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Contents
#
# test/unit/bio/appl/mafft/test_report.rb - Unit test for Bio::Alignment::MultiFastaFormat
#
# Copyright:: Copyright (C) 2007
# 2005 Naohisa Goto <ng@bioruby.org>
# License:: The Ruby License
#
# $Id:$
#
# loading helper routine for testing bioruby
require 'pathname'
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
'bioruby_test_helper.rb')).cleanpath.to_s
# libraries needed for the tests
require 'test/unit'
require 'bio/appl/mafft/report'
module Bio
class TestAlignmentMultiFastaFormat < Test::Unit::TestCase
def setup
@na = Bio::Alignment::MultiFastaFormat.new <<__END_OF_NASEQS__
>naseq1
TAGATTTCGAATTTCTAGnGAACCGAACCGkACAGCCTTACATyATTCAGACCAATGTGT
TACCAATTCGAGTATACAAGAACAGTGATAAGGTACCAAACAACGACTTCTTCCCGAACC
>naseq2
TAGATTTCGAATCTAGGGAATCCGATACGGACAGCCTTACATTATTCAGACCAATGTGTA
TACCAATTCGAGAATACAAGAACGTGATAAGGTACCCAAACAACGACTTCTTCCCGAACC
>naseq3
TAGATTTCGAATCTAGGGAATCCGATACCGGACAGCCTTACATTATTCAGACCAATGTGT
TACCAATTCGAGAATACAAGAACGTGATAAGGTACCCAAACAACGACTTCTTCCCGAACC
__END_OF_NASEQS__
@aa = Bio::Alignment::MultiFastaFormat.new <<__END_OF_AASEQS__
>aaseq1
MVHWTAEEKQLITGLWGKVNVAECGAEALARLLIVYPWTQRFFASFGNLSSPTAILGNPMVRAHGKKVLT
>aaseq2
MLTAEEKAAVTGFWGKVKVDEVGAEALGRLLVVYPWTQRFFEHFGDLSSADAVMNNAKVKAHGKKVLDSF
>aaseq3
MVHLTDAEKSAVSCLWAKVNPDEVGGEALGRLLVVYPWTQRYFDSFGDLSSASAIMGNPKVKAHGKKVIT
>aaseq4
MVHLTDAEKAAVNGLWGKVNPDDVGGEALGRLLVVYPWTQRYFDSFGDLSSASAIMGNPKVKAHGKKVIN
__END_OF_AASEQS__
end #def setup
def test_alignment
assert_equal(120, @na.alignment.alignment_length)
assert_equal(70, @aa.alignment.alignment_length)
end
def test_entries
assert_equal(3, @na.entries.size)
assert_equal(4, @aa.entries.size)
end
def test_determine_seq_method
@na.alignment
assert_equal(:naseq, @na.instance_eval { @seq_method })
@aa.alignment
assert_equal(:aaseq, @aa.instance_eval { @seq_method })
end
end #class TestAlignmentMultiFastaFormat
end #module Bio
Version data entries
15 entries across 15 versions & 1 rubygems