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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: LinkageMap.t,v 1.1 2002/02/11 09:31:34 heikki Exp $
#
use strict;
BEGIN {
use vars qw($DEBUG);
$DEBUG = $ENV{'BIOPERLDEBUG'};
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
plan tests => 16;
}
END {
}
require 'dumpvar.pl';
use Bio::Map::LinkagePosition;
use Bio::Map::Microsatellite;
use Bio::Map::LinkageMap;
ok 1 ;
my $verbose = 0;
ok my $map = new Bio::Map::LinkageMap('-verbose' => $verbose,
'-name' => 'Leviathon',
'-type' => 'Genetic',
'-units' => 'cM',
'-species' => "Brassica");
ok ref($map), 'Bio::Map::LinkageMap';
ok $map->name, 'Leviathon';
ok $map->type, 'Genetic';
ok $map->units, 'cM';
ok $map->species, 'Brassica';
ok $map->unique_id, '1';
ok my $position = new Bio::Map::LinkagePosition('-order' => 2,
'-map' => $map,
'-value' => 22.3
);
ok $position->order, 2;
ok $position->map, $map,
ok $position->value, 22.3;
ok my $o_usat = new Bio::Map::Microsatellite('-name' => "Chad marker",
'-position' => $position);
ok $o_usat->name, 'Chad marker';
ok $o_usat->position, $position ;
ok $map->add_element($o_usat);
#use Data::Dumper; print Dumper($map);
#----------------------------
#ok my $position2 = new Bio::Map::LinkagePosition(-order => qw(3 4 5),
# );
# print("position2 looks like this:\n");
# dumpValue($position2);
#ok(($position2->each_position_value('fakemap'))[0] == 0);
#ok $position2->order, 3;
#-------------
#ok($position->order, 2);
#ok(($position->each_position_value($map))[0], 22.3);
# what should be printed if this was ok?
# ok(1);
#ok my $o_usat = new Bio::Map::Microsatellite('-name' => "Chad marker",
# '-position' => $position);
#
#ok $o_usat->name, 'Chad marker';
#ok $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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