test/unit/bio/appl/blast/test_report.rb in bio-1.4.3.0001 vs test/unit/bio/appl/blast/test_report.rb in bio-1.5.0
- old
+ new
@@ -60,11 +60,11 @@
Bio::Blast::Report.new(text)
end
end
end #module TestBlastReportHelper
- class TestBlastReport < Test::Unit::TestCase
+ module TemplateTestBlastReport
include TestBlastReportHelper
def setup
@report = create_report_object
end
@@ -88,13 +88,11 @@
def test_version
assert_equal('blastp 2.2.10 [Oct-19-2004]', @report.version)
end
def test_reference
- xml_quoted_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."
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('b0002.faa', @report.db)
@@ -201,13 +199,14 @@
end
def test_message
assert_equal(nil, @report.message)
end
- end
-
- class TestBlastReportIteration < Test::Unit::TestCase
+ end #module TemplateTestBlastReport
+
+
+ module TemplateTestBlastReportIteration
include TestBlastReportHelper
def setup
report = create_report_object
@itr = report.iterations.first
@@ -229,13 +228,14 @@
end
def test_message
assert_equal(nil, @itr.message)
end
- end
+ end #module TemplateTestBlastReportIteration
- class TestBlastReportHit < Test::Unit::TestCase
+
+ module TemplateTestBlastReportHit
include TestBlastReportHelper
def setup
report = create_report_object
@hit = report.hits.first
@@ -341,13 +341,14 @@
end
def test_Hit_lap_at
assert_equal([1, 820, 1, 820], @hit.lap_at)
end
- end
+ end #module TemplateTestBlastReportHit
- class TestBlastReportHsp < Test::Unit::TestCase
+
+ module TemplateTestBlastReportHsp
include TestBlastReportHelper
def setup
report = create_report_object
@hsp = report.hits.first.hsps.first
@@ -442,41 +443,67 @@
def test_Hsp_mismatch_count
assert_nothing_raised { @hsp.mismatch_count }
end
- end
+ end #module TestBlastReportHsp
- class TestBlastReportREXML < TestBlastReport
+ class TestBlastReport < Test::Unit::TestCase
+ include TemplateTestBlastReport
end
- class TestBlastReportIterationREXML < TestBlastReportIteration
+ class TestBlastReportIteration < Test::Unit::TestCase
+ include TemplateTestBlastReportIteration
end
- class TestBlastReportHitREXML < TestBlastReportHit
+ class TestBlastReportHit < Test::Unit::TestCase
+ include TemplateTestBlastReportHit
end
- class TestBlastReportHspREXML < TestBlastReportHsp
+ class TestBlastReportHsp < Test::Unit::TestCase
+ include TemplateTestBlastReportHsp
end
+ class TestBlastReportREXML < Test::Unit::TestCase
+ include TemplateTestBlastReport
+ end
+
+ class TestBlastReportIterationREXML < Test::Unit::TestCase
+ include TemplateTestBlastReportIteration
+ end
+
+ class TestBlastReportHitREXML < Test::Unit::TestCase
+ include TemplateTestBlastReportHit
+ end
+
+ class TestBlastReportHspREXML < Test::Unit::TestCase
+ include TemplateTestBlastReportHsp
+ end
+
if defined? XMLParser then
- class TestBlastReportXMLParser < TestBlastReport
+ class TestBlastReportXMLParser < Test::Unit::TestCase
+ include TemplateTestBlastReport
end
- class TestBlastReportIterationXMLParser < TestBlastReportIteration
+ class TestBlastReportIterationXMLParser < Test::Unit::TestCase
+ include TemplateTestBlastReportIteration
end
- class TestBlastReportHitXMLParser < TestBlastReportHit
+ class TestBlastReportHitXMLParser < Test::Unit::TestCase
+ include TemplateTestBlastReportHit
end
- class TestBlastReportHspXMLParser < TestBlastReportHsp
+ class TestBlastReportHspXMLParser < Test::Unit::TestCase
+ include TemplateTestBlastReportHsp
end
end #if defined? XMLParser
- class TestBlastReportDefault < TestBlastReport
