branch-1-6/Bio/PopGen/MarkerI.pm

   1 # $Id $
   2 #
   3 # BioPerl module for Bio::PopGen::MarkerI
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Jason Stajich <jason@bioperl.org>
   8 #
   9 # Copyright Jason Stajich
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::PopGen::MarkerI - A Population Genetic conceptual marker
  18
  19 =head1 SYNOPSIS
  20
  21 # Get a Bio::PopGen::MarkerI somehow - like using a Bio::PopGen::Marker
  22
  23   my $name = $marker->name();            # marker name
  24   my $description = $marker->description(); # description
  25   my $type = $marker->type();            # coded type of the marker
  26   my $unique_id = $marker->unique_id;    # optional unique ID
  27
  28   my @alleles = $marker->get_Alleles();  # the known alleles
  29   my %allele_freqs = $marker->get_Allele_Frequencies(); # keys are marker names
  30                                          # vals are frequencies
  31                                          # may change to handle multiple populations
  32
  33
  34 =head1 DESCRIPTION
  35
  36 This is the basic interface for Markers which one can associate
  37 alleles with for calculating Theta and Pi.
  38
  39 =head1 FEEDBACK
  40
  41 =head2 Mailing Lists
  42
  43 User feedback is an integral part of the evolution of this and other
  44 Bioperl modules. Send your comments and suggestions preferably to
  45 the Bioperl mailing list.  Your participation is much appreciated.
  46
  47   bioperl-l@bioperl.org                  - General discussion
  48   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  49
  50 =head2 Support
  51
  52 Please direct usage questions or support issues to the mailing list:
  53
  54 I<bioperl-l@bioperl.org>
  55
  56 rather than to the module maintainer directly. Many experienced and
  57 reponsive experts will be able look at the problem and quickly
  58 address it. Please include a thorough description of the problem
  59 with code and data examples if at all possible.
  60
  61 =head2 Reporting Bugs
  62
  63 Report bugs to the Bioperl bug tracking system to help us keep track
  64 of the bugs and their resolution. Bug reports can be submitted via
  65 email or the web:
  66
  67   http://bugzilla.open-bio.org/
  68
  69 =head1 AUTHOR - Jason Stajich
  70
  71 Email jason-at-bioperl.org
  72
  73 =head1 CONTRIBUTORS
  74
  75 Matthew Hahn, matthew.hahn-at-duke.edu
  76
  77 =head1 APPENDIX
  78
  79 The rest of the documentation details each of the object methods.
  80 Internal methods are usually preceded with a _
  81
  82 =cut
  83
  84
  85 # Let the code begin...
  86
  87
  88 package Bio::PopGen::MarkerI;
  89 use strict;
  90
  91
  92 use base qw(Bio::Root::RootI Bio::AnnotatableI);
  93
  94
  95 =head2 name
  96
  97  Title   : name
  98  Usage   : my $name = $marker->name();
  99  Function: Get the name of the marker
 100  Returns : string representing the name of the marker
 101  Args    :
 102
 103
 104 =cut
 105
 106 sub name{
 107    $_[0]->throw_not_implemented();
 108 }
 109
 110
 111 =head2 description
 112
 113  Title   : description
 114  Usage   : my $desc = $marker->description
 115  Function: Get the marker description free text
 116  Returns : string
 117  Args    : [optional] string
 118
 119
 120 =cut
 121
 122 sub description{
 123     $_[0]->throw_not_implemented();
 124 }
 125
 126 =head2 type
 127
 128  Title   : type
 129  Usage   : my $type = $marker->type;
 130  Function: Get coded string for marker type
 131  Returns : string
 132  Args    : [optional] string
 133
 134
 135 =cut
 136
 137 sub type{
 138    my ($self) = @_;
 139    $self->throw_not_implemented();
 140 }
 141
 142
 143 =head2 unique_id
 144
 145  Title   : unique_id
 146  Usage   : my $id = $marker->unique_id;
 147  Function: Get the unique marker ID
 148  Returns : unique ID string
 149  Args    : [optional ] string
 150
 151
 152 =cut
 153
 154 sub unique_id{
 155    my ($self) = @_;
 156     $self->throw_not_implemented();
 157 }
 158
 159
 160 =head2 annotation
 161
 162  Title   : annotation
 163  Usage   : $obj->annotation($seq_obj)
 164  Function: retrieve the attached annotation object
 165  Returns : Bio::AnnotationCollectionI or none;
 166
 167 See L<Bio::AnnotationCollectionI> and L<Bio::Annotation::Collection>
 168 for more information. This method comes through extension from
 169 L<Bio::AnnotatableI>.
 170
 171
 172 =cut
 173
 174
 175 sub annotation{
 176    my ($self,@args) = @_;
 177    $self->throw_not_implemented();
 178 }
 179
 180
 181 =head2 get_Alleles
 182
 183  Title   : get_Alleles
 184  Usage   : my @alleles = $marker->get_Alleles();
 185  Function: Get the available marker alleles if they are known and stored
 186  Returns : Array of strings
 187  Args    : none
 188
 189
 190 =cut
 191
 192 sub get_Alleles{
 193    my ($self) = @_;
 194    $self->throw_not_implemented();
 195 }
 196
 197
 198 =head2 get_Allele_Frequencies
 199
 200  Title   : get_Allele_Frequencies
 201  Usage   : my %allele_freqs = $marker->get_Allele_Frequencies;
 202  Function: Get the alleles and their frequency (set relative to
 203            a given population - you may want to create different
 204            markers with the same name for different populations
 205            with this current implementation
 206  Returns : Associative array (hash) where keys are the names of the alleles
 207  Args    : none
 208
 209
 210 =cut
 211
 212 sub get_Allele_Frequencies{
 213    my ($self) = @_;
 214     $self->throw_not_implemented();
 215 }
 216
 217 1;