', @sim4.query_id)
+    end
+
+    def test_query_len
+      assert_equal(284, @sim4.query_len)
+    end
+
+  end #class TestSim4Report4
+
+  class TestSim4ReportHit4 < TestSim4ReportHit
+
+    def setup
+      @hit = TestDataForSim4Report.report4.hits.first
+    end
+
+    def test_align
+      a = [
+           [ "TTTTAGCCGGCACGAGATTG AGCGTATGATCACGCGCGCGGCCTCCT CAGAGTGATGCATGATACAACTT AT ",
+             "||||||||||||||||||||-||||-||||||||||||||||||||||-|-|||| ||||||||||||||||- |-",
+             "TTTTAGCCGGCACGAGATTGCAGCG ATGATCACGCGCGCGGCCTCCTAC GAGTCATGCATGATACAACTTCTTG"],
+           [ "         ",
+             ">>>...>>>",
+             "GTT...GAT" ],
+           [ "ATATGTACTTAGCTGGCAACCGAGATTTACTTTCGAAGCACTGTGATGAACCCGCGGCCCTTTGAGCGCT",
+             "|||||||||||||-|||||||||||||||||||||||| |||||||||||||||||-|||||||||||||",
+             "ATATGTACTTAGC GGCAACCGAGATTTACTTTCGAAGGACTGTGATGAACCCGCG CCCTTTGAGCGCT" ],
+           [ "", "", "" ],
+           [ "TATATATGTACTTAGCGG ACACCGAGATTTACTTTCGAAGGACTGTGGATGAACCCGCGCCCTTTGAGCGCT",
+             "||||||||||||||||||-|-|||||||||||||||||||||||||||-||||||||||||||||||||||||",
+             "TATATATGTACTTAGCGGCA ACCGAGATTTACTTTCGAAGGACTGTG ATGAACCCGCGCCCTTTGAGCGCT" ]
+          ]
+      assert_equal(a, @hit.align)
+    end
+
+    def test_complement?
+      assert_equal(true, @hit.complement?)
+    end
+
+    def test_definition
+      assert_equal('genome4', @hit.definition)
+    end
+
+    def test_each
+      count = 0
+      assert_nothing_raised {
+        @hit.each do |x|
+          count += 1
+        end
+      }
+      assert_equal(3, count)
+      @hit.each do |x|
+        assert_instance_of(Bio::Sim4::Report::SegmentPair, x)
+      end
+    end
+
+    def exec_test_exons(meth)
+      assert_kind_of(Array, @hit.__send__(meth))
+      assert_equal(3, @hit.__send__(meth).size)
+      @hit.__send__(meth).each do |x|
+        assert_instance_of(Bio::Sim4::Report::SegmentPair, x)
+      end
+    end
+    private :exec_test_exons
+
+    def test_hit_id
+      assert_equal('genome4', @hit.hit_id)
+    end
+
+    def test_introns
+      assert_kind_of(Array, @hit.introns)
+      assert_equal(2, @hit.introns.size)
+      @hit.introns.each do |x|
+        assert_instance_of(Bio::Sim4::Report::SegmentPair, x)
+      end
+    end
+
+    def test_len
+      assert_equal(770, @hit.len)
+    end
+
+    def test_query_def
+      assert_equal('mrna4c', @hit.query_def)
+    end
+
+    def test_query_id
+      assert_equal('mrna4c', @hit.query_id)
+    end
+
+    def test_query_len
+      assert_equal(284, @hit.query_len)
+    end
+
+    def test_segmentpairs
+      assert_kind_of(Array, @hit.segmentpairs)
+      assert_equal(5, @hit.segmentpairs.size)
+      @hit.segmentpairs.each do |x|
+        assert_instance_of(Bio::Sim4::Report::SegmentPair, x)
+      end
+    end
+
+    def exec_test_seq1_len(sd)
+      assert_equal(284, sd.len)
+    end
+    private :exec_test_seq1_len
+
+    def test_seq1
+      sd = @hit.seq1
+      assert_instance_of(Bio::Sim4::Report::SeqDesc, sd)
+      assert_equal('mrna4c', sd.entry_id)
+      assert_equal('mrna4c', sd.definition)
+      assert_equal('sample41-1c.fst', sd.filename)
+      exec_test_seq1_len(sd)
+    end
+
+    def test_seq2
+      sd = @hit.seq2
+      assert_instance_of(Bio::Sim4::Report::SeqDesc, sd)
+      assert_equal('genome4', sd.entry_id)
+      assert_equal('genome4', sd.definition)
+      assert_equal(770, sd.len)
