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#
# = test/unit/bio/test_map.rb - Unit test for Bio::Map
#
# Copyright:: Copyright (C) 2006
# Jan Aerts <jan.aerts@bbsrc.ac.uk>
# 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/map'
module Bio
class TestMapSimple < Test::Unit::TestCase
def setup
@marker1 = Bio::Map::Marker.new('marker1')
@marker2 = Bio::Map::Marker.new('marker2')
@map1 = Bio::Map::SimpleMap.new('map1', 'some_type', 500, 'some_unit')
end
def test_attributes
assert_equal("marker1", @marker1.name)
assert_equal("marker2", @marker2.name)
assert_equal([], @marker1.mappings_as_marker)
assert_equal([], @marker2.mappings_as_marker)
assert_equal("map1", @map1.name)
assert_equal("some_unit", @map1.units)
assert_equal("some_type", @map1.type)
assert_equal([], @map1.mappings_as_map)
end
end
class TestMapping < Test::Unit::TestCase
def setup
@marker1 = Bio::Map::Marker.new('marker1')
@marker2 = Bio::Map::Marker.new('marker2')
@marker3 = Bio::Map::Marker.new('marker3')
@map1 = Bio::Map::SimpleMap.new('map1', 'some_type', 'some_unit')
@map2 = Bio::Map::SimpleMap.new('map2', 'some_other_type', 'some_other_unit')
end
def test_add_mapping_as_map
@map1.add_mapping_as_map(@marker2, '5')
assert_equal(1, @map1.mappings_as_map.length)
assert_equal(1, @marker2.mappings_as_marker.length)
assert_equal(0, @marker1.mappings_as_marker.length)
assert_kind_of(Bio::Locations, @map1.mappings_as_map[0].location)
assert_kind_of(Bio::Locations, @marker2.mappings_as_marker[0].location)
end
def test_add_mapping_as_marker
@marker1.add_mapping_as_marker(@map1, '5')
assert_equal(1, @map1.mappings_as_map.length, 'Mapping as map')
assert_equal(1, @marker1.mappings_as_marker.length, 'Mapping as marker')
assert_kind_of(Bio::Locations, @map1.mappings_as_map[0].location)
assert_kind_of(Bio::Locations, @marker1.mappings_as_marker[0].location)
end
def test_mapped_to?
@marker1.add_mapping_as_marker(@map1, '5')
assert_equal(true, @marker1.mapped_to?(@map1))
assert_equal(false, @marker3.mapped_to?(@map1))
end
def test_contains_marker?
@marker1.add_mapping_as_marker(@map1, '5')
assert_equal(true, @map1.contains_marker?(@marker1))
assert_equal(false, @map1.contains_marker?(@marker3))
end
def test_mappings_as_map_each
@map1.add_mapping_as_map(@marker1, '5')
@marker2.add_mapping_as_marker(@map1, '7')
mappings = 0
@map1.mappings_as_map.each do |mapping|
mappings += 1
end
assert_equal(2, mappings)
end
def test_mappings_as_marker_each
@map1.add_mapping_as_map(@marker1, '5')
@marker1.add_mapping_as_marker(@map1, '7')
mappings = 0
@marker1.mappings_as_marker.each do |mapping|
mappings += 1
end
assert_equal(2, mappings)
end
def test_multiple_mappings_between_same_marker_and_map
@map1.add_mapping_as_map(@marker1, '5')
@map1.add_mapping_as_map(@marker1, '37')
@marker1.add_mapping_as_marker(@map1, '53')
assert_equal(3, @marker1.mappings_as_marker.length)
@marker1.add_mapping_as_marker(@map1, '53') # This mapping should _not_ be added, because it's already defined.
