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1 # $Id: Taxonomy.pm,v 1.1 2002/11/19 00:36:47 kortsch Exp $
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2 #
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3 # BioPerl module for Bio::Taxonomy
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4 #
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5 # Cared for by Dan Kortschak
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6 #
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7 # You may distribute this module under the same terms as perl itself
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8
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9 # POD documentation - main docs before the code
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10
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11 =head1 NAME
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12
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13 Bio::Taxonomy - Conversion used bt the Taxonomy classes
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14
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15 =head1 SYNOPSIS
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16
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17 use Bio::Taxonomy;
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18
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19 =head1 DESCRIPTION
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20
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21 Provides methods for converting classifications into taxonomic
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22 structures.
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23
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24 =head1 CONTACT
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25
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26 Dan Kortschak email B<kortschak@rsbs.anu.edu.au>
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27
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28 =head1 APPENDIX
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29
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30 The rest of the documentation details each of the object
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31 methods. Internal methods are usually preceded with a _
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32
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33 =cut
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34
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35
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36 # code begins...
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37
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38
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39 package Bio::Taxonomy;
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40 use vars qw(@ISA);
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41 use strict;
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42
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43 # Object preamble - inherits from Bio::Root::Object
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44 use Bio::Root::Root;
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45
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46 @ISA = qw(Bio::Root::Root);
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47
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48
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49 =head2 new
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50
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51 Title : new
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52 Usage : my $obj = new Bio::Taxonomy();
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53 Function: Builds a new Bio::Taxonomy object
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54 Returns : Bio::Taxonomy
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55 Args : -method -> method used to decide classification
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56 (none|trust|lookup)
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57 -ranks -> what ranks are there
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58
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59 =cut
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60
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61
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62 sub new {
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63 my ($class,@args) = @_;
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64
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65 my $self = $class->SUPER::new(@args);
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66
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67 $self->{'_method'}='none';
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68 $self->{'_ranks'}=[];
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69 $self->{'_rank_hash'}={};
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70
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71 my ($method,$ranks,$order) = $self->_rearrange([qw(METHOD RANKS ORDER)], @args);
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72
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73 if ($method) {
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74 $self->method($method);
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75 }
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76
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77 if (defined $ranks &&
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78 (ref($ranks) eq "ARRAY") ) {
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79 $self->ranks(@$ranks);
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80 } else {
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81 # default ranks
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82 # I think these are in the right order, but not sure:
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83 # some parvorder|suborder and varietas|subspecies seem
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84 # to be at the same level - any taxonomists?
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85 # I don't expect that these will actually be used except as a way
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86 # to find what ranks there are in taxonomic use
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87 $self->ranks(('root',
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88 'superkingdom',
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89 'kingdom',
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90 'superphylum',
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91 'phylum',
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92 'subphylum',
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93 'superclass',
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94 'class',
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95 'subclass',
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96 'infraclass',
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97 'superorder',
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98 'order',
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99 'suborder',
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100 'parvorder',
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101 'infraorder',
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102 'superfamily',
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103 'family',
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104 'subfamily',
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105 'tribe',
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106 'subtribe',
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107 'genus',
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108 'subgenus',
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109 'species group',
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110 'species subgroup',
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111 'species',
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112 'subspecies',
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113 'varietas',
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114 'forma',
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115 'no rank'));
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116 }
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117
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118 return $self;
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119 }
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120
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121
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122 =head2 method
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123
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124 Title : method
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125 Usage : $obj = taxonomy->method($method);
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126 Function: set or return the method used to decide classification
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127 Returns : $obj
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128 Args : $obj
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129
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130 =cut
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131
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132
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133 sub method {
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134 my ($self,$value) = @_;
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135 if (defined $value && $value=~/none|trust|lookup/) {
