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