Raw content of Bio::EnsEMBL::SeqFeatureI
<![CDATA[=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 It is deprecated and has been replaced by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;
]]>