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# -*-Perl-*- Test Harness script for Bioperl
# $Id: Linkage.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 18);
use_ok('Bio::Map::LinkagePosition');
use_ok('Bio::Map::Microsatellite');
use_ok('Bio::Map::LinkageMap');
}
#require_ok('dumpvar.pl');
my $verbose = test_debug();
ok my $map = Bio::Map::LinkageMap->new('-verbose' => $verbose,
'-name' => 'Leviathon',
'-type' => 'Genetic',
'-units' => 'cM',
'-species' => "Brassica");
is ref($map), 'Bio::Map::LinkageMap';
is $map->name, 'Leviathon';
is $map->type, 'Genetic';
is $map->units, 'cM';
is $map->species, 'Brassica';
is $map->unique_id, '1';
ok my $position = Bio::Map::LinkagePosition->new('-order' => 2,
'-map' => $map,
'-value' => 22.3
);
is $position->order, 2;
ok my $map2 = $position->map;
is $position->value, 22.3;
ok my $o_usat = Bio::Map::Microsatellite->new('-name' => "Chad marker",
'-position' => $position);
is $o_usat->name, 'Chad marker';
is $o_usat->position, $position ;
ok $map->add_element($o_usat);
#use Data::Dumper; print Dumper($map);
#----------------------------
#ok my $position2 = Bio::Map::LinkagePosition->new(-order => qw(3 4 5),
# );
# print("position2 looks like this:\n");
# dumpValue($position2);
#is(($position2->each_position_value('fakemap'))[0], 0);
#is $position2->order, 3;
#-------------
#is($position->order, 2);
#is(($position->each_position_value($map))[0], 22.3);
# what should be printed if this was ok?
# ok(1);
#ok my $o_usat = Bio::Map::Microsatellite->new('-name' => "Chad marker",
# '-position' => $position);
#
#is $o_usat->name, 'Chad marker';
#is $o_usat->position, $position ;
#ok $map->add_element($o_usat);
# what should be printed if this is ok?
#dumpValue($map);
# add more tests
# see also t/microsatellite.t and t/linkageposition.t
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