view release on metacpan or  search on metacpan

lib/Bio/Phylo/Forest.pm  view on Meta::CPAN

    sub insert {
        my $self = shift;
        if ( $self->can_contain(@_) ) {
            my $seen_default = 0;
            for my $tree ( reverse @_ ) {
                if ( $tree->is_default ) {
                    if ( not $seen_default ) {
                        $seen_default++;
                    }
                    else {
                        $tree->set_not_default;
                    }
                }
            }
            if ($seen_default) {
                if ( my $tree = $self->get_default_tree ) {
                    $tree->set_not_default;
                }
            }
            $self->SUPER::insert(@_);
        }
        else {
            throw 'ObjectMismatch' => "Failed insertion: @_ [in $self]";
        }
    }

=item get_default_tree()

lib/Bio/Phylo/Forest/Tree.pm  view on Meta::CPAN

 Comments: This is a flag to indicate that the invocant
           is the default tree in a forest, i.e. to
           capture the '*' token in nexus files.

=cut

    sub set_as_default {
        my $self = shift;
        if ( my $forest = $self->_get_container ) {
            if ( my $tree = $forest->get_default_tree ) {
                $tree->set_not_default;
            }
        }
        $default{ $self->get_id } = 1;
        return $self;
    }

=item set_not_default()

Sets tree to NOT be the default tree in a forest

 Type    : Mutator
 Title   : set_not_default
 Usage   : $tree->set_not_default;
 Function: Sets tree to not be default tree in forest
 Returns : $tree
 Args    : NONE
 Comments: This is a flag to indicate that the invocant
           is the default tree in a forest, i.e. to
           capture the '*' token in nexus files.

=cut

    sub set_not_default {
        my $self = shift;
        $default{ $self->get_id } = 0;
        return $self;
    }

=back

=head2 TESTS

=over