assert_equal(3, @marker1.mappings_as_marker.length)
@map1.add_mapping_as_map(@marker1, '53')
assert_equal(3, @marker1.mappings_as_marker.length)
end
def test_positions_on
@map1.add_mapping_as_map(@marker1, '5')
assert_equal(1, @marker1.mappings_as_marker.length)
assert_equal('5', @marker1.positions_on(@map1).collect{|p| p.first.from.to_s}.join(',')) # FIXME: Test is not correct (uses Location.first)
@map1.add_mapping_as_map(@marker1, '37')
assert_equal('5,37', @marker1.positions_on(@map1).collect{|p| p.first.from.to_s}.sort{|a,b| a.to_i <=> b.to_i}.join(',')) # FIXME: Test is not correct (uses Location.first)
end
def test_mappings_on
@map1.add_mapping_as_map(@marker1, '5')
@map1.add_mapping_as_map(@marker1, '37')
assert_equal('5,37', @marker1.mappings_on(@map1).sort{|a,b| a.location[0].from.to_i <=> b.location[0].from.to_i}.collect{|m| m.location[0].from}.join(',')) # FIXME: Test is not correct (uses Location.first)
end
def test_mapping_location_comparison
@map1.add_mapping_as_map(@marker1, '5')
@map1.add_mapping_as_map(@marker2, '5')
@map1.add_mapping_as_map(@marker3, '17')
mapping1 = @marker1.mappings_on(@map1)[0]
mapping2 = @marker2.mappings_on(@map1)[0]
mapping3 = @marker3.mappings_on(@map1)[0]
assert_equal(true, mapping1 == mapping2)
assert_equal(false, mapping1 < mapping2)
assert_equal(false, mapping1 > mapping2)
assert_equal(false, mapping1 == mapping3)
assert_equal(true, mapping1 < mapping3)
assert_equal(false, mapping1 > mapping3)
@map2.add_mapping_as_map(@marker1, '23')
mapping4 = @marker1.mappings_on(@map2)[0]
assert_raise(RuntimeError) { mapping2 < mapping4 }
end
def test_raise_error_kind_of
marker_without_class = 'marker1'
assert_raise(RuntimeError) { @map1.add_mapping_as_map(marker_without_class, '5') }
assert_raise(RuntimeError) { @map1.contains_marker?(marker_without_class) }
map_without_class = 'map1'
assert_raise(RuntimeError) { @marker1.add_mapping_as_marker(map_without_class, '5') }
assert_raise(RuntimeError) { @marker1.mapped_to?(map_without_class) }
assert_raise(RuntimeError) { @marker1.positions_on(map_without_class) }
assert_raise(RuntimeError) { @marker1.mappings_on(map_without_class) }
@map1.add_mapping_as_map(@marker1, '5')
mapping1 = @marker1.mappings_on(@map1)[0]
assert_raise(RuntimeError) { mapping1 > 'some_mapping' }
end
end
class CloneToActLikeMap
include Bio::Map::ActsLikeMap
def initialize
@mappings_as_map = Array.new
end
attr_accessor :mappings_as_map
end
class TestActsLikeMap < Test::Unit::TestCase
def setup
@clone = CloneToActLikeMap.new
end
def test_mixin
assert_instance_of(CloneToActLikeMap, @clone)
assert_respond_to(@clone, 'contains_marker?')
assert_respond_to(@clone, 'add_mapping_as_map')
assert_equal(0, @clone.mappings_as_map.length)
end
end
class CloneToActLikeMarker
include Bio::Map::ActsLikeMarker
def initialize
@mappings_as_marker = Array.new
end
attr_accessor :mappings_as_marker
end
class TestActsLikeMarker < Test::Unit::TestCase
def setup
@clone = CloneToActLikeMarker.new
end
def test_mixin
assert_instance_of(CloneToActLikeMarker, @clone)
assert_respond_to(@clone, 'mapped_to?')
assert_respond_to(@clone, 'add_mapping_as_marker')
end
end
class CloneToActLikeMapAndMarker
include Bio::Map::ActsLikeMap
include Bio::Map::ActsLikeMarker
def initialize
@mappings_as_map = Array.new
@mappings_as_marker = Array.new
end
attr_accessor :mappings_as_map, :mappings_as_marker
end
class TestActsLikeMapAndMarker < Test::Unit::TestCase
def setup
@clone_a = CloneToActLikeMapAndMarker.new
@clone_b = CloneToActLikeMapAndMarker.new
@clone_a.add_mapping_as_map(@clone_b, nil)
end
def test_mixin
assert_instance_of(CloneToActLikeMapAndMarker, @clone_a)
assert_respond_to(@clone_a, 'contains_marker?')
assert_respond_to(@clone_a, 'add_mapping_as_map')
assert_respond_to(@clone_a, 'mapped_to?')
assert_respond_to(@clone_a, 'add_mapping_as_marker')
assert_equal(1, @clone_a.mappings_as_map.length)
assert_equal(0, @clone_a.mappings_as_marker.length)
assert_equal(0, @clone_b.mappings_as_map.length)
assert_equal(1, @clone_b.mappings_as_marker.length)
end
end
end
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