+ class TestBlastReportDefault < Test::Unit::TestCase
+ include TemplateTestBlastReport
+
undef test_entrez_query
undef test_filter
undef test_hsp_len
undef test_inclusion
undef test_parameters
@@ -517,17 +544,20 @@
end
def test_gapped_entropy
assert_equal(0.140, @report.gapped_entropy)
end
- end
+ end #class TestBlastReportDefault
- class TestBlastReportIterationDefault < TestBlastReportIteration
+ class TestBlastReportIterationDefault < Test::Unit::TestCase
+ include TemplateTestBlastReportIteration
undef test_statistics
end
- class TestBlastReportHitDefault < TestBlastReportHit
+ class TestBlastReportHitDefault < Test::Unit::TestCase
+ include TemplateTestBlastReportHit
+
undef test_Hit_accession
undef test_Hit_hit_id
undef test_Hit_num
undef test_Hit_query_def
undef test_Hit_query_id
@@ -558,13 +588,15 @@
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
+ end #class TestBlastReportHitDefault
- class TestBlastReportHspDefault < TestBlastReportHsp
+ class TestBlastReportHspDefault < Test::Unit::TestCase
+ include TemplateTestBlastReportHsp
+
undef test_Hsp_density
undef test_Hsp_mismatch_count
undef test_Hsp_num
undef test_Hsp_pattern_from
undef test_Hsp_pattern_to
@@ -610,12 +642,13 @@
def test_Hsp_query_frame
# differs from XML because not available in the default BLASTP format
assert_equal(nil, @hsp.query_frame)
end
- end
+ end #class TestBlastReportHspDefault
+
module TestBlastReportTabularHelper
def def_test_assert_nil(test_method)
str = test_method.to_s
name = str.sub(/test(\_(Hit|Hsp))?\_/, '')
method = name.intern
@@ -632,14 +665,15 @@
define_method(test_method) do
assert_nil(instance_variable_get(instance).__send__(method))
end
end
- end #module
+ end #module TestBlastReportTabularHelper
- class TestBlastReportTabular < TestBlastReport
+ class TestBlastReportTabular < Test::Unit::TestCase
extend TestBlastReportTabularHelper
+ include TemplateTestBlastReport
def_test_assert_nil :test_db
def_test_assert_nil :test_db_len
def_test_assert_nil :test_db_num
def_test_assert_nil :test_eff_space
@@ -676,20 +710,22 @@
def test_statistics
assert_equal({}, @report.statistics)
end
end #class TestBlastReportTabular
- class TestBlastReportIterationTabular < TestBlastReportIteration
+ class TestBlastReportIterationTabular < Test::Unit::TestCase
+ include TemplateTestBlastReportIteration
# No statistics information available in the "-m 8" format
def test_statistics
assert_equal({}, @itr.statistics)
end
end #class TestBlastReportIterationTabular
- class TestBlastReportHitTabular < TestBlastReportHit
+ class TestBlastReportHitTabular < Test::Unit::TestCase
extend TestBlastReportTabularHelper
+ include TemplateTestBlastReportHit
def_test_assert_nil :test_Hit_hit_id
def_test_assert_nil :test_Hit_identity
def_test_assert_nil :test_Hit_len
def_test_assert_nil :test_Hit_midline
@@ -712,12 +748,13 @@
# differs from XML because of the limited data
assert_equal("eco:b0002", @hit.query_id)
end
end #class TestBlastReportHitTabular
- class TestBlastReportHspTabular < TestBlastReportHsp
+ class TestBlastReportHspTabular < Test::Unit::TestCase
extend TestBlastReportTabularHelper
+ include TemplateTestBlastReportHsp
def_test_assert_nil :test_Hsp_density
def_test_assert_nil :test_Hsp_hit_frame
def_test_assert_nil :test_Hsp_hseq
def_test_assert_nil :test_Hsp_identity
@@ -736,11 +773,11 @@
########################################################################
# Tests for new BLAST XML format (blastall 2.2.14 or later)
# with the result of multiple query sequences
########################################################################
