Raw content of Bio::EnsEMBL::SeqFeatureI =head1 LICENSE Copyright (c) 1999-2009 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 /info/about/code_licence.html =head1 CONTACT Please email comments or questions to the public Ensembl developers list at <ensembl-dev@ebi.ac.uk>. Questions may also be sent to the Ensembl help desk at <helpdesk@ensembl.org>. =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 It is deprecated and has been replaced by Bio::EnsEMBL::Feature.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;