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#
# BioPerl module for Bio::SeqFeature::Gene::GeneStructureI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# 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::GeneStructureI - A feature representing an arbitrarily
complex structure of a gene
=head1 SYNOPSIS
#documentation needed
=head1 DESCRIPTION
A feature representing a gene structure.
=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://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=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 the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Hilmar Lapp
Email hlapp@gmx.net
=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::GeneStructureI;
use strict;
use Carp;
use base qw(Bio::SeqFeatureI);
=head2 transcripts
Title : transcripts()
Usage : @transcripts = $gene->transcripts();
Function: Get the transcript features/sites of this gene structure.
See Bio::SeqFeature::Gene::TranscriptI for properties of the
returned objects.
Returns : An array of Bio::SeqFeature::Gene::TranscriptI implementing objects
representing the promoter regions or sites.
Args :
=cut
sub transcripts {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 promoters
Title : promoters()
Usage : @prom_sites = $gene->promoters();
Function: Get the promoter features/sites of this gene structure.
Note that OO-modeling of regulatory elements is not stable yet.
This means that this method might change or even disappear in a
future release. Be aware of this if you use it.
Returns : An array of Bio::SeqFeatureI implementing objects representing the
promoter regions or sites.
Args :
=cut
sub promoters {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 exons
Title : exons()
Usage : @exons = $gene->exons();
@inital = $gene->exons('Initial');
Function: Get all exon features or all exons of specified type of this gene
structure.
Refer to the documentation of the class that produced this gene
structure object for information about the possible types.
See Bio::SeqFeature::Gene::ExonI for properties of the
returned objects.
Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
representing the exon regions.
Args : An optional string specifying the type of the exon.
=cut
sub exons {
my ($self, $type) = @_;
$self->throw_not_implemented();
}
=head2 introns
Title : introns()
Usage : @introns = $gene->introns();
Function: Get all introns of this gene structure.
Returns : An array of Bio::SeqFeatureI implementing objects representing the
introns.
Args :
=cut
sub introns {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 poly_A_sites
Title : poly_A_sites()
Usage : @polyAsites = $gene->poly_A_sites();
Function: Get the poly-adenylation features/sites of this gene structure.
Returns : An array of Bio::SeqFeatureI implementing objects representing the
poly-adenylation regions or sites.
Args :
=cut
sub poly_A_sites {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 utrs
Title : utrs()
Usage : @utr_sites = $gene->utrs();
Function: Get the UTR features/sites of this gene structure.
See Bio::SeqFeature::Gene::ExonI for properties of the
returned objects.
Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
representing the UTR regions or sites.
Args :
=cut
sub utrs {
my ($self) = @_;
$self->throw_not_implemented();
}
1;
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