NAME

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

VERSION

version 0.191620

SYNOPSIS

    # TODO

DESCRIPTION

    # TODO

ATTRIBUTES

qualifiers

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

locations

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

METHODS

count_qualifiers

Returns the number of Qualifiers of the Motif.

    # $motif is a Bio::Palantir::Parser::Motif
    my $count = $motif->count_qualifiers;

This method does not accept any arguments.

all_qualifiers

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

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

This method does not accept any arguments.

get_qualifier

Returns one Qualifier of the Motif 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.

    # $motif is a Bio::Palantir::Parser::Motif
    my $qualifier = $motif->get_qualifier($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.

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

This method does not accept any arguments.

name

Returns the value of the element <motif_name>.

    # $motif is a Bio::Palantir::Parser::Motif
    my $name = $motif->name;

This method does not accept any arguments.

type

Returns the value of the element <motif_type>.

    # $motif is a Bio::Palantir::Parser::Motif
    my $type = $motif->type;

This method does not accept any arguments.

sequence

Returns the value of the element <sequence>.

    # $motif is a Bio::Palantir::Parser::Motif
    my $sequence = $motif->sequence;

This method does not accept any arguments.

detail

Returns the value of the element <detail>.

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

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.