Raw content of Bio::SeqFeature::Gene::TranscriptI
<![CDATA[# $Id: TranscriptI.pm,v 1.7 2002/10/22 07:38:41 lapp Exp $
#
# BioPerl module for Bio::SeqFeature::Gene::TranscriptI
#
# 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::SeqFeature::Gene::TranscriptI - Interface for a feature representing a
transcript of exons, promoter(s), UTR, and a poly-adenylation site.
=head1 SYNOPSIS
#documentation needed
=head1 DESCRIPTION
A feature representing a transcript.
=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::SeqFeature::Gene::TranscriptI;
use vars qw(@ISA);
use strict;
use Carp;
use Bio::SeqFeatureI;
@ISA = qw(Bio::SeqFeatureI);
=head2 promoters
Title : promoters()
Usage : @proms = $transcript->promoters();
Function: Get the promoter features of this transcript.
Note that OO-modeling of regulatory elements is not stable yet.
This means that this method might change or even disappear in a
future release. Be aware of this if you use it.
Returns : An array of Bio::SeqFeatureI implementing objects representing the
promoter regions or sites.
Args :
=cut
sub promoters {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 exons
Title : exons()
Usage : @exons = $transcript->exons();
@inital = $transcript->exons('Initial');
Function: Get the individual exons this transcript comprises of, or all exons
of a specified type.
Refer to the documentation of the class that produced this
transcript object for information about the possible types.
See Bio::SeqFeature::Gene::ExonI for properties of the
returned objects.
Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
Args : An optional string specifying the type of the exon.
=cut
sub exons {
my ($self, $type) = @_;
$self->throw_not_implemented();
}
=head2 introns
Title : introns()
Usage : @introns = $transcript->introns();
Function: Get all introns this transcript comprises of.
Returns : An array of Bio::SeqFeatureI implementing objects representing the
introns.
Args :
=cut
sub introns {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 poly_A_site
Title : poly_A_site()
Usage : $polyAsite = $transcript->poly_A_site();
Function: Get the poly-adenylation site of this transcript.
Returns : A Bio::SeqFeatureI implementing object.
Args :
=cut
sub poly_A_site {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 utrs
Title : utrs()
Usage : @utr_sites = $transcript->utrs();
Function: Get the UTR regions this transcript comprises of.
See Bio::SeqFeature::Gene::ExonI for properties of the
returned objects.
Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
Args :
=cut
sub utrs {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 mrna
Title : mrna()
Usage : $mrna = $transcript->mrna();
Function: Get the mRNA of the transcript as a sequence object.
Returns : A Bio::PrimarySeqI implementing object.
Args :
=cut
sub mrna {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 cds
Title : cds()
Usage : $cds = $transcript->cds();
Function: Get the CDS (coding sequence) of the transcript as a sequence
object.
Returns : A Bio::PrimarySeqI implementing object.
Args :
=cut
sub cds {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 protein
Title : protein()
Usage : $protein = $transcript->protein();
Function: Get the protein encoded by the transcript as a sequence object.
Returns : A Bio::PrimarySeqI implementing object.
Args :
=cut
sub protein {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 parent
Title : parent
Usage : $obj->parent($newval)
Function: get the parent gene of the transcript
Returns : value of parent - a Bio::SeqFeature::Gene::GeneStructureI-compliant object
Args : a Bio::SeqFeature::Gene::GeneStructureI-compliant object (optional)
=cut
sub parent{
my ($self,$value) = @_;
if( defined $value) {
if ($value->isa("Bio::SeqFeature::Gene::GeneStructureI")) {
$self->{'parent'} = $value;
} else {
$self->throw("$value must be a Bio::SeqFeature::Gene::GeneStructureI")
}
}
return $self->{'parent'};
}
1;
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