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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/SeqFeature/Gene/ExonI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,117 @@
+# $Id: ExonI.pm,v 1.6 2002/10/22 07:38:41 lapp Exp $
+#
+# BioPerl module for Bio::SeqFeature::Gene::ExonI
+#
+# 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::ExonI - Interface for a feature representing an exon
+
+=head1 SYNOPSIS
+
+See documentation of methods.
+
+=head1 DESCRIPTION
+
+A feature representing an exon. An exon in this definition is
+transcribed and at least for one particular transcript not spliced out
+of the pre-mRNA. However, it does not necessarily code for amino acid.
+
+=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::ExonI;
+use vars qw(@ISA);
+use strict;
+
+use Carp;
+use Bio::SeqFeatureI;
+
+@ISA = qw(Bio::SeqFeatureI);
+
+
+=head2 is_coding
+
+ Title   : is_coding
+ Usage   : if($exon->is_coding()) {
+                   # do something
+           }
+ Function: Whether or not the exon codes for amino acid.
+ Returns : TRUE if the object represents a feature translated into protein,
+           and FALSE otherwise.
+ Args    : 
+
+
+=cut
+
+sub is_coding {
+    my ($self) = @_;
+    $self->throw_not_implemented();
+}
+
+=head2 cds
+
+ Title   : cds()
+ Usage   : $cds = $exon->cds();
+ Function: Get the coding sequence of the exon as a sequence object.
+
+           The returned sequence object must be in frame 0, i.e., the first
+           base starts a codon.
+
+           An implementation may return undef, indicating that a coding
+           sequence does not exist, e.g. for a UTR (untranslated region).
+
+ Returns : A L<Bio::PrimarySeqI> implementing object.
+ Args    : 
+
+
+=cut
+
+sub cds {
+    my ($self) = @_;
+    $self->throw_not_implemented();
+}
+
+1;