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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
##
my $error;
use strict;
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
$error = 0;
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
plan tests => 17;
}
use Bio::Tree::Node;
use Bio::Tree::AlleleNode;
ok(1);
my $node1 = new Bio::Tree::Node();
my $node2 = new Bio::Tree::Node();
ok($node1->is_Leaf() );
ok($node1->ancestor, undef);
my $pnode = new Bio::Tree::Node();
$pnode->add_Descendent($node1);
ok($node1->ancestor, $pnode);
$pnode->add_Descendent($node2);
ok($node2->ancestor, $pnode);
ok(! $pnode->is_Leaf);
my $phylo_node = new Bio::Tree::Node(-bootstrap => 0.25,
-id => 'ADH_BOV',
-desc => 'Taxon 1');
$node1->add_Descendent($phylo_node);
ok(! $node1->is_Leaf);
ok($phylo_node->ancestor, $node1);
ok($phylo_node->id, 'ADH_BOV');
ok($phylo_node->bootstrap, 0.25);
ok($phylo_node->description, 'Taxon 1');
my $allele_node = new Bio::Tree::AlleleNode();
$allele_node->add_Genotype(new Bio::PopGen::Genotype(-marker_name => 'm1',
-alleles=> [ 0 ]));
$allele_node->add_Genotype(new Bio::PopGen::Genotype(-marker_name => 'm3',
-alleles=> [ 1,1 ]));
$allele_node->add_Genotype(new Bio::PopGen::Genotype(-marker_name => 'm4',
-alleles=> [ 0,4 ]));
ok($allele_node);
my @mkrs = $allele_node->get_marker_names;
ok(@mkrs, 3);
my ($m3) = $allele_node->get_Genotypes(-marker => 'm3');
ok($m3->get_Alleles, 2);
my ($a1) = $allele_node->get_Genotypes(-marker => 'm1')->get_Alleles;
ok($a1, 0);
my ($a2,$a3) = $allele_node->get_Genotypes(-marker => 'm4')->get_Alleles;
ok($a2, 0);
ok($a3, 4);
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