Raw content of Bio::EnsEMBL::DnaPepAlignFeature
<![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::DnaPepAlignFeature - Ensembl specific dna-pep pairwise
alignment feature
=head1 SYNOPSIS
See BaseAlignFeature
=cut
package Bio::EnsEMBL::DnaPepAlignFeature;
use strict;
use Bio::EnsEMBL::BaseAlignFeature;
use vars qw(@ISA);
@ISA = qw( Bio::EnsEMBL::BaseAlignFeature );
=head2 new_fast
Arg [1] : hashref $hashref
A hashref which will be blessed into a PepDnaAlignFeature.
Example : none
Description: This allows for very fast object creation when a large number
of DnaPepAlignFeatures needs to be created. This is a bit of
a hack but necessary when thousands of features need to be
generated within a couple of seconds for web display. It is
not recommended that this method be called unless you know what
you are doing. It requires knowledge of the internals of this
class and its superclasses.
Returntype : Bio::EnsEMBL::DnaPepAlignFeature
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor
Status : Stable
=cut
sub new_fast {
my ($class, $hashref) = @_;
return bless $hashref, $class;
}
=head2 _hit_unit
Arg [1] : none
Example : none
Description: PRIVATE implementation of abstract superclass method. Returns
1 as the 'unit' used for the hit sequence.
Returntype : int
Exceptions : none
Caller : Bio::EnsEMBL::BaseAlignFeature
Status : Stable
=cut
sub _hit_unit {
return 1;
}
=head2 _query_unit
Arg [1] : none
Example : none
Description: PRIVATE implementation of abstract superclass method. Returns
3 as the 'unit' used for the query sequence.
Returntype : int
Exceptions : none
Caller : Bio::EnsEMBL::BaseAlignFeature
Status : Stable
=cut
sub _query_unit {
return 3;
}
1;
]]>