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# TFBS module for TFBS::PatternGen::Gibbs::Motif
#
# Copyright Boris Lenhard and Wynand Alkema
#
# You may distribute this module under the same terms as perl itself
#
# POD
# POD
=head1 NAME
TFBS::PatternGen::Gibbs::Motif - class for unprocessed motifs and associated
numerical scores created by the Gibbs program
=head1 SYNOPSIS
=head1 DESCRIPTION
TFBS::PatternGen::Gibbs::Motif is used to store and manipulate unprocessed
motifs and associated numerical scores created by the Gibbs program. You do not
normally want to create a TFBS::PatternGen::Gibbs::Motif yourself. They are created
by running TFBS::PatternGen::Gibbs
=head1 FEEDBACK
Please send bug reports and other comments to the author.
=head1 AUTHOR - Boris Lenhard and Wynand Alkema
Boris Lenhard E<lt>Boris.Lenhard@cgb.ki.seE<gt>
Wynand Alkema E<lt>Wynand.Alkema@cgb.ki.seE<gt>
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are preceded with an underscore.
=cut
# the code begins here:
package TFBS::PatternGen::Gibbs::Motif;
use vars qw(@ISA);
use strict;
use TFBS::Matrix::PFM;
use TFBS::PatternGen::Motif::Matrix;
@ISA = qw(TFBS::PatternGen::Motif::Matrix);
=head2 MAP
Title : MAP
Usage : my $map_score = $motif->MAP;
Function: returns MAP score for the detected motif
(This is a backward compatibility method. For consistency,
you should use $motif->tag('MAP_score') instead
Returns : float (a scalar)
Args : none
=head2 Other methods
TFBS::PatterGen::Motif::Gibbs inherits from TFBS::PatternGen::Motif,
which inherits from TFBS::Matrix. Please consult the documentation of those modules
for additional available methods.
=cut
sub MAP{
my ($self) = @_;
return $self->tag("MAP_score");
}
sub _calculate_PFM {
my $self = shift;
unless ($self->{'nr_hits'}) {
$self->throw(ref($self).
" objects must be created with a (nonzero)".
" -nr_hits parameter in constructor"
);
}
my @PFM;
foreach my $rowref ( @{$self->{'matrix'}} ) {
my @PFMrow;
foreach my $element (@$rowref) {
push @PFMrow, int($self->{'nr_hits'}*$element/100 + 0.5);
}
push @PFM, [@PFMrow];
}
return \@PFM;
}
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