Raw content of Bio::Tools::Prediction::Exon
<![CDATA[# $Id: Exon.pm,v 1.10 2002/10/22 07:38:48 lapp Exp $
#
# BioPerl module for Bio::Tools::Prediction::Exon
#
# Cared for by Hilmar Lapp <hlapp@gmx.net>
#
# Copyright Hilmar Lapp
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Prediction::Exon - A predicted exon feature
=head1 SYNOPSIS
See documentation of methods.
=head1 DESCRIPTION
A feature representing a predicted exon. This class actually inherits
off Bio::SeqFeature::Gene::Exon and therefore has all that
functionality (also implements Bio::SeqFeatureI), plus a few methods
supporting predicted features, like various scores and a
significance. Even though these were inspired by GenScan results, at
least a subset should be generally useable for exon prediction
results.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Hilmar Lapp
Email hlapp@gmx.net
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::Prediction::Exon;
use vars qw(@ISA);
use strict;
use Bio::SeqFeature::Gene::Exon;
@ISA = qw(Bio::SeqFeature::Gene::Exon);
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($primary) = $self->_rearrange([qw(PRIMARY)],@args);
return $self;
}
=head2 predicted_cds
Title : predicted_cds
Usage : $predicted_cds_dna = $exon->predicted_cds();
$exon->predicted_cds($predicted_cds_dna);
Function: Get/Set the CDS (coding sequence) as predicted by a program.
This method is independent of an attached_seq. There is no
guarantee whatsoever that the returned CDS has anything to do
(e.g., matches) with the sequence covered by the exons as annotated
through this object.
Example :
Returns : A Bio::PrimarySeqI implementing object holding the DNA sequence
defined as coding by a prediction of a program.
Args : On set, a Bio::PrimarySeqI implementing object holding the DNA
sequence defined as coding by a prediction of a program.
=cut
sub predicted_cds {
my ($self, $cds) = @_;
if(defined($cds)) {
$self->{'_predicted_cds'} = $cds;
}
return $self->{'_predicted_cds'};
}
=head2 predicted_protein
Title : predicted_protein
Usage : $predicted_protein_seq = $exon->predicted_protein();
$exon->predicted_protein($predicted_protein_seq);
Function: Get/Set the protein translation as predicted by a program.
This method is independent of an attached_seq. There is no
guarantee whatsoever that the returned translation has anything to
do with the sequence covered by the exons as annotated
through this object, or the sequence returned by predicted_cds(),
although it should usually be just the standard translation.
Example :
Returns : A Bio::PrimarySeqI implementing object holding the protein
translation as predicted by a program.
Args : On set, a Bio::PrimarySeqI implementing object holding the protein
translation as predicted by a program.
=cut
sub predicted_protein {
my ($self, $aa) = @_;
if(defined($aa)) {
$self->{'_predicted_aa'} = $aa;
}
return $self->{'_predicted_aa'};
}
=head2 significance
Title : significance
Usage : $evalue = $obj->significance();
$obj->significance($evalue);
Function:
Returns :
Args :
=cut
sub significance {
my ($self, $value) = @_;
return $self->_tag_value('signif', $value);
}
=head2 start_signal_score
Title : start_signal_score
Usage : $sc = $obj->start_signal_score();
$obj->start_signal_score($evalue);
Function: Get/Set a score for the exon start signal (acceptor splice site
or initiation signal).
Returns :
Args :
=cut
sub start_signal_score {
my ($self, $value) = @_;
return $self->_tag_value('AccScore', $value);
}
=head2 end_signal_score
Title : end_signal_score
Usage : $sc = $obj->end_signal_score();
$obj->end_signal_score($evalue);
Function: Get/Set a score for the exon end signal (donor splice site
or termination signal).
Returns :
Args :
=cut
sub end_signal_score {
my ($self, $value) = @_;
return $self->_tag_value('DonScore', $value);
}
=head2 coding_signal_score
Title : coding_signal_score
Usage : $sc = $obj->coding_signal_score();
$obj->coding_signal_score($evalue);
Function: Get/Set a score for the exon coding signal (e.g., coding potential).
Returns :
Args :
=cut
sub coding_signal_score {
my ($self, $value) = @_;
return $self->_tag_value('CodScore', $value);
}
#
# Everything else is just inherited from SeqFeature::Generic.
#
1;
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