/ 
Bio-Palantir-0.211420
River stage zero No dependents
/ Bio::Palantir::Roles::Modulable::Module

NAME

Bio::Palantir::Roles::Modulable::Module

VERSION

version 0.211420

SYNOPSIS

# TODO

DESCRIPTION

# TODO

ATTRIBUTES

domains

ArrayRef of Bio::Palantir::Parser::Domain

METHODS

count_domains

Returns the number of Domains of the Module.

# $module is a Bio::Palantir::Parser::Module
my $count = $module->count_domains;

This method does not accept any arguments.

all_domains

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

# $module is a Bio::Palantir::Parser::Module
my @domains = $module->all_domains;

This method does not accept any arguments.

get_domain

Returns one Domain of the Module by its index. You can also use negative index numbers, just as with Perl's core array handling. If the specified Domain does not exist, this method will return undef.

# $module is a Bio::Palantir::Parser::Module
my $domain = $module->get_domain($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.

# $module is a Bio::Palantir::Parser::Module
while (my $domain = $module->next_domain) {
    # process $domain
    # ...
}

This method does not accept any arguments.

sort_domains

Returns a array of sorted domains by increasing start coordinate (by default, the list of domains should be built in the right order, so it is a security here).

    # $module is a Bio::Palantir::Roles::Modulable::Module
	my @sorted_domains = $module->sort_domains;

This method does not accept any arguments.

genomic_dna_begin

Returns the begin of the genomic DNA coordinate of the module.

    # $module is a Bio::Palantir::Roles::Modulable::Module
	my $genomic_dna_begin = $module->genomic_dna_begin;

genomic_dna_end

Returns the end of the genomic DNA coordinate of the module.

    # $module is a Bio::Palantir::Roles::Modulable::Module
	my $genomic_dna_end = $module->genomic_dna_end;

get_domain_functions

Returns the list of functions from the domains constituting the module.

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.