- class TestBlastReportMulti < Test::Unit::TestCase
+ module TemplateTestBlastReportMulti
include TestBlastReportHelper
def setup
@report = create_report_object('blastp-multi')
@overall = [ @report ] + @report.reports
@@ -953,13 +990,13 @@
def test_message
@overall.each do |r|
assert_equal(nil, r.message)
end
end
- end
-
- class TestBlastReportIterationMulti < Test::Unit::TestCase
+ end #module TemplateTestBlastReportMulti
+
+ module TemplateTestBlastReportIterationMulti
include TestBlastReportHelper
def setup
report = create_report_object('blastp-multi')
@itr = report.reports[4].iterations[0]
@@ -1003,13 +1040,13 @@
end
def test_message
assert_equal(nil, @itr.message)
end
- end
+ end #module TemplateTestBlastReportIterationMulti
- class TestBlastReportHitMulti < Test::Unit::TestCase
+ module TemplateTestBlastReportHitMulti
include TestBlastReportHelper
def setup
report = create_report_object('blastp-multi')
@hit = report.reports[4].iterations[0].hits[1]
@@ -1117,13 +1154,13 @@
end
def test_Hit_lap_at
assert_equal([190, 311, 569, 668], @hit.lap_at)
end
- end
+ end #module TemplateTestBlastReportHitMulti
- class TestBlastReportHspMulti < Test::Unit::TestCase
+ module TemplateTestBlastReportHspMulti
include TestBlastReportHelper
def setup
report = create_report_object('blastp-multi')
@hsp = report.reports[4].iterations[0].hits[1].hsps[0]
@@ -1218,37 +1255,62 @@
def test_Hsp_mismatch_count
assert_nothing_raised { @hsp.mismatch_count }
end
- end
+ end #module TemplateTestBlastReportHspMulti
+
+ class TestBlastReportMulti < Test::Unit::TestCase
+ include TemplateTestBlastReportMulti
+ end
+
+ class TestBlastReportIterationMulti < Test::Unit::TestCase
+ include TemplateTestBlastReportIterationMulti
+ end
+
+ class TestBlastReportHitMulti < Test::Unit::TestCase
+ include TemplateTestBlastReportHitMulti
+ end
+
+ class TestBlastReportHspMulti < Test::Unit::TestCase
+ include TemplateTestBlastReportHspMulti
+ end
+
# Tests for REXML version
- class TestBlastReportMultiREXML < TestBlastReportMulti
+ class TestBlastReportMultiREXML < Test::Unit::TestCase
+ include TemplateTestBlastReportMulti
end
- class TestBlastReportIterationMultiREXML < TestBlastReportIterationMulti
+ class TestBlastReportIterationMultiREXML < Test::Unit::TestCase
+ include TemplateTestBlastReportIterationMulti
end
- class TestBlastReportHitMultiREXML < TestBlastReportHitMulti
+ class TestBlastReportHitMultiREXML < Test::Unit::TestCase
+ include TemplateTestBlastReportHitMulti
end
- class TestBlastReportHspMultiREXML < TestBlastReportHspMulti
+ class TestBlastReportHspMultiREXML < Test::Unit::TestCase
+ include TemplateTestBlastReportHspMulti
end
# Tests for XMLParser version
if defined? XMLParser then
- class TestBlastReportMultiXMLParser < TestBlastReportMulti
+ class TestBlastReportMultiXMLParser < Test::Unit::TestCase
+ include TemplateTestBlastReportMulti
end
- class TestBlastReportIterationMultiXMLParser < TestBlastReportIterationMulti
+ class TestBlastReportIterationMultiXMLParser < Test::Unit::TestCase
+ include TemplateTestBlastReportIterationMulti
end
- class TestBlastReportHitMultiXMLParser < TestBlastReportHitMulti
+ class TestBlastReportHitMultiXMLParser < Test::Unit::TestCase
+ include TemplateTestBlastReportHitMulti
end
- class TestBlastReportHspMultiXMLParser < TestBlastReportHspMulti
+ class TestBlastReportHspMultiXMLParser < Test::Unit::TestCase
+ include TemplateTestBlastReportHspMulti
end
end #if defined? XMLParser
end # module Bio