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# -*-Perl-*- Test Harness script for Bioperl
# $Id: TaxonTree.t 15112 2008-12-08 18:12:38Z sendu $
# These modules are now deprecated, don't bother testing them. --sendubala
## I am pretty sure this module is going the way of the dodo bird so
## I am not sure how much work to put into fixing the tests/module
## --jasonstajich
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 0);
}
if (0) {
use Bio::Taxonomy::Taxon;
ok(1);
ok my $taxonL = Bio::Taxonomy::Taxon->new;
ok $taxonL->description('this could be anything');
ok $taxonL->taxon('could this be called name?');
ok $taxonL->id('could this be called taxid?');
skip 1, $taxonL->branch_length('should accept only numerical values?');
ok $taxonL->branch_length(5);
ok $taxonL->id('could this be called taxid?');
ok $taxonL->rank('species');
ok $taxonL->rank, 'species';
# ok $taxonL->has_rank, 'species'; #why two methods that do mostly the same thing, but work differently?
skip 1, $taxonL->rank('foo is not a rank, class variable @RANK not initialised');
ok $taxonL->to_string, '"could this be called taxid?":5';
my $taxonR = Bio::Taxonomy::Taxon->new();
my $taxon = Bio::Taxonomy::Taxon->new(-id =>'ancient', -taxon => 'genus');
ok $taxon->id(), 'ancient';
ok $taxon->taxon(), 'genus';
ok $taxon->internal_id, 2;
ok $taxonL->internal_id, 0; # would not it be better to start numebering from 1?
ok $taxon->add_Descendent($taxonL);
$taxon->add_Descendent($taxonR);
ok scalar $taxon->each_Descendent, 2; # dies
ok $taxon->remove_Descendent($taxonR); # better to return number of Descendants removed
ok $taxon->remove_all_Descendents();
$taxon->add_Descendent($taxonL);
ok $taxonL->ancestor->id, 'ancient';
ok $taxonL->branch_length(5);
ok $taxonL->is_Leaf, 1;
ok $taxon->is_Leaf, 0;
ok $taxon->height, 6;
ok $taxonL->height, 5;
ok $taxon->invalidate_height, undef;
ok $taxonL->classify(1), 2;
skip(1,"skip classify weirdness");
# ok $taxonL->classify(0), 2, 'ancestor has rank, but implementation prevents showing anything more than one value';
skip(1,"skip classify weirdness");
#ok $taxonL->has_rank, 1, 'documentation claims this returns a boolean; and that it queries ancestors rank?, needs an agrument but does not test it';
skip(1,"skip classify weirdness");
#ok $taxonL->has_rank('species'), 1;
#ok $taxon->has_taxon(); # why docs and code talk about ancestor?
#ok $taxonL->has_taxon('genus'); returns undef or oan object, not boolean
ok $taxon->distance_to_root, 0;
ok $taxonL->distance_to_root, 1;
#ok $taxonL->recent_common_ancestor($taxon)->id, 'ancient';
#use Data::Dumper;
#print Dumper $taxonL->classify();
skip(1, 'Skip this weird function');
# ok $taxonL->has_rank('species'), 1;
#ok my $species = $taxonL->species;
##################################################################################################
# tests for Bio::Taxonomy::Tree;
# code from synopsis
use Bio::Species;
use Bio::Taxonomy::Tree;
use Bio::Taxonomy;
my $human=Bio::Species->new();
my $chimp=Bio::Species->new();
my $bonobo=Bio::Species->new();
$human->classification(qw( sapiens Homo Hominidae
Catarrhini Primates Eutheria
Mammalia Euteleostomi Vertebrata
Craniata Chordata
Metazoa Eukaryota ));
$chimp->classification(qw( troglodytes Pan Hominidae
Catarrhini Primates Eutheria
Mammalia Euteleostomi Vertebrata
Craniata Chordata
Metazoa Eukaryota ));
$bonobo->classification(qw( paniscus Pan Hominidae
Catarrhini Primates Eutheria
Mammalia Euteleostomi Vertebrata
Craniata Chordata
Metazoa Eukaryota ));
# ranks passed to $taxonomy match ranks of species
my @ranks = ('superkingdom','kingdom','phylum','subphylum',
'no rank 1','no rank 2','class','no rank 3','order',
'suborder','family','genus','species');
my $taxonomy=Bio::Taxonomy->new(-ranks => \@ranks,
-method => 'trust',
-order => -1);
ok my $tree1=Bio::Taxonomy::Tree->new();
my $tree2=Bio::Taxonomy::Tree->new();
$tree1->make_species_branch($human,$taxonomy);
$tree2->make_species_branch($chimp,$taxonomy);
my ($homo_sapiens) = $tree1->get_leaves;
ok ref $homo_sapiens, 'Bio::Taxonomy::Taxon';
ok $tree1->splice($tree2);
ok $tree1->add_species($bonobo,$taxonomy);
ok join (", ", map {$_->taxon} $tree1->get_leaves), 'Homo sapiens, Pan troglodytes, Pan paniscus';
ok $tree1->remove_branch($homo_sapiens);
ok join (", ", map {$_->taxon} $tree1->get_leaves), 'Pan troglodytes, Pan paniscus';
}
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