#
# test/unit/bio/db/embl/test_embl.rb - Unit test for Bio::EMBL
#
# Copyright::  Copyright (C) 2005 Mitsuteru 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__), ['..'] * 4,
                            'bioruby_test_helper.rb')).cleanpath.to_s

# libraries needed for the tests
require 'test/unit'
require 'bio/db/embl/embl'

module Bio
  class TestEMBL < Test::Unit::TestCase
    def setup
      output = File.read(File.join(BioRubyTestDataPath, 'embl', 'AB090716.embl'))
      @obj = Bio::EMBL.new(output)
    end

    def test_id_line
      assert(@obj.id_line)
    end

    def test_id_line_iterator
      assert(@obj.id_line { |key, value| })
    end

    def test_id_line_entry_name
      assert_equal('AB090716', @obj.id_line('ENTRY_NAME'))
    end

    def test_id_line_data_class
      assert_equal('standard', @obj.id_line('DATA_CLASS'))
    end

    def test_id_line_molecule_type
      assert_equal('genomic DNA', @obj.id_line('MOLECULE_TYPE'))
    end

    def test_id_line_division
      assert_equal('VRT', @obj.id_line('DIVISION'))
    end

    def test_id_line_sequence_length
      assert_equal(166, @obj.id_line('SEQUENCE_LENGTH'))
    end

    def test_entry
      entry_id = 'AB090716'
      assert_equal(entry_id, @obj.entry)
      assert_equal(entry_id, @obj.entry_name)
      assert_equal(entry_id, @obj.entry_id)
    end

    def test_molecule
      molecule = 'genomic DNA'
      assert_equal(molecule, @obj.molecule)
      assert_equal(molecule, @obj.molecule_type)
    end

    def test_division
      assert_equal('VRT', @obj.division)
    end

    def test_sequence_length
      seqlen = 166
      assert_equal(seqlen, @obj.sequence_length)
      assert_equal(seqlen, @obj.seqlen)
    end

    # Bio::EMBLDB::COMMON#ac
    def test_ac
      ac = ['AB090716']
      assert_equal(ac, @obj.ac)
      assert_equal(ac, @obj.accessions)
    end

    # Bio::EMBLDB::COMMON#accession
    def test_accession
      assert_equal('AB090716', @obj.accession)
    end

    def test_sv
      assert_equal('AB090716.1', @obj.sv)
    end

    def test_version
      assert_equal(1, @obj.version)
    end

    def test_dt
      assert(@obj.dt)
    end

    def test_dt_iterator
      assert(@obj.dt { |key, value| })
    end

    def test_dt_created
      assert_equal('25-OCT-2002 (Rel. 73, Created)', @obj.dt('created'))
    end

    def test_dt_updated
      assert_equal('29-NOV-2002 (Rel. 73, Last updated, Version 2)', @obj.dt('updated'))
    end

    # Bio::EMBLDB::COMMON#de
    def test_de
      assert_equal(
        "Haplochromis sp. 'muzu, rukwa' LWS gene for long wavelength-sensitive opsin, partial cds, specimen_voucher:specimen No. HT-9361.", @obj.de
      )
    end

    # Bio::EMBLDB::COMMON#kw
    def test_kw
      assert_equal([], @obj.kw)
      assert_equal([], @obj.keywords)
    end

    def test_os
      assert_equal("Haplochromis sp. 'muzu, rukwa'", @obj.os[0]['os'])
      assert_nil(@obj.os[0]['name'])
    end

    # Bio::EMBLDB::COMMON#oc
    def test_oc
      assert_equal('Eukaryota', @obj.oc.first)
    end

    # Bio::EMBLDB::COMMON#og
    def test_og
      assert_equal([], @obj.og)
    end

    # Bio::EMBLDB::COMMON#ref
    def test_ref
      assert_equal(2, @obj.ref.size)
    end

    # Bio::EMBLDB::COMMON#references
    def test_references
      assert_equal(Array, @obj.references.class)
    end

    # Bio::EMBLDB::COMMON#dr
    def test_dr
      assert_equal({}, @obj.dr)
    end

    def test_fh
      assert_equal('Key Location/Qualifiers', @obj.fh)
    end

    def test_ft
      assert_equal(Array, @obj.ft.class)
    end

    def test_ft_iterator
      @obj.ft.each do |feature|
        assert_equal(Bio::Feature, feature.class)
      end
    end

    def test_ft_accessor
      assert_equal('CDS', @obj.ft[1].feature)
    end

    def test_each_cds
      @obj.each_cds do |x|
        assert_equal('CDS', x.feature)
      end
    end

    def test_each_gene
      @obj.each_gene do |x|
        assert_equal('gene', x.feature)
      end
    end

    def test_cc
      assert_equal('', @obj.cc)
    end

    #    def test_xx
    #    end

    def test_sq
      data = { 'a' => 29, 'c' => 42, 'ntlen' => 166, 'g' => 41, 't' => 54, 'other' => 0 }
      assert_equal(data, @obj.sq)
    end

    def test_sq_get
      assert_equal(29, @obj.sq('a'))
    end

    def test_seq
      seq = 'gttctggcctcatggactgaagacttcctgtggacctgatgtgttcagtggaagtgaagaccctggagtacagtcctacatgattgttctcatgattacttgctgtttcatccccctggctatcatcatcctgtgctaccttgctgtgtggatggccatccgtgct'
      assert_equal(seq, @obj.seq)
      assert_equal(seq, @obj.naseq)
      assert_equal(seq, @obj.ntseq)
    end
  end
end