+      #assert_equal('sample40-2.fst', sd.filename)
+      assert_equal('sample40-2.fst (genome4)', sd.filename)
+    end
+
+    def test_target_def
+      assert_equal('genome4', @hit.target_def)
+    end
+
+    def test_target_id
+      assert_equal('genome4', @hit.target_id)
+    end
+
+    def test_target_len
+      assert_equal(770, @hit.target_len)
+    end
+  end #class TestSim4ReportHit4
+
+  class TestSim4ReportSegmentPair4_exon < TestSim4ReportSegmentPair_exon
+    def setup
+      @exon = TestDataForSim4Report.report4.hits[0].exons[1]
+    end
+
+    def test_align_len
+      assert_equal(70, @exon.align_len)
+    end
+
+    def test_direction
+      assert_equal("==", @exon.direction)
+    end
+
+    def test_hit_from
+      assert_equal(563, @exon.hit_from)
+    end
+
+    def test_hit_to
+      assert_equal(630, @exon.hit_to)
+    end
+
+    def test_hseq
+      hseq = "ATATGTACTTAGC GGCAACCGAGATTTACTTTCGAAGGACTGTGATGAACCCGCG CCCTTTGAGCGCT"
+      assert_equal(hseq, @exon.hseq)
+    end
+
+    def test_midline
+      midline = "|||||||||||||-|||||||||||||||||||||||| |||||||||||||||||-|||||||||||||"
+      assert_equal(midline, @exon.midline)
+    end
+
+    def test_percent_identity
+      #assert_equal(95, @exon.percent_identity)
+      assert_equal("95", @exon.percent_identity)
+    end
+
+    def test_qseq
+      qseq = "ATATGTACTTAGCTGGCAACCGAGATTTACTTTCGAAGCACTGTGATGAACCCGCGGCCCTTTGAGCGCT"
+      assert_equal(qseq, @exon.qseq)
+    end
+
+    def test_query_from
+      assert_equal(73, @exon.query_from)
+    end
+
+    def test_query_to
+      assert_equal(142, @exon.query_to)
+    end
+
+    def exec_test_seq1_from_to(seg)
+      assert_equal(73, seg.from)
+      assert_equal(142, seg.to)
+    end
+    private :exec_test_seq1_from_to
+
+    def test_seq1
+      assert_instance_of(Bio::Sim4::Report::Segment, @exon.seq1)
+      assert_equal("ATATGTACTTAGCTGGCAACCGAGATTTACTTTCGAAGCACTGTGATGAACCCGCGGCCCTTTGAGCGCT",
+                   @exon.seq1.seq)
+      exec_test_seq1_from_to(@exon.seq1)
+    end
+
+    def test_seq2
+      assert_instance_of(Bio::Sim4::Report::Segment, @exon.seq2)
+      assert_equal(563, @exon.seq2.from)
+      assert_equal(630, @exon.seq2.to)
+      assert_equal("ATATGTACTTAGC GGCAACCGAGATTTACTTTCGAAGGACTGTGATGAACCCGCG CCCTTTGAGCGCT",
+                   @exon.seq2.seq)
+    end
+  end #class TestSim4ReportSegmentPair4_exon
+
+
+  class TestSim4ReportSegmentPair4_intron < TestSim4ReportSegmentPair_intron
+    def setup
+      @intron = TestDataForSim4Report.report4.hits[0].introns[0]
+    end
+
+    def test_hit_from
+      assert_equal(425, @intron.hit_from)
+    end
+
+    def test_hit_to
+      assert_equal(562, @intron.hit_to)
+    end
+
+    def test_hseq
+      hseq = "GTT...GAT"
+      assert_equal(hseq, @intron.hseq)
+    end
+
+    def test_midline
+      midline = ">>>...>>>"
+      assert_equal(midline, @intron.midline)
+    end
+
+    def test_seq2
+      assert_instance_of(Bio::Sim4::Report::Segment, @intron.seq2)
+      assert_equal(425, @intron.seq2.from)
+      assert_equal(562, @intron.seq2.to)
+      assert_equal("GTT...GAT", @intron.seq2.seq)
+    end
+  end #class TestSim4ReportSegmentPair4_intron
+
+
+  class TestSim4ReportSegmentPair4_intron1 < Test::Unit::TestCase
+    def setup
+      @intron = TestDataForSim4Report.report4.hits[0].introns[1]
+    end
+
+    def test_align_len
+      assert_equal(0, @intron.align_len)
+    end
+
+    def test_direction
