NAME

Bio::Palantir::Parser::Root - BiosynML DTD-derived internal class

VERSION

version 0.192540

SYNOPSIS

    # TODO

DESCRIPTION

    # TODO

ATTRIBUTES

clusters

ArrayRef of Bio::Palantir::Parser::Cluster

genes

ArrayRef of Bio::Palantir::Parser::Gene

domains

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

motifs

ArrayRef of Bio::Palantir::Parser::Motif

METHODS

count_clusters

Returns the number of Clusters of the Root.

    # $root is a Bio::Palantir::Parser::Root
    my $count = $root->count_clusters;

This method does not accept any arguments.

all_clusters

Returns all the Clusters of the Root (not an array reference).

    # $root is a Bio::Palantir::Parser::Root
    my @clusters = $root->all_clusters;

This method does not accept any arguments.

get_cluster

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

    # $root is a Bio::Palantir::Parser::Root
    my $cluster = $root->get_cluster($index);
    croak "Cluster $index not found!" unless defined $cluster;

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

next_cluster

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

    # $root is a Bio::Palantir::Parser::Root
    while (my $cluster = $root->next_cluster) {
        # process $cluster
        # ...
    }

This method does not accept any arguments.

count_genes

Returns the number of Genes of the Root.

    # $root is a Bio::Palantir::Parser::Root
    my $count = $root->count_genes;

This method does not accept any arguments.

all_genes

Returns all the Genes of the Root (not an array reference).

    # $root is a Bio::Palantir::Parser::Root
    my @genes = $root->all_genes;

This method does not accept any arguments.

get_gene

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

    # $root is a Bio::Palantir::Parser::Root
    my $gene = $root->get_gene($index);
    croak "Gene $index not found!" unless defined $gene;

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

next_gene

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

    # $root is a Bio::Palantir::Parser::Root
    while (my $gene = $root->next_gene) {
        # process $gene
        # ...
    }

This method does not accept any arguments.

count_domains

Returns the number of Domains of the Root.

    # $root is a Bio::Palantir::Parser::Root
    my $count = $root->count_domains;

This method does not accept any arguments.

all_domains

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

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

This method does not accept any arguments.

get_domain

Returns one Domain of the Root 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.

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

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

This method does not accept any arguments.

count_motifs

Returns the number of Motifs of the Root.

    # $root is a Bio::Palantir::Parser::Root
    my $count = $root->count_motifs;

This method does not accept any arguments.

all_motifs

Returns all the Motifs of the Root (not an array reference).

    # $root is a Bio::Palantir::Parser::Root
    my @motifs = $root->all_motifs;

This method does not accept any arguments.

get_motif

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

    # $root is a Bio::Palantir::Parser::Root
    my $motif = $root->get_motif($index);
    croak "Motif $index not found!" unless defined $motif;

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

next_motif

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

    # $root is a Bio::Palantir::Parser::Root
    while (my $motif = $root->next_motif) {
        # process $motif
        # ...
    }

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.