Bio::Palantir::Parser::Root - BiosynML DTD-derived internal class
version 0.191620
# TODO
ArrayRef of Bio::Palantir::Parser::Cluster
ArrayRef of Bio::Palantir::Parser::Gene
ArrayRef of Bio::Palantir::Parser::Domain
ArrayRef of Bio::Palantir::Parser::Motif
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.
Returns all the Clusters of the Root (not an array reference).
# $root is a Bio::Palantir::Parser::Root my @clusters = $root->all_clusters;
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.
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).
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 # ... }
Returns the number of Genes of the Root.
# $root is a Bio::Palantir::Parser::Root my $count = $root->count_genes;
Returns all the Genes of the Root (not an array reference).
# $root is a Bio::Palantir::Parser::Root my @genes = $root->all_genes;
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;
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 # ... }
Returns the number of Domains of the Root.
# $root is a Bio::Palantir::Parser::Root my $count = $root->count_domains;
Returns all the Domains of the Root (not an array reference).
# $root is a Bio::Palantir::Parser::Root my @domains = $root->all_domains;
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;
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 # ... }
Returns the number of Motifs of the Root.
# $root is a Bio::Palantir::Parser::Root my $count = $root->count_motifs;
Returns all the Motifs of the Root (not an array reference).
# $root is a Bio::Palantir::Parser::Root my @motifs = $root->all_motifs;
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;
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 # ... }
Loic MEUNIER <lmeunier@uliege.be>
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.
To install Bio::Palantir, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Palantir
CPAN shell
perl -MCPAN -e shell install Bio::Palantir
For more information on module installation, please visit the detailed CPAN module installation guide.