NAME

Bio::Palantir::Refiner::GenePlus - Refiner internal class for handling GenePlus objects

VERSION

version 0.192540

SYNOPSIS

    # TODO

DESCRIPTION

    # TODO

ATTRIBUTES

domains

ArrayRef of Bio::Palantir::Refiner::Domain

exp_domains

ArrayRef of Bio::Palantir::Refiner::Domain

METHODS

count_domains

Returns the number of Domains of the Gene.

    # $gene is a Bio::Palantir::Refiner::Gene
    my $count = $gene->count_domains;

This method does not accept any arguments.

all_domains

Returns all the Domains of the Gene (not an array reference).

    # $gene is a Bio::Palantir::Refiner::Gene
    my @domains = $gene->all_domains;

This method does not accept any arguments.

get_domain

    # $gene is a Bio::Palantir::Refiner::Gene
    my $domain = $gene->get_domain($index);
    croak "Domain $index not found!" unless defined $domain;

This method accepts just one argument (and not an array slice).

next_domain

Shifts the first Domain of the array off and returns it, shortening the array by 1 and moving everything down. If there are no more Domains in the array, returns undef.

    # $gene is a Bio::Palantir::Refiner::Gene
    while (my $domain = $gene->next_domain) {
        # process $domain
        # ...
    }

This method does not accept any arguments.

count_exp_domains

Returns the number of Domains of the Gene.

    # $gene is a Bio::Palantir::Refiner::Gene
    my $count = $gene->count_exp_domains;

This method does not accept any arguments.

all_exp_domains

Returns all the Domains of the Gene (not an array reference).

    # $gene is a Bio::Palantir::Refiner::Gene
    my @exp_domains = $gene->all_exp_domains;

This method does not accept any arguments.

get_exp_domain

    # $gene is a Bio::Palantir::Refiner::Gene
    my $exp_domain = $gene->get_exp_domain($index);
    croak "Domain $index not found!" unless defined $exp_domain;

This method accepts just one argument (and not an array slice).

next_exp_domain

Shifts the first Domain of the array off and returns it, shortening the array by 1 and moving everything down. If there are no more Domains in the array, returns undef.

    # $gene is a Bio::Palantir::Refiner::Gene
    while (my $exp_domain = $gene->next_exp_domain) {
        # process $exp_domain
        # ...
    }

This method does not accept any arguments.

AUTHOR

Loic MEUNIER <lmeunier@uliege.be>

COPYRIGHT AND LICENSE

This software is copyright (c) 2019 by University of Liege / Unit of Eukaryotic Phylogenomics / Loic MEUNIER and Denis BAURAIN.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.