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#
# = test/unit/bio/sequence/test_aa.rb - Unit test for Bio::Sequencce::AA
#
# 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/aa'
module Bio
class TestSequenceAANew < Test::Unit::TestCase
def test_new
str = "RRLEHTFVFL RNFSLMLLRY"
assert(Bio::Sequence::AA.new(str))
end
def test_new_t
str = "RRLEHTFVFLRNFSLMLLRY"
str_t = "RRLEHTFVFL\tRNFSLMLLRY"
assert_equal(str, Bio::Sequence::AA.new(str_t))
end
def test_new_n
str = "RRLEHTFVFLRNFSLMLLRY"
str_n = "RRLEHTFVFL\nRNFSLMLLRY"
assert_equal(str, Bio::Sequence::AA.new(str_n))
end
def test_new_r
str = "RRLEHTFVFLRNFSLMLLRY"
str_r = "RRLEHTFVFL\n\rRNFSLMLLRY"
assert_equal(str, Bio::Sequence::AA.new(str_r))
end
end
class TestSequenceAA < Test::Unit::TestCase
def setup
str = "RRLEHTFVFLRNFSLMLLRY"
@obj = Bio::Sequence::AA.new(str)
end
def test_to_s
str = "RRLEHTFVFLRNFSLMLLRY"
assert_equal(str, @obj.to_s)
end
def test_molecular_weight
assert_in_delta(2612.105, @obj.molecular_weight, 1e-4)
end
def test_to_re
re = /RRLEHTFVFLRNFSLMLLRY/
assert_equal(re, @obj.to_re)
@obj[1, 1] = 'B'
re = /R[DNB]LEHTFVFLRNFSLMLLRY/
assert_equal(re, @obj.to_re)
end
def test_codes
ary = ["Arg", "Arg", "Leu", "Glu", "His", "Thr", "Phe", "Val",
"Phe", "Leu", "Arg", "Asn", "Phe", "Ser", "Leu", "Met",
"Leu", "Leu", "Arg", "Tyr"]
assert_equal(ary, @obj.codes)
end
def test_names
ary = ["arginine", "arginine", "leucine", "glutamic acid",
"histidine", "threonine", "phenylalanine", "valine",
"phenylalanine", "leucine", "arginine", "asparagine",
"phenylalanine", "serine", "leucine", "methionine",
"leucine", "leucine", "arginine", "tyrosine"]
assert_equal(ary, @obj.names)
end
end
require 'bio/sequence/aa'
class TestSequenceAACompat < Test::Unit::TestCase
def test_aa_self_randomize
composition = Bio::Sequence::AA.new("WWDTGAK").composition
assert(Bio::Sequence::AA.randomize(composition))
end
end
end
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