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#
# test/unit/bio/sequence/test_compat.rb - Unit test for Bio::Sequencce::Compat
#
# Copyright:: Copyright (C) 2006 Mitsuteru C. Nakao <n@bioruby.org>
# License:: The Ruby License
#
# $Id:$
#
# loading helper routine for testing bioruby
require 'pathname'
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
'bioruby_test_helper.rb')).cleanpath.to_s
# libraries needed for the tests
require 'test/unit'
require 'bio/sequence'
require 'bio/sequence/compat'
module Bio; module TestSequenceCompat
class TSequence < String
include Bio::Sequence::Common
end
class TestSequenceCompat < Test::Unit::TestCase
def setup
@obj = TSequence.new('atgcatgcatgcatgcaaaa')
end
def test_to_s
str = 'atgcatgcatgcatgcaaaa'
assert_equal(str, @obj.to_s)
end
end
class TestSequenceCommonCompat < Test::Unit::TestCase
# Test Sequence#to_fasta
def test_to_fasta
sequence = TSequence.new("agtc" * 10)
header = "the header"
str = ">the header\n" + ("agtc" * 5) + "\n" + ("agtc" * 5) + "\n"
assert_equal(str, sequence.to_fasta(header, 20))
end
end
require 'bio/sequence/na'
class TestSequenceNACompat < Test::Unit::TestCase
def test_na_self_randomize
composition = Bio::Sequence::NA.new("acgtacgt").composition
assert(Bio::Sequence::NA.randomize(composition))
end
end
require 'bio/sequence/aa'
class TestSequenceNACompat < Test::Unit::TestCase
def test_aa_self_randomize
composition = Bio::Sequence::AA.new("WWDTGAK").composition
assert(Bio::Sequence::AA.randomize(composition))
end
end
end; end #module Bio; module TestSequenceCompat
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