diff variant_effect_predictor/Bio/EnsEMBL/SeqFeatureI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/SeqFeatureI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,178 @@
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::SeqFeatureI
+
+=head1 DESCRIPTION
+
+Do not use this class. It is deprecated and has been replaced by 
+Bio::EnsEMBL::Feature.
+
+=head1 METHODS
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::EnsEMBL::SeqFeatureI;
+
+use vars qw(@ISA);
+use strict;
+use Carp;
+
+# Object preamble - inherits from Bio::Root::Object
+
+use Bio::SeqFeatureI;
+use Bio::EnsEMBL::Root;
+
+@ISA = qw(Bio::EnsEMBL::Root Bio::SeqFeatureI);
+
+
+=head1 Abstract methods
+
+These methods must be implemented in all subclasses.
+
+
+=head2 analysis
+
+ Title   : analysis
+ Usage   : $sf->analysis();
+ Function: Store details of the program/database
+           and versions used to create this feature.
+           
+ Example :
+ Returns : 
+ Args    :
+
+
+=cut
+
+sub analysis {
+   my ($self,$value) = @_;
+
+   $self->throw("Have not implemeneted analysis");
+
+}
+
+=head2 validate
+
+ Title   : validate
+ Usage   : $sf->validate;
+ Function: Checks whether all the data is present in the
+           object.
+ Example :
+ Returns : 
+ Args    :
+
+
+=cut
+
+sub validate {
+   my ($self,$value) = @_;
+
+   $self->throw("Have not implemeneted validate");
+
+
+}
+
+
+sub id {
+    my ($self,$value) = @_;
+
+    $self->throw("Have not implemented id");
+}
+
+=head2 percent_id
+
+ Title   : percent_id
+ Usage   : $pid = $feat->percent_id()
+           $feat->percent_id($pid)
+ Function: get/set on percentage identity information
+ Returns : float
+ Args    : none if get, the new value if set
+
+=cut
+
+sub percent_id {
+    my ($self) = @_;
+    $self->throw("percent_id() not yet implemented");
+}
+
+=head2 e_value
+
+ Title   : p_value
+ Usage   : $p_val = $feat->p_value()
+           $feat->p_value($p_val)
+ Function: get/set on p value information
+ Returns : float
+ Args    : none if get, the new value if set
+
+=cut
+
+sub e_value {
+    my ($self) = @_;
+    $self->throw("e value() not yet implemented");
+}
+
+=head2 phase
+
+ Title   : phase
+ Usage   : $phase = $feat->phase()
+           $feat->phase($phase)
+ Function: get/set on start phase of predicted exon feature
+ Returns : [0,1,2]
+ Args    : none if get, 0,1 or 2 if set. 
+
+=cut
+
+sub phase {
+    my ($self) = @_;
+    $self->throw("phase() not yet implemented");
+}
+
+=head2 end_phase
+
+ Title   : end_phase
+ Usage   : $end_phase = $feat->end_phase()
+           $feat->end_phase($end_phase)
+ Function: get/set on end phase of predicted exon feature
+ Returns : [0,1,2]
+ Args    : none if get, 0,1 or 2 if set. 
+
+=cut
+
+sub end_phase {
+    my ($self) = @_;
+    $self->throw("end_phase() not yet implemented");
+}
+
+
+# this is a bit too sneaky. 
+sub location {
+    my ($self)= @_;
+    return $self;
+}
+
+
+1;