#
# = 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 = %w[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
