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Bio-Palantir-0.211420
River stage zero No dependents
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/ Bio::Palantir::Parser::Domain

NAME

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

VERSION

version 0.211420

SYNOPSIS

    # TODO

DESCRIPTION

    # TODO

ATTRIBUTES

motifs

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

gene_locations

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

protein_locations

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

METHODS

count_motifs

Returns the number of Motifs of the Domain.

    # $domain is a Bio::Palantir::Parser::Domain
    my $count = $domain->count_motifs;

This method does not accept any arguments.

all_motifs

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

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

This method does not accept any arguments.

get_motif

Returns one Motif of the Domain 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.

    # $domain is a Bio::Palantir::Parser::Domain
    my $motif = $domain->get_motif($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.

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

This method does not accept any arguments.

protein_sequence

Returns the value of the element <location}-{protein}->{sequence>>.

    # $domain is a Bio::Palantir::Parser::Domain
    my $protein_sequence = $domain->protein_sequence;

This method does not accept any arguments.

protein_name

Returns the value of the element <location}-{protein}->{name>>.

    # $domain is a Bio::Palantir::Parser::Domain
    my $protein_name = $domain->protein_name;

This method does not accept any arguments.

nodeid

Returns the value of the element <nodeid>.

    # $domain is a Bio::Palantir::Parser::Domain
    my $nodeid = $domain->nodeid;

This method does not accept any arguments.

function

Returns the value of the element <function>.

    # $domain is a Bio::Palantir::Parser::Domain
    my $function = $domain->function;

This method does not accept any arguments.

subtype

Returns the value of the element <subtype>.

    # $domain is a Bio::Palantir::Parser::Domain
    my $subtype = $domain->subtype;

This method does not accept any arguments.

dstatus

Returns the value of the element <dstatus>.

    # $domain is a Bio::Palantir::Parser::Domain
    my $dstatus = $domain->dstatus;

This method does not accept any arguments.

label

Returns the value of the element <label>.

    # $domain is a Bio::Palantir::Parser::Domain
    my $label = $domain->label;

This method does not accept any arguments.

chemistry

Returns the value of the element <chemistry>.

    # $domain is a Bio::Palantir::Parser::Domain
    my $chemistry = $domain->chemistry;

This method does not accept any arguments.

substrate

Returns the value of the element <substrate>.

    # $domain is a Bio::Palantir::Parser::Domain
    my $substrate = $domain->substrate;

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.