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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/SeqFeature/Gene/TranscriptI.pm	Thu Apr 11 02:01:53 2013 -0400
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+# $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 <[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::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.
+
+  [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::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;
+
+
+
+
+
+