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1 # $Id: MarkerI.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::MarkerI
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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::MarkerI - Interface for basic marker functionality
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16
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17 =head1 SYNOPSIS
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18
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19 Give standard usage here
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20
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21 =head1 DESCRIPTION
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22
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23 Describe the interface here
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24
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25 =head1 FEEDBACK
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26
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27 =head2 Mailing Lists
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28
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29 User feedback is an integral part of the evolution of this and other
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30 Bioperl modules. Send your comments and suggestions preferably to
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31 the Bioperl mailing list. Your participation is much appreciated.
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32
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33 bioperl-l@bioperl.org - General discussion
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34 http://bioperl.org/MailList.shtml - About the mailing lists
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35
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36 =head2 Reporting Bugs
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37
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38 Report bugs to the Bioperl bug tracking system to help us keep track
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39 of the bugs and their resolution. Bug reports can be submitted via
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40 email or the web:
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41
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42 bioperl-bugs@bioperl.org
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43 http://bugzilla.bioperl.org/
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44
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45 =head1 AUTHOR - Jason Stajich
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46
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47 Email jason@bioperl.org
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48
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49 Describe contact details here
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50
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51 =head1 CONTRIBUTORS
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52
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53 Heikki Lehvaslaiho heikki@ebi.ac.uk
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54 Lincoln Stein lstein@cshl.org
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55 Jason Stajich jason@bioperl.org
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56 Chad Matsalla bioinformatics1@dieselwurks.com
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57
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58 =head1 APPENDIX
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59
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60 The rest of the documentation details each of the object methods.
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61 Internal methods are usually preceded with a _
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62
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63 =cut
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64
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65
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66 # Let the code begin...
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67
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68
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69 package Bio::Map::MarkerI;
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70 use vars qw(@ISA);
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71 use strict;
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72 use Bio::Map::MappableI;
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73
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74 @ISA = qw(Bio::Map::MappableI);
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75
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76 =head2 name($new_name)
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77
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78 Title : name($new_name)
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79 Usage : my $name = $o_usat->name($new_name) _or_
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80 my $name = $o_usat->name()
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81 Function: Get/Set the name for this Marker
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82 Returns : A scalar representing the current name of this Marker
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83 Args : If provided, the current name of this Marker
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84 will be set to $new_name.
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85
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86 =cut
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87
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88 sub name {
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89 my ($self) = @_;
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90 $self->throw_not_implemented();
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91 }
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92
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93 =head2 add_position
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94
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95 Title : add_position
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96 Usage : $position->add_position($map,'100')
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97 Function: Add a numeric or string position to the PositionI container
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98 Returns : none
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99 Args : Map - Reference to Bio::Map::MapI
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100 String or Numeric coding for a position on a map
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101
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102 =cut
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103
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104 sub add_position{
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105 my ($self,$map,$value) = @_;
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106 $self->throw_not_implemented();
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107 }
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108
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109
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110 =head2 each_position
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111
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112 Title : positions
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113 Usage : my @positions = $position->each_position_value('mapname');
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114 Function: Retrieve a list of positions coded as strings or ints
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115 Returns : Array of position values
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116 Args : none
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117
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118 =cut
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119
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120 sub each_position {
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121 my ($self,$mapname) = @_;
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122 $self->throw_not_implemented();
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123 }
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124
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125 =head2 purge_positions
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126
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127 Title : purge_positions
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128 Usage : $position->purge_positions
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129 Function: Remove all the position values stored for a Marker
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130 Returns : none
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131 Args : [optional] only purge values for a given map
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132
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133 =cut
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134
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135 sub purge_position_values{
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136 my ($self, $map) = @_;
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137 $self->throw_not_implemented();
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138 }
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139
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140 =head2 known_maps
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141
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142 Title : known_maps
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143 Usage : my @maps = $marker->known_maps
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144 Function: Returns the list of maps that this position has values for
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145 Returns : list of Bio::Map::MapI unique ids
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146 Args : none
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147
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148 =cut
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149
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150 sub known_maps{
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151 my ($self) = @_;
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152 $self->throw_not_implemented();
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153 }
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154
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155 =head2 in_map
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156
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157 Title : in_map
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158 Usage : if ( $position->in_map($map) ) {}
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159 Function: Tests if a position has values in a specific map
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160 Returns : boolean
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161 Args : a map unique id OR Bio::Map::MapI
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162
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163
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164 =cut
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165
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166 sub in_map{
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167 my ($self,@args) = @_;
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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 get_position_object
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172
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173 Title : get_position_class
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174 Usage : my $pos = $marker->get_position_object();
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175 Function: To get an object of the default Position class
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176 for this Marker. Subclasses should redefine this method.
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177 The Position needs to be L<Bio::Map::PositionI>.
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178 Returns : L<Bio::Map::PositionI>
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179 Args : none
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180
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181 =cut
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182
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183 sub get_position_object {
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184 my ($self) = @_;
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185 $self->throw_not_implemented();
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186 }
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187
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188
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189 =head2 tuple
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190
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191 Title : tuple
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192 Usage : ($me, $you) = $self->_tuple($compare)
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193 Function: Utility method to extract numbers and test for missing values.
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194 Makes writing subsequent tests easier.
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195 Returns : a tuple of values or ranges
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196 Args : Bio::Map::MappableI or Bio::Map::PositionI
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197
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198 =cut
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199
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200 sub tuple {
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201 my ($self,@args) = @_;
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202 $self->throw_not_implemented();
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203 }
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204
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205
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206 =head2 Bio::Map::MappableI methods
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207
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208 =cut
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209
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210
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211 =head2 position
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212
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213 Title : position
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214 Usage : my position_string = $position->position('mapname');
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215 Function: Get/Set method for single value positions.
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216 Gives a simplified interface when only one map and
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217 one position per marker is used.
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218 Returns : a position value
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219 Args : optional:
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220 Map - Reference to Bio::Map::MapI
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221 String or Numeric coding for a position on a map
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222
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223 =cut
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224
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225 sub position{
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226 my ($self,$map, $value) = @_;
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227 $self->throw_not_implemented();
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228 }
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229
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230 =head2 equals
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231
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232 Title : equals
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233 Usage : if( $mappable->equals($mapable2)) ...
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234 Function: Test if a position is equal to another position
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235 Returns : boolean
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236 Args : Bio::Map::MappableI
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237
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238 =head2 less_than
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239
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240 Title : less_than
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241 Usage : if( $mappable->less_than($m2) ) ...
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242 Function: Tests if a position is less than another position
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243 Returns : boolean
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244 Args : Bio::Map::MappableI
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245
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246 =head2 greater_than
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247
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248 Title : greater_than
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249 Usage : if( $mappable->greater_than($m2) ) ...
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250 Function: Tests if position is greater than another position
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251 Returns : boolean
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252 Args : Bio::Map::MappableI
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253
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254 =cut
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255
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256 1;
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