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Bio-Palantir-0.211420
River stage zero No dependents
/ Bio::Palantir::Refiner::GenePlus

NAME

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

VERSION

version 0.211420

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.