diff variant_effect_predictor/Bio/SeqFeature/Gene/GeneStructureI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/SeqFeature/Gene/GeneStructureI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,195 @@
+# $Id: GeneStructureI.pm,v 1.8 2002/10/22 07:38:41 lapp Exp $
+#
+# BioPerl module for Bio::SeqFeature::Gene::GeneStructureI
+#
+# Cared for by Hilmar Lapp <[e-mail]>
+#
+# 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::GeneStructure - A feature representing an arbitrarily
+           complex structure of a gene
+
+=head1 SYNOPSIS
+
+  #documentaion 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.
+
+  [e-mail]          - 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:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Hilmar Lapp
+
+Email [e-mail]
+
+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::GeneStructureI;
+use vars qw(@ISA);
+use strict;
+
+use Carp;
+use Bio::SeqFeatureI;
+
+@ISA = 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;