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1 # $Id: MappableI.pm,v 1.9 2002/10/22 07:45:15 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Map::MappableI
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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::MappableI - An object that can be placed in a map
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16
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17 =head1 SYNOPSIS
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18
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19 # get a Bio::Map::MappableI somehow
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20 my $position = $element->map_position();
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21 # these methods will be important for building sorted lists
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22 if( $position->equals($p2) ) {
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23 # do something
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24 } elsif( $position->less_tha($p2) ) {}
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25 elsif( $position->greater_than($p2) ) { }
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26
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27
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28 =head1 DESCRIPTION
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29
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30 This object handles the generic notion of an element placed on a
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31 (linear) Map. Elements can have multiple positions in a map such as
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32 is the case of Restriction enzyme cut sites on a sequence map. For
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33 exact information about an element's position in a map one must query
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34 the associate PositionI object which is accessible through the
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35 position() method.
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36
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37 =head1 FEEDBACK
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38
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39 =head2 Mailing Lists
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40
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41 User feedback is an integral part of the evolution of this and other
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42 Bioperl modules. Send your comments and suggestions preferably to
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43 the Bioperl mailing list. Your participation is much appreciated.
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44
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45 bioperl-l@bioperl.org - General discussion
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46 http://bioperl.org/MailList.shtml - About the mailing lists
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47
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48 =head2 Reporting Bugs
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49
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50 Report bugs to the Bioperl bug tracking system to help us keep track
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51 of the bugs and their resolution. Bug reports can be submitted via
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52 email or the web:
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53
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54 bioperl-bugs@bioperl.org
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55 http://bugzilla.bioperl.org/
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56
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57 =head1 AUTHOR - Jason Stajich
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58
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59 Email jason@bioperl.org
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60
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61 =head1 CONTRIBUTORS
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62
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63 Heikki Lehvaslaiho heikki@ebi.ac.uk
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64 Lincoln Stein lstein@cshl.org
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65
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66 =head1 APPENDIX
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67
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68 The rest of the documentation details each of the object methods.
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69 Internal methods are usually preceded with a _
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70
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71 =cut
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72
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73
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74 # 'Let the code begin...
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75
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76
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77 package Bio::Map::MappableI;
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78 use vars qw(@ISA);
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79 use strict;
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80 use Bio::Root::RootI;
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81 use Carp;
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82
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83 @ISA = qw(Bio::Root::RootI);
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84
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85 =head2 position
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86
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87 Title : position
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88 Usage : my $position = $mappable->position();
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89 Function: Get/Set the Bio::Map::PositionI for a mappable element
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90 Returns : Bio::Map::PositionI
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91 Args : (optional) Bio::Map::PositionI
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92
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93 =cut
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94
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95 sub position{
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96 my ($self,@args) = @_;
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97 $self->throw_not_implemented();
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98 }
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99
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100 =head2 equals
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101
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102 Title : equals
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103 Usage : if( $mappable->equals($mapable2)) ...
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104 Function: Test if a position is equal to another position
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105 Returns : boolean
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106 Args : Bio::Map::MappableI or Bio::Map::PositionI
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107
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108 =cut
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109
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110 sub equals{
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111 my ($self,@args) = @_;
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112 $self->throw_not_implemented();
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113 }
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114
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115 =head2 less_than
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116
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117 Title : less_than
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118 Usage : if( $mappable->less_than($m2) ) ...
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119 Function: Tests if a position is less than another position
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120 Returns : boolean
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121 Args : Bio::Map::MappableI or Bio::Map::PositionI
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122
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123 =cut
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124
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125 sub less_than{
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126 my ($self,@args) = @_;
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127 $self->throw_not_implemented();
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128 }
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129
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130 =head2 greater_than
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131
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132 Title : greater_than
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133 Usage : if( $mappable->greater_than($m2) ) ...
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134 Function: Tests if position is greater than another position
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135 Returns : boolean
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136 Args : Bio::Map::MappableI or Bio::Map::PositionI
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137
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138 =cut
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139
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140 sub greater_than{
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141 my ($self,@args) = @_;
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142 $self->throw_not_implemented();
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143 }
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144
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145 1;
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