NAME

Bio::Palantir::Roles::Modulable::Module - BiosynML DTD-derived internal class

VERSION

version 0.191620

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::FastParsers::Biosynml::Module
        my @sorted_domains = $module->sort_domains;

This method does not accept any arguments.

size

Returns the size of the module.

    # $module is a Bio::FastParsers::Biosynml::Module
        my $size = $module->size;

coordinates

Returns the coordinates of the module.

    # $module is a Bio::FastParsers::Biosynml::Module
        my $coordinates = $module->coordinates;

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.

cpanm Bio::Palantir

perl -MCPAN -e shell
install Bio::Palantir