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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::ProjectionSegment - part of the list that is returned from
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24 project function calls
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25
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26 =head1 SYNOPSIS
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27
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28 $slice =
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29 $sa->fetch_by_region( 'chromosome', 'X', 1_000_000, 2_000_000 );
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30
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31 my $projection = $slice->project("clone");
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32
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33 foreach my $projection_segment (@$projection) {
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34 print( " from_start ", $projection_segment->from_start(), "\n" );
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35 print( " from_end ", $projection_segment->from_end(), "\n" );
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36 print( " to_Slice ",
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37 $projection_segment->to_Slice()->name(), "\n" );
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38 }
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39
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40 =head1 DESCRIPTION
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41
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42 The ProjectionSegment is a helper object to make the arrays returned by
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43 project more accessible. Instead of writing $segment->[0], $segment->[1]
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44 or $segment->[2] its possible to use the more descriptive notation of
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45 $segment->from_start(), $segement->from_end(), $segment->to_Slice().
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46
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47 =head1 METHODS
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48
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49 =cut
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50
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51 package Bio::EnsEMBL::ProjectionSegment;
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52
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53 #
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54 # WARNING: THIS CLASS IS REPRESENTED BY A BLESSED ARRAY REFERENCE
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55 # NOT A HASH REFERENCE
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56 #
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57
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58
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59
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60
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61
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62 =head2 from_start
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63
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64 Args : none
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65 Example : $coord_in_fetaure_start = $segment->from_start()
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66 Description: First element in projects returned segment lists
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67 Returntype : int
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68 Exceptions : none
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69 Caller : general
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70 Status : Stable
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71
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72 =cut
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73
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74 sub from_start {
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75 my $self = shift;
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76 return $self->[0];
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77 }
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78
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79
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80
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81 =head2 from_end
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82
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83 Args : none
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84 Example : $coord_in_feature_end = $segment->from_end()
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85 Description: Second element in projects returned segment lists
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86 Returntype : int
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87 Exceptions : none
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88 Caller : general
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89 Status : Stable
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90
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91 =cut
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92
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93 sub from_end {
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94 my $self = shift;
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95 return $self->[1];
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96 }
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97
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98
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99
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100
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101 =head2 to_Slice
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102
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103 Args : none
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104 Example : $target_slice = $segment->to_Slice()
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105 Description: Third element in projects returned segment lists
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106 Returntype : Bio::EnsEMBL::Slice
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107 Exceptions : none
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108 Caller : general
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109 Status : Stable
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110
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111 =cut
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112
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113 sub to_Slice {
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114 my $self = shift;
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115 return $self->[2];
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116 }
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117
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118
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119
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120 1;
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