comparison variant_effect_predictor/Bio/EnsEMBL/DnaPepAlignFeature.pm @ 0:1f6dce3d34e0

Uploaded
author mahtabm
date Thu, 11 Apr 2013 02:01:53 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:1f6dce3d34e0
1 =head1 LICENSE
2
3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
4 Genome Research Limited. All rights reserved.
5
6 This software is distributed under a modified Apache license.
7 For license details, please see
8
9 http://www.ensembl.org/info/about/code_licence.html
10
11 =head1 CONTACT
12
13 Please email comments or questions to the public Ensembl
14 developers list at <dev@ensembl.org>.
15
16 Questions may also be sent to the Ensembl help desk at
17 <helpdesk@ensembl.org>.
18
19 =cut
20
21 =head1 NAME
22
23 Bio::EnsEMBL::DnaPepAlignFeature - Ensembl specific dna-pep pairwise
24 alignment feature
25
26 =head1 SYNOPSIS
27
28 See BaseAlignFeature
29
30 =cut
31
32
33 package Bio::EnsEMBL::DnaPepAlignFeature;
34
35 use strict;
36
37 use Bio::EnsEMBL::BaseAlignFeature;
38 use Scalar::Util qw(weaken isweak);
39
40 use vars qw(@ISA);
41
42 @ISA = qw( Bio::EnsEMBL::BaseAlignFeature );
43
44
45 =head2 new_fast
46
47 Arg [1] : hashref $hashref
48 A hashref which will be blessed into a PepDnaAlignFeature.
49 Example : none
50 Description: This allows for very fast object creation when a large number
51 of DnaPepAlignFeatures needs to be created. This is a bit of
52 a hack but necessary when thousands of features need to be
53 generated within a couple of seconds for web display. It is
54 not recommended that this method be called unless you know what
55 you are doing. It requires knowledge of the internals of this
56 class and its superclasses.
57 Returntype : Bio::EnsEMBL::DnaPepAlignFeature
58 Exceptions : none
59 Caller : Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor
60 Status : Stable
61
62 =cut
63
64 sub new_fast {
65 my ($class, $hashref) = @_;
66 my $self = bless $hashref, $class;
67 weaken($self->{adaptor}) if ( ! isweak($self->{adaptor}) );
68 return $self;
69 }
70
71
72 =head2 _hit_unit
73
74 Arg [1] : none
75 Description: PRIVATE implementation of abstract superclass method. Returns
76 1 as the 'unit' used for the hit sequence.
77 Returntype : int
78 Exceptions : none
79 Caller : Bio::EnsEMBL::BaseAlignFeature
80 Status : Stable
81
82
83 =cut
84
85 sub _hit_unit {
86 return 1;
87 }
88
89
90 =head2 _query_unit
91
92 Arg [1] : none
93 Description: PRIVATE implementation of abstract superclass method. Returns
94 3 as the 'unit' used for the query sequence.
95 Returntype : int
96 Exceptions : none
97 Caller : Bio::EnsEMBL::BaseAlignFeature
98 Status : Stable
99
100
101 =cut
102
103 sub _query_unit {
104 return 3;
105 }
106
107
108
109
110 1;