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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::PepDnaAlignFeature - Ensembl specific pep-dna 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 =head1 METHODS
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31
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32 =cut
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33
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34 package Bio::EnsEMBL::PepDnaAlignFeature;
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35
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36 use Bio::EnsEMBL::BaseAlignFeature;
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37
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38 use vars qw(@ISA);
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39 use strict;
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40
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41 @ISA = qw( Bio::EnsEMBL::BaseAlignFeature );
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42
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43 =head2 transform
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44
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45 Arg [1] : none
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46 Example : none
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47 Description: Overwrites Bio:EnsEMBL:Feature->transform as
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48 to give error message
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49 Status : Stable
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50
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51 =cut
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52
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53 sub transform {
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54 my $self = shift;
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55
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56 $self->throw( "PepDnaAlignFeatures cant be transformed as".
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57 " they are not on EnsEMBL coord system" );
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58 }
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59
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60 =head2 _hit_unit
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61
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62 Arg [1] : none
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63 Example : none
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64 Description: PRIVATE implementation of abstract superclass method. Returns
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65 3 as the 'unit' used for the hit sequence.
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66 Returntype : int
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67 Exceptions : none
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68 Caller : Bio::EnsEMBL::BaseAlignFeature
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69 Status : Stable
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70
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71
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72 =cut
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73
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74 sub _hit_unit {
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75 return 3;
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76 }
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77
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78 =head2 _query_unit
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79
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80 Arg [1] : none
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81 Example : none
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82 Description: PRIVATE implementation of abstract superclass method. Returns
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83 1 as the 'unit' used for the query sequence.
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84 Returntype : int
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85 Exceptions : none
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86 Caller : Bio::EnsEMBL::BaseAlignFeature
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87 Status : Stable
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88
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89
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90 =cut
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91
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92 sub _query_unit {
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93 return 1;
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94 }
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95
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96 1;
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