Mercurial > repos > mahtabm > ensembl
diff variant_effect_predictor/Bio/EnsEMBL/DnaPepAlignFeature.pm @ 0:1f6dce3d34e0
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author | mahtabm |
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date | Thu, 11 Apr 2013 02:01:53 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/variant_effect_predictor/Bio/EnsEMBL/DnaPepAlignFeature.pm Thu Apr 11 02:01:53 2013 -0400 @@ -0,0 +1,110 @@ +=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 <dev@ensembl.org>. + + 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 Scalar::Util qw(weaken isweak); + +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) = @_; + my $self = bless $hashref, $class; + weaken($self->{adaptor}) if ( ! isweak($self->{adaptor}) ); + return $self; +} + + +=head2 _hit_unit + + Arg [1] : 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 + 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;