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136 $self->{'_method'} = $value;
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137 }
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138 return $self->{'_method'};
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139 }
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140
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141
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142 =head2 classify
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143
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144 Title : classify
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145 Usage : @obj[][0-1] = taxonomy->classify($species);
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146 Function: return a ranked classification
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147 Returns : @obj of taxa and ranks as word pairs separated by "@"
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148 Args : Bio::Species object
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149
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150 =cut
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151
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152
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153 sub classify {
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154 my ($self,$value) = @_;
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155 my @ranks;
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156
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157 if (! $value->isa('Bio::Species') ) {
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158 $self->throw("Trying to classify $value which is not a Bio::Species object");
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159 }
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160
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161 my @classes=reverse($value->classification);
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162
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163 if ($self->method eq 'none') {
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164 for (my $i=0; $i < @classes-2; $i++) {
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165 ($ranks[$i][0],$ranks[$i][1])=($classes[$i],'no rank');
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166 }
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167 push @ranks,[$classes[-2],'genus'];
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168 push @ranks,[$value->binomial,'species'];
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169 } elsif ($self->method eq 'trust') {
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170 if (scalar(@classes)==scalar($self->ranks)) {
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171 for (my $i=0; $i < @classes; $i++) {
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172 if ($self->rank_of_number($i) eq 'species') {
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173 push @ranks,[$value->binomial,$self->rank_of_number($i)];
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174 } else {
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175 push @ranks,[$classes[$i],$self->rank_of_number($i)];
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176 }
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177 }
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178 } else {
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179 $self->throw("Species object and taxonomy object cannot be reconciled");
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180 }
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181 } elsif ($self->method eq 'lookup') {
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182 # this will lookup a DB for the rank of a taxon name
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183 # I imagine that some kind of Bio::DB class will be need to
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184 # be given to the taxonomy object to act as an DB interface
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185 # (I'm not sure how useful this is though - if you have a DB of
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186 # taxonomy - why would you be doing things this way?)
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187 $self->throw("Not yet implemented");
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188 }
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189
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190 return @ranks;
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191 }
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192
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193
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194 =head2 level_of_rank
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195
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196 Title : level_of_rank
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197 Usage : $obj = taxonomy->level_of_rank($obj);
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198 Function: returns the level of a rank name
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199 Returns : $obj
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200 Args : $obj
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201
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202 =cut
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203
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204
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205 sub level_of {
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206 my ($self,$value) = @_;
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207
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208 return $self->{'_rank_hash'}{$value};
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209 }
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210
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211
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212 =head2 rank_of_number
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213
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214 Title : rank_of_number
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215 Usage : $obj = taxonomy->rank_of_number($obj);
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216 Function: returns the rank name of a rank level
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217 Returns : $obj
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218 Args : $obj
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219
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220 =cut
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221
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222
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223 sub rank_of_number {
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224 my ($self,$value) = @_;
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225
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226 return ${$self->{'_ranks'}}[$value];
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227 }
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228
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229
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230 =head2 ranks
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231
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232 Title : ranks
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233 Usage : @obj = taxonomy->ranks(@obj);
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234 Function: set or return all ranks
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235 Returns : @obj
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236 Args : @obj
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237
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238 =cut
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239
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240
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241 sub ranks {
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242 my ($self,@value) = @_;
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243
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244 # currently this makes no uniqueness sanity check (this should be done)
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245 # I am think that adding a way of converting multiple 'no rank' ranks
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246 # to unique 'no rank #' ranks so that the level of a 'no rank' is
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247 # abstracted way from the user - I'm not sure of the vlaue of this
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248
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249 if (defined @value) {
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250 $self->{'_ranks'}=\@value;
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251 }
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252
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253 for (my $i=0; $i <= @{$self->{'_ranks'}}-1; $i++) {
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254 $self->{'_rank_hash'}{$self->{'_ranks'}[$i]}=$i unless $self->{'_ranks'}[$i] eq 'no rank';
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255 }
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256
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257 return @{$self->{'_ranks'}};
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258 }
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259
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260
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261 1;
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