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Bio/Species.pm  view on Meta::CPAN

sub validate_species_name {
    my( $self, $string ) = @_;

    return 1 if $string eq "sp.";
    return 1 if $string =~ /strain/;
    return 1 if $string =~ /^[a-z][\w\s-]+$/i;
    $self->throw("Invalid species name '$string'");
}

sub validate_name {
    return 1;
}

=head2 organelle

 Title   : organelle
 Usage   : $self->organelle( $organelle );
           $organelle = $self->organelle();
 Function: Get or set the organelle name
 Example : $self->organelle('Chloroplast')
 Returns : The organelle name in a string
 Args    : String, which is the organelle name
 Note    : TODO: We currently do not know where the organelle definition will
           eventually go.  This is stored in the source seqfeature, though,
           so the information isn't lost.

=cut

sub organelle {
    my($self) = shift;
    return $self->{'_organelle'} = shift if @_;
    return $self->{'_organelle'};
}

=head2 Delegation

The following methods delegate to the internal Bio::Taxon instance. This is
mainly to allow code continue using older methods, with the mind to migrate to
using Bio::Taxon and related methods when this class is deprecated.

=cut 

sub node_name {shift->taxon->node_name(@_)}
sub scientific_name {shift->taxon->node_name(@_)}

sub id {shift->taxon->id(@_)}
sub object_id {shift->taxon->id(@_)}
sub ncbi_taxid {shift->taxon->ncbi_taxid(@_)}
sub rank {shift->taxon->rank(@_)}
sub division {shift->taxon->division(@_)}

sub common_names {shift->taxon->common_names(@_)}
sub common_name {shift->taxon->common_names(@_)}

sub genetic_code {shift->taxon->genetic_code(@_)}
sub mitochondrial_genetic_code {shift->taxon->mitochondrial_genetic_code(@_)}

sub create_date { shift->taxon->create_date(@_)}
sub pub_date { shift->taxon->pub_date(@_)}
sub update_date { shift->taxon->update_date(@_)}

sub db_handle { shift->taxon->db_handle(@_)}

sub parent_id { shift->taxon->parent_id(@_)}
sub parent_taxon_id { shift->taxon->parent_id(@_)}

sub version { shift->taxon->version(@_)}
sub authority { shift->taxon->authority(@_)}
sub namespace { shift->taxon->namespace(@_)}

sub ancestor { shift->taxon->ancestor(@_)}
sub get_Parent_Node { shift->taxon->get_Parent_Node(@_)}
sub each_Descendent { shift->taxon->each_Descendent(@_)}
sub get_Children_Nodes { shift->taxon->get_Children_Nodes(@_)}
sub remove_Descendant { shift->taxon->remove_Descendant(@_)}

sub name { shift->taxon->name(@_)}

=head2 taxon

 Title    : taxon
 Usage    : $obj->taxon
 Function : retrieve the internal Bio::Taxon instance
 Returns  : A Bio::Taxon. If one is not previously set,
            an instance is created lazily
 Args     : Bio::Taxon (optional)
 
=cut

sub taxon {
    my ($self, $taxon) = @_;
    if (!$self->{taxon} || $taxon) {
        $taxon ||= Bio::Taxon->new();
        $self->{taxon} = $taxon;
    }
    $self->{taxon};
}

=head2 tree

 Title    : tree
 Usage    : $obj->tree
 Function : Returns a Bio::Tree::Tree object
 Returns  : A Bio::Tree::Tree. If one is not previously set,
            an instance is created lazily
 Args     : Bio::Tree::Tree (optional)
 
=cut

sub tree {
    my ($self, $tree) = @_;
    if (!$self->{tree} || $tree) {
        $tree ||= Bio::Tree::Tree->new();
        delete $tree->{_root_cleanup_methods};
        $self->{tree} = $tree;
    }
    $self->{tree};
}

sub DESTROY {