Mercurial > repos > mahtabm > ensembl
comparison 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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-1:000000000000 | 0:1f6dce3d34e0 |
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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; |