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#
# test/unit/bio/test_feature.rb - Unit test for Features/Feature classes
#
# 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__), ['..'] * 2,
'bioruby_test_helper.rb')).cleanpath.to_s
# libraries needed for the tests
require 'test/unit'
require 'bio/feature'
require 'bio/compat/features'
module Bio
class TestQualifier < Test::Unit::TestCase
def setup
qualifier = 'gene'
value = 'CDS'
@obj = Bio::Feature::Qualifier.new(qualifier, value)
end
def test_qualifier
assert_equal('gene', @obj.qualifier)
end
def test_value
assert_equal('CDS', @obj.value)
end
end
class TestFeature < Test::Unit::TestCase
def setup
@qualifier = Bio::Feature::Qualifier.new('organism', 'Arabidopsis thaliana')
feature = "source"
position = '1..615'
qualifiers = [@qualifier]
@obj = Bio::Feature.new(feature, position, qualifiers)
end
def test_new
assert(Bio::Feature.new)
end
def test_feature
assert_equal("source", @obj.feature)
end
def test_position
assert_equal('1..615', @obj.position)
end
def test_qualifiers
assert_equal([@qualifier], @obj.qualifiers)
end
def test_locations
assert_equal(1, @obj.locations.first.from)
assert_equal(615, @obj.locations.first.to)
end
def test_append_nil
assert(@obj.append(nil))
assert_equal(1, @obj.qualifiers.size)
end
def test_append
qualifier = Bio::Feature::Qualifier.new('db_xref', 'taxon:3702')
assert(@obj.append(qualifier))
assert_equal('db_xref', @obj.qualifiers.last.qualifier)
end
def test_each
@obj.each do |qua|
assert_equal('Arabidopsis thaliana', qua.value)
end
end
def test_assoc
@obj.append(Bio::Feature::Qualifier.new("organism", "Arabidopsis thaliana"))
assert_equal({"organism" => "Arabidopsis thaliana"}, @obj.assoc)
end
end
class TestFeatures < Test::Unit::TestCase
class NullStderr
def initialize
@log = []
end
def write(*arg)
#p arg
@log.push([ :write, *arg ])
nil
end
def method_missing(*arg)
#p arg
@log.push arg
nil
end
end #class NullStderr
def setup
# To suppress warning messages, $stderr is replaced by dummy object.
@stderr_orig = $stderr
$stderr = NullStderr.new
@obj = Bio::Features.new([Bio::Feature.new('gene', '1..615', [])])
end
def teardown
# bring back $stderr
$stderr = @stderr_orig
end
def test_features
assert_equal(1, @obj.features.size)
end
def test_append
assert(@obj.append(Bio::Feature.new('gene', '1..615', [])))
assert_equal(2, @obj.features.size)
end
def test_each
@obj.each do |feature|
assert_equal('gene', feature.feature)
end
end
def test_arg # def [](*arg)
assert_equal('gene', @obj[0].feature)
end
end
end
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