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# -*-Perl-*- Test Harness script for Bioperl
# $Id: TreeIO.t 14580 2008-03-01 17:01:30Z cjfields $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 24);
use_ok('Bio::TreeIO');
}
my $verbose = test_debug();
# try lintree parsing
my $treeio = Bio::TreeIO->new(-format => 'lintree',
-file => test_input_file('crab.njb'));
my ($tree, @leaves, $node);
while( $tree = $treeio->next_tree ) {
isa_ok($tree, 'Bio::Tree::TreeI');
my @nodes = $tree->get_nodes;
@leaves = $tree->get_leaf_nodes;
is(@leaves, 13);
#\maj is(@nodes, 25);
is(@nodes, 24);
($node) = $tree->find_node(-id => '18');
ok($node);
is($node->id, '18');
is($node->branch_length, '0.030579');
is($node->bootstrap, 998);
}
$treeio = Bio::TreeIO->new(-format => 'lintree',
-file => test_input_file('crab.nj'));
$tree = $treeio->next_tree;
isa_ok($tree, 'Bio::Tree::TreeI');
my @nodes = $tree->get_nodes;
@leaves = $tree->get_leaf_nodes;
is(@leaves, 13);
#/maj is(@nodes, 25);
is(@nodes, 24); #/maj
($node) = $tree->find_node('18');
is($node->id, '18');
is($node->branch_length, '0.028117');
($node) = $tree->find_node(-id => 'C-vittat');
is($node->id, 'C-vittat');
is($node->branch_length, '0.087619');
is($node->ancestor->id, '14');
$treeio = Bio::TreeIO->new(-format => 'lintree',
-file => test_input_file('crab.dat.cn'));
$tree = $treeio->next_tree;
isa_ok($tree, 'Bio::Tree::TreeI');
@nodes = $tree->get_nodes;
@leaves = $tree->get_leaf_nodes;
is(@leaves, 13, "Leaf nodes");
#/maj is(@nodes, 25, "All nodes");
is(@nodes, 24, "All nodes"); #/maj
($node) = $tree->find_node('18');
is($node->id, '18');
is($node->branch_length, '0.029044');
($node) = $tree->find_node(-id => 'C-vittat');
is($node->id, 'C-vittat');
is($node->branch_length, '0.097855');
is($node->ancestor->id, '14');
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