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1 # $Id: MapI.pm,v 1.6 2002/10/22 07:45:15 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Map::MapI
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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::MapI - Interface for describing Map objects in bioperl
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16
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17 =head1 SYNOPSIS
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18
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19 # get a MapI somehowe
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20 my $name = $map->name(); # string
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21 my $length = $map->length(); # integer
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22 my $species= $map->species; # Bio::Species
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23 my $type = $map->type(); # genetic/sts/rh/
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24
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25 =head1 DESCRIPTION
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26
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27 This object describes the basic functionality of a Map in bioperl.
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28 Maps are anything from Genetic Map to Sequence Map to and Assembly Map
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29 to Restriction Enzyme to FPC.
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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 =head1 CONTRIBUTORS
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56
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57 Lincoln Stein, lstein@cshl.org
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58 Heikki Lehvaslaiho, heikki@ebi.ac.uk
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59
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60 =head1 APPENDIX
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61
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62 The rest of the documentation details each of the object methods.
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63 Internal methods are usually preceded with a _
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64
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65 =cut
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66
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67 # Let the code begin...
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68
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69 package Bio::Map::MapI;
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70 use vars qw(@ISA);
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71 use strict;
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72 use Bio::Root::RootI;
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73 use Carp;
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74
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75 @ISA = qw(Bio::Root::RootI);
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76
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77 =head2 species
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78
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79 Title : species
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80 Usage : my $species = $map->species;
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81 Function: Get/Set Species for a map
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82 Returns : L<Bio::Species> object
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83 Args : (optional) Bio::Species
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84
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85 =cut
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86
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87 sub species{
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88 my ($self) = @_;
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89 $self->throw_not_implemented();
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90 }
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91
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92 =head2 units
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93
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94 Title : units
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95 Usage : $map->units('cM');
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96 Function: Get/Set units for a map
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97 Returns : units for a map
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98 Args : units for a map (string)
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99
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100 =cut
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101
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102 sub units{
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103 my ($self) = @_;
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104 $self->throw_not_implemented();
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105 }
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106
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107 =head2 type
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108
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109 Title : type
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110 Usage : my $type = $map->type
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111 Function: Get/Set Map type
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112 Returns : String coding map type
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113 Args : (optional) string
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114
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115 =cut
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116
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117 sub type {
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118 my ($self) = @_;
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119 $self->throw_not_implemented();
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120 }
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121
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122 =head2 name
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123
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124 Title : name
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125 Usage : my $name = $map->name
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126 Function: Get/Set Map name
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127 Returns : Map name
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128 Args : (optional) string
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129
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130 =cut
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131
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132 sub name {
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133 my ($self) = @_;
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134 $self->throw_not_implemented();
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135 }
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136
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137 =head2 length
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138
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139 Title : length
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140 Usage : my $length = $map->length();
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141 Function: Retrieves the length of the map,
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142 It is possible for the length to be unknown
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143 for maps such as Restriction Enzyme, will return undef
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144 in that case
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145 Returns : integer representing length of map in current units
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146 will return undef if length is not calculateable
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147 Args : none
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148
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149 =cut
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150
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151 sub length{
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152 my ($self) = @_;
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153 $self->throw_not_implemented();
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154 }
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155
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156 =head2 unique_id
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157
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158 Title : unique_id
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159 Usage : my $id = $map->unique_id;
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160 Function: Get/Set the unique ID for this map
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161 Returns : a unique identifier
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162 Args : [optional] new identifier to set
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163
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164 =cut
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165
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166 sub unique_id{
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167 my ($self,$id) = @_;
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168 $self->throw_not_implemented();
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169 }
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170
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171 =head2 add_element
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172
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173 Title : add_element
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174 Usage : $map->add_element($marker)
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175 Function: Add a Bio::Map::MappableI object to the Map
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176 Returns : none
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177 Args : Bio::Map::MappableI object
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178
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179 =cut
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180
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181 sub add_element{
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182 my ($self) = @_;
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183 $self->throw_not_implemented();
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184 }
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185
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186 =head2 each_element
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187
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188 Title : each_element
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189 Usage : my @elements = $map->each_element;
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190 Function: Retrieves all the elements in a map
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191 unordered
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192 Returns : Array of Map elements (L<Bio::Map::MarkerI>)
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193 Args :
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194
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195
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196 =cut
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197
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198 sub each_element{
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199 my ($self) = @_;
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200 $self->throw_not_implemented();
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201 }
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202
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203 1;
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