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1 # $Id: PositionI.pm,v 1.8 2002/10/22 07:45:16 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Map::PositionI
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4 #
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5 # Cared for by Jason Stajich <jason@bioperl.org>
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6 #
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7 # Copyright Jason Stajich
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::Map::PositionI - Abstracts the notion of a position having
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16 a value in the context of a marker and a Map
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17
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18 =head1 SYNOPSIS
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19
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20 # do not use directly
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21
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22 =head1 DESCRIPTION
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23
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24 This object stores one of the postions a that a mappable object
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25 (e.g. Marker) may have in a map (e.g. restriction enzymes or a SNP
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26 mapped to several chromosomes).
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27
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28 The method numeric() returns the position in a form that can be
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29 compared between other positions of the same type.
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30
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31 =head1 FEEDBACK
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32
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33 =head2 Mailing Lists
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34
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35 User feedback is an integral part of the evolution of this and other
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36 Bioperl modules. Send your comments and suggestions preferably to
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37 the Bioperl mailing list. Your participation is much appreciated.
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38
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39 bioperl-l@bioperl.org - General discussion
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40 http://bioperl.org/MailList.shtml - About the mailing lists
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41
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42 =head2 Reporting Bugs
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43
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44 Report bugs to the Bioperl bug tracking system to help us keep track
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45 of the bugs and their resolution. Bug reports can be submitted via
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46 email or the web:
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47
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48 bioperl-bugs@bioperl.org
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49 http://bugzilla.bioperl.org/
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50
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51 =head1 AUTHOR - Jason Stajich
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52
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53 Email jason@bioperl.org
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54
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55 Describe contact details here
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56
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57 =head1 CONTRIBUTORS
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58
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59 Lincoln Stein, lstein@cshl.org
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60 Heikki Lehvaslaiho, heikki@ebi.ac.uk
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61
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62 =head1 APPENDIX
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63
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64 The rest of the documentation details each of the object methods.
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65 Internal methods are usually preceded with a _
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66
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67 =cut
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68
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69
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70 # Let the code begin...
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71
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72
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73 package Bio::Map::PositionI;
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74 use vars qw(@ISA);
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75 use strict;
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76 use Bio::Root::RootI;
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77 use Carp;
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78
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79 @ISA = qw(Bio::Root::RootI);
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80
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81
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82 =head2 map
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83
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84 Title : map
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85 Usage : my $id = map->$map;
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86 Function: Get/Set the map the position is in.
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87 Returns : L<Bio::Map::MapI>
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88 Args : [optional] new L<Bio::Map::MapI>
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89
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90 =cut
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91
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92 sub map {
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93 my ($self, $value) = @_;
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94 $self->throw_not_implemented();
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95 }
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96
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97 =head2 marker
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98
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99 Title : marker
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100 Usage : my $id = marker->$marker;
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101 Function: Get/Set the marker the position is in.
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102 Returns : L<Bio::Map::MarkerI>
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103 Args : [optional] new L<Bio::Map::MarkerI>
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104
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105 =cut
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106
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107 sub marker {
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108 my ($self, $value) = @_;
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109 $self->throw_not_implemented();
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110 }
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111
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112
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113 =head2 value
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114
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115 Title : value
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116 Usage : my $pos = $position->value;
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117 Function: Get/Set the value for this position
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118 Returns : scalar, value
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119 Args : [optional] new value to set
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120
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121 =cut
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122
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123 sub value {
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124 my ($self, $value) = @_;
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125 $self->throw_not_implemented();
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126 }
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127
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128 =head2 numeric
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129
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130 Title : numeric
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131 Usage : my $num = $position->numeric;
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132 Function: Read-only method that is guarantied to return
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133 representation for this position that can be compared with others
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134 Returns : numeric (int, real or range)
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135 Args : none
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136
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137 =cut
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138
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139 sub numeric {
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140 my ($self) = @_;
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141 $self->throw_not_implemented();
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142 }
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143
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144 1;
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