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SENDU / bioperl-1.5.2_004-RCc / t / TaxonTree.t 

            

              
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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
##
# These modules are now deprecated, don't bother testing them.
## 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
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 => 1;
}
ok(1);
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 = new Bio::Taxonomy::Taxon;
         
        my $taxon = new Bio::Taxonomy::Taxon(-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=new Bio::Species;
        my $chimp=new Bio::Species;
        my $bonobo=new Bio::Species;
         
        $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=new Bio::Taxonomy(-ranks => \@ranks,
                                                                   -method => 'trust',
                                                                   -order => -1);
         
         
        ok my $tree1=new Bio::Taxonomy::Tree;
        my $tree2=new Bio::Taxonomy::Tree;
         
        $tree1->make_species_branch($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';
}