Bio/Map/CytoMap.pm

   1 #
   2 # BioPerl module for Bio::Map::CytoMap
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Sendu Bala <bix@sendu.me.uk>
   7 #
   8 # Copyright Heikki Lehvaslaiho
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::Map::CytoMap - A Bio::MapI compliant map implementation handling cytogenic bands
  17
  18 =head1 SYNOPSIS
  19
  20     use Bio::Map::CytoMap;
  21     my $map = Bio::Map::CytoMap->new(-name => 'human1',
  22                                       -species => $human);
  23     foreach my $marker ( @markers ) { # get a list of markers somewhere
  24         $map->add_element($marker);
  25     }
  26
  27 =head1 DESCRIPTION
  28
  29 This is the simple implementation of cytogenetic maps based on
  30 L<Bio::Map::MapI>.  It handles the essential storage of name, species,
  31 type, and units as well as in memory representation of the elements of
  32 a map.
  33
  34 For CytoMaps type is hard coded to be 'cytogeneticmap' and
  35 units are set to '' but can be set to something else.
  36
  37 =head1 FEEDBACK
  38
  39 =head2 Mailing Lists
  40
  41 User feedback is an integral part of the evolution of this and other
  42 Bioperl modules. Send your comments and suggestions preferably to
  43 the Bioperl mailing list.  Your participation is much appreciated.
  44
  45   bioperl-l@bioperl.org                  - General discussion
  46   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  47
  48 =head2 Support
  49
  50 Please direct usage questions or support issues to the mailing list:
  51
  52 I<bioperl-l@bioperl.org>
  53
  54 rather than to the module maintainer directly. Many experienced and
  55 reponsive experts will be able look at the problem and quickly
  56 address it. Please include a thorough description of the problem
  57 with code and data examples if at all possible.
  58
  59 =head2 Reporting Bugs
  60
  61 Report bugs to the Bioperl bug tracking system to help us keep track
  62 of the bugs and their resolution. Bug reports can be submitted via the
  63 web:
  64
  65   https://github.com/bioperl/bioperl-live/issues
  66
  67 =head1 AUTHOR - Heikki Lehvaslaiho
  68
  69 Email heikki-at-bioperl-dot-org
  70
  71 =head1 CONTRIBUTORS
  72
  73 Jason Stajich      jason@bioperl.org
  74 Lincoln Stein      lstein@cshl.org
  75 Sendu Bala         bix@sendu.me.uk
  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 package Bio::Map::CytoMap;
  85 use vars qw($MAPCOUNT);
  86 use strict;
  87
  88
  89 use base qw(Bio::Map::SimpleMap);
  90 BEGIN { $MAPCOUNT = 1; }
  91
  92 =head2 new
  93
  94  Title   : new
  95  Usage   : my $obj = Bio::Map::CytoMap->new();
  96  Function: Builds a new Bio::Map::CytoMap object
  97  Returns : Bio::Map::CytoMap
  98  Args    : -name    => name of map (string)
  99            -species => species for this map (Bio::Species) [optional]
 100            -elements=> elements to initialize with
 101                        (arrayref of Bio::Map::MappableI objects) [optional]
 102
 103            -uid     => Unique Id
 104
 105 =cut
 106
 107 sub new {
 108     my ($class, @args) = @_;
 109
 110     my $self = $class->SUPER::new(@args);
 111
 112     $self->{'_uid'} = $MAPCOUNT++;
 113     my ($uid) = $self->_rearrange([qw(UID)], @args);
 114     defined $uid && $self->unique_id($uid);
 115
 116     return $self;
 117 }
 118
 119 =head2 type
 120
 121  Title   : type
 122  Usage   : my $type = $map->type
 123  Function: Get hard-coded Map type
 124  Returns : String coding Map type (always 'cyto')
 125  Args    : none
 126
 127 =cut
 128
 129 sub type {
 130    return 'cyto';
 131 }
 132
 133 =head2 length
 134
 135  Title   : length
 136  Usage   : my $length = $map->length();
 137  Function: Retrieves the length of the map,
 138  Returns : 0 since length is not calculatable for cytogenetic maps
 139  Args    : none
 140
 141 =cut
 142
 143 sub length {
 144    return 0;
 145 }
 146
 147 1;