+      assert_equal(nil, @intron.direction)
+    end
+
+    def test_hit_from
+      assert_equal(631, @intron.hit_from)
+    end
+
+    def test_hit_to
+      assert_equal(699, @intron.hit_to)
+    end
+
+    def test_hseq
+      assert_equal("", @intron.hseq)
+    end
+
+    def test_midline
+      assert_equal("", @intron.midline)
+    end
+
+    def test_percent_identity
+      assert_equal(nil, @intron.percent_identity)
+    end
+
+    def test_qseq
+      assert_equal("", @intron.qseq)
+    end
+
+    def test_query_from
+      assert_equal(143, @intron.query_from)
+    end
+
+    def test_query_to
+      assert_equal(212, @intron.query_to)
+    end
+
+    def test_seq1
+      assert_instance_of(Bio::Sim4::Report::Segment, @intron.seq1)
+      assert_equal(143, @intron.seq1.from)
+      assert_equal(212, @intron.seq1.to)
+      assert_equal("", @intron.seq1.seq)
+    end
+
+    def test_seq2
+      assert_instance_of(Bio::Sim4::Report::Segment, @intron.seq2)
+      assert_equal(631, @intron.seq2.from)
+      assert_equal(699, @intron.seq2.to)
+      assert_equal("", @intron.seq2.seq)
+    end
+  end #class TestSim4ReportSegmentPair4_intron1
+
+
+  class TestSim4ReportSeqDesc < Test::Unit::TestCase
+    def setup
+      @str1 = 'seq1 = c_NC_000011.5_101050001-101075000.fst, 25000 bp'
+      @str2 = '>ref|NC_000011.5|NC_000011:c101075000-101050001 Homo sapiens chromosome 11, complete sequence'
+
+      @seqdesc = Bio::Sim4::Report::SeqDesc.parse(@str1, @str2)
+    end
+
+    def test_entry_id
+      assert_equal('ref|NC_000011.5|NC_000011:c101075000-101050001',
+                   @seqdesc.entry_id)
+    end
+
+    def test_definition
+      assert_equal("ref|NC_000011.5|NC_000011:c101075000-101050001 Homo sapiens chromosome 11, complete sequence",
+                   @seqdesc.definition)
+    end
+
+    def test_len
+      assert_equal(25000, @seqdesc.len)
+    end
+
+    def test_filename
+      assert_equal('c_NC_000011.5_101050001-101075000.fst', @seqdesc.filename)
+    end
+
+    def test_self_parse
+      assert_instance_of(Bio::Sim4::Report::SeqDesc,
+                         Bio::Sim4::Report::SeqDesc.parse(@str1, @str2))
+
+      assert_instance_of(Bio::Sim4::Report::SeqDesc,
+                         Bio::Sim4::Report::SeqDesc.parse(@str1))
+    end
+
+    def test_self_new
+      assert_instance_of(Bio::Sim4::Report::SeqDesc,
+                         Bio::Sim4::Report::SeqDesc.new('SEQID',
+                                                        'SEQDEF',
+                                                        123,
+                                                        'file.sim4'))
+    end
+  end #class TestSim4ReportSeqDesc
+
+
+  class TestSim4ReportSegment < Test::Unit::TestCase
+    def setup
+      @seq = "TCTACACATCACTAGCGTGGGTGGGCGGAAAGAGCAGCTCGCCACT CAAGCTAA".freeze
+      @segment = Bio::Sim4::Report::Segment.new("123", "176", @seq.dup)
+    end
+
+    def test_from
+      assert_equal(123, @segment.from)
+    end
+
+    def test_to
+      assert_equal(176, @segment.to)
+    end
+
+    def test_seq
+      assert_equal(@seq, @segment.seq)
+    end
+
+    def test_self_new
+      assert_instance_of(Bio::Sim4::Report::Segment,
+                         Bio::Sim4::Report::Segment.new(1,9))
+      assert_instance_of(Bio::Sim4::Report::Segment,
+                         Bio::Sim4::Report::Segment.new(2,4, "ATG"))
+    end
+  end #class TestSim4ReportSegment
+
+end #module Bio