NAME

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

VERSION

version 0.191800

SYNOPSIS

    # TODO

DESCRIPTION

    # TODO

ATTRIBUTES

domains

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

orphan_motifs

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

qualifiers

ArrayRef of Bio::Palantir::Parser::Qualifier

locations

Bio::Palantir::Parser::Location composed object

METHODS

count_domains

Returns the number of Domains of the Gene.

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

This method does not accept any arguments.

get_domain

Returns one Domain of the Gene 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.

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

This method does not accept any arguments.

count_orphan_motifs

Returns the number of Motifs of the Gene.

    # $gene is a Bio::Palantir::Parser::Gene
    my $count = $gene->count_orphan_motifs;

This method does not accept any arguments.

all_orphan_motifs

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

    # $gene is a Bio::Palantir::Parser::Gene
    my @orphan_motifs = $gene->all_orphan_motifs;

This method does not accept any arguments.

get_orphan_motif

Returns one Motif of the Gene 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.

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

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

next_orphan_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.

    # $gene is a Bio::Palantir::Parser::Gene
    while (my $orphan_motif = $gene->next_orphan_motif) {
        # process $orphan_motif
        # ...
    }

This method does not accept any arguments.

count_qualifiers

Returns the number of Qualifiers of the Gene.

    # $gene is a Bio::Palantir::Parser::Gene
    my $count = $gene->count_qualifiers;

This method does not accept any arguments.

all_qualifiers

Returns all the Qualifiers of the Gene (not an array reference).

    # $gene is a Bio::Palantir::Parser::Gene
    my @qualifiers = $gene->all_qualifiers;

This method does not accept any arguments.

get_qualifier

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

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

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

next_qualifier

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

    # $gene is a Bio::Palantir::Parser::Gene
    while (my $qualifier = $gene->next_qualifier) {
        # process $qualifier
        # ...
    }

This method does not accept any arguments.

name

Returns the value of the element <gene_name>.

    # $gene is a Bio::Palantir::Parser::Gene
    my $name = $gene->name;

This method does not accept any arguments.

sequence

Returns the value of the element <sequence>.

    # $gene is a Bio::Palantir::Parser::Gene
    my $sequence = $gene->sequence;

This method does not accept any arguments.

operon

Returns the value of the element <operon>.

    # $gene is a Bio::Palantir::Parser::Gene
    my $operon = $gene->operon;

This method does not accept any arguments.

transcript_id

Returns the value of the element <transcript_id>.

    # $gene is a Bio::FastParsers::Biosynml::Gene
    my $transcript_id = $gene->transcript_id;

This method does not accept any arguments.

protein_sequence

Returns the value of the element <protein_sequence>.

    # $gene is a Bio::FastParsers::Biosynml::Gene
    my $protein_sequence = $gene->protein_sequence;

This method does not accept any arguments.

gene_id

Returns the value of the element <gene_id>.

    # $gene is a Bio::FastParsers::Biosynml::Gene
    my $gene_id = $gene->gene_id;

This method does not accept any arguments.

protein_id

Returns the value of the element <protein_id>.

    # $gene is a Bio::FastParsers::Biosynml::Gene
    my $protein_id = $gene->protein_id;

This method does not accept any arguments.

product_id

Returns the value of the element <product_id>.

    # $gene is a Bio::FastParsers::Biosynml::Gene
    my $product_id = $gene->product_id;

This method does not accept any arguments.

locus_tag

Returns the value of the element <locus_tag>.

    # $gene is a Bio::FastParsers::Biosynml::Gene
    my $locus_tag = $gene->locus_tag;

This method does not accept any arguments.

smcog

Returns the value of the element <smcog>.

    # $gene is a Bio::FastParsers::Biosynml::Gene
    my $smcog = $gene->smcog;

This method does not accept any arguments.

uniprot_id

Returns the value of the element <uniprot_id>.

    # $gene is a Bio::FastParsers::Biosynml::Gene
    my $uniprot_id = $gene->uniprot_id;

This method does not accept any arguments.

go_ids

Returns the values of the elements <go_ids>.

    # $gene is a Bio::FastParsers::Biosynml::Gene
        my @go_ids = $gene->go_ids;

This method does not accept any arguments.

uniparc_id

Returns the value of the element <uniparc_id>.

    # $gene is a Bio::FastParsers::Biosynml::Gene
    my $uniparc_id = $gene->uniparc_id;

This method does not accept any arguments.

type

Returns the value of the element <type>.

    # $gene is a Bio::FastParsers::Biosynml::Gene
    my $type = $gene->type;

This method does not accept any arguments.

domains_detail

Returns the value of the element <domains_detail>.

    # $gene is a Bio::FastParsers::Biosynml::Gene
    my $domains_detail = $gene->domains_detail;

This method does not accept any arguments.

kind

Returns the value of the element <kind>.

    # $gene is a Bio::FastParsers::Biosynml::Gene
    my $kind = $gene->kind;

This method does not accept any arguments.

subtype

Returns the value of the element <subtype>.

    # $gene is a Bio::FastParsers::Biosynml::Gene
    my $subtype = $gene->subtype;

This method does not accept any arguments.

bgc_domains

Returns the values of the elements <bgc_domains>.

    # $gene is a Bio::FastParsers::Biosynml::Gene
        my @bgc_domains = $gene->bgc_domains;

This method does not accept any arguments.

monomers

Returns the values of the elements <monomers>.

    # $gene is a Bio::FastParsers::Biosynml::Gene
        my @monomers = $gene->monomers;

This method does not accept any arguments.

nrpspredictor_monomers

Returns the values of the elements <nrpspredictor_monomers>.

    # $gene is a Bio::FastParsers::Biosynml::Gene
        my @nrpspredictor_monomers = $gene->nrpspredictor_monomers;

This method does not accept any arguments.

stachelhaus_monomers

Returns the values of the elements <stachelhaus_monomers>.

    # $gene is a Bio::FastParsers::Biosynml::Gene
        my @stachelhaus_monomers = $gene->stachelhaus_monomers;

This method does not accept any arguments.

minowa_monomers

Returns the values of the elements <minowa_monomers>.

    # $gene is a Bio::FastParsers::Biosynml::Gene
        my @minowa_monomers = $gene->minowa_monomers;

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.