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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: Map.t,v 1.2 2002/02/11 19:04:21 jason 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 => 48;
}
END {
}
#
# Let's test first the map class : Bio::Map::SimpleMap
#
use Data::Dumper;
use Bio::Map::SimpleMap;
ok 1;
ok my $map = new Bio::Map::SimpleMap(-name => 'my');
ok $map->type('cyto');
ok $map->type, 'cyto';
ok $map->units, '';
ok $map->length, 0, "Length is ". $map->length;
ok $map->name, 'my';
ok $map->species('human'), 'human';
ok $map->species, 'human';
ok $map->unique_id, '1';
#
# Secondly, create Markers for the Map
#
use Bio::Map::Marker;
ok 1;
#
# Four ways of adding a position:
#
# 1. position gets a map object and a value as arguments
ok my $marker1 = new Bio::Map::Marker();
ok $marker1->name('gene1'), 'Unnamed marker' ;
ok $marker1->name(), 'gene1';
ok $marker1->position($map, 100);
ok $marker1->position->value, 100;
ok $marker1->map, $map;
#
# Now that we have a Marker, let's
# make sure the basic Position class works
#
use Bio::Map::Position;
ok 1;
ok my $pos = new Bio::Map::Position();
ok $pos->map($map);
ok $pos->map(), $map;
ok $pos->marker($marker1);
ok $pos->marker(), $marker1;
ok $pos->value('999');
ok $pos->value(), '999';
ok $pos->numeric, 999;
# ... and then continue testing the Marker
# 2. position is set in the constructor
ok my $marker2 = new Bio::Map::Marker(-name => 'gene2',
-position => [$map, 200]
);
ok ( $marker2->map, $map);
ok ($marker2->position->value, 200);
# 3. marker is first added into map,
# then marker knows the the position belongs to
ok my $marker3 = new Bio::Map::Marker(-name => 'gene3');
ok $map->add_element($marker3);
ok $marker3->map, $map;
ok $marker3->position(300);
ok $marker3->position->value, 300;
ok my $position = $marker3->position($map);
# 4. A Position is explicitely created
ok my $cpos = new Bio::Map::Position(-map => $map,
-value => 500);
ok $marker3->position($cpos);
my $cpos2 = $marker3->position($cpos);
ok $cpos2 eq $cpos;
ok $marker3->position->value, 500;
#
# Next, what do markers know about Maps?
#
ok $marker3->known_maps, qw ( 1 );
ok $marker3->in_map(1);
ok ! $marker3->in_map(2);
#
# Lastly, let's test the comparison methods
#
ok $marker1->equals($marker1);
ok ! $marker1->equals($marker3);
ok $marker1->less_than($marker3);
ok ! $marker1->greater_than($marker3);
ok ! $marker3->less_than($marker1);
ok $marker3->greater_than($marker1);
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