Bio/Map/CytoMap.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Map::CytoMap
   4 #
   5 # Cared for by Sendu Bala <bix@sendu.me.uk>
   6 #
   7 # Copyright Heikki Lehvaslaiho
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::Map::CytoMap - A Bio::MapI compliant map implementation handling cytogenic bands
  16
  17 =head1 SYNOPSIS
  18
  19     use Bio::Map::CytoMap;
  20     my $map = Bio::Map::CytoMap->new(-name => 'human1',
  21                                       -species => $human);
  22     foreach my $marker ( @markers ) { # get a list of markers somewhere
  23         $map->add_element($marker);
  24     }
  25
  26 =head1 DESCRIPTION
  27
  28 This is the simple implementation of cytogenetic maps based on
  29 L<Bio::Map::MapI>.  It handles the essential storage of name, species,
  30 type, and units as well as in memory representation of the elements of
  31 a map.
  32
  33 For CytoMaps type is hard coded to be 'cytogeneticmap' and
  34 units are set to '' but can be set to something else.
  35
  36 =head1 FEEDBACK
  37
  38 =head2 Mailing Lists
  39
  40 User feedback is an integral part of the evolution of this and other
  41 Bioperl modules. Send your comments and suggestions preferably to
  42 the Bioperl mailing list.  Your participation is much appreciated.
  43
  44   bioperl-l@bioperl.org                  - General discussion
  45   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  46
  47 =head2 Reporting Bugs
  48
  49 Report bugs to the Bioperl bug tracking system to help us keep track
  50 of the bugs and their resolution. Bug reports can be submitted via the
  51 web:
  52
  53   http://bugzilla.open-bio.org/
  54
  55 =head1 AUTHOR - Heikki Lehvaslaiho
  56
  57 Email heikki-at-bioperl-dot-org
  58
  59 =head1 CONTRIBUTORS
  60
  61 Jason Stajich      jason@bioperl.org
  62 Lincoln Stein      lstein@cshl.org
  63 Sendu Bala         bix@sendu.me.uk
  64
  65 =head1 APPENDIX
  66
  67 The rest of the documentation details each of the object methods.
  68 Internal methods are usually preceded with a _
  69
  70 =cut
  71
  72 package Bio::Map::CytoMap;
  73 use vars qw($MAPCOUNT);
  74 use strict;
  75
  76
  77 use base qw(Bio::Map::SimpleMap);
  78 BEGIN { $MAPCOUNT = 1; }
  79
  80 =head2 new
  81
  82  Title   : new
  83  Usage   : my $obj = Bio::Map::CytoMap->new();
  84  Function: Builds a new Bio::Map::CytoMap object
  85  Returns : Bio::Map::CytoMap
  86  Args    : -name    => name of map (string)
  87            -species => species for this map (Bio::Species) [optional]
  88            -elements=> elements to initialize with
  89                        (arrayref of Bio::Map::MappableI objects) [optional]
  90
  91            -uid     => Unique Id
  92
  93 =cut
  94
  95 sub new {
  96     my ($class, @args) = @_;
  97
  98     my $self = $class->SUPER::new(@args);
  99
 100     $self->{'_uid'} = $MAPCOUNT++;
 101     my ($uid) = $self->_rearrange([qw(UID)], @args);
 102     defined $uid && $self->unique_id($uid);
 103
 104     return $self;
 105 }
 106
 107 =head2 type
 108
 109  Title   : type
 110  Usage   : my $type = $map->type
 111  Function: Get hard-coded Map type
 112  Returns : String coding Map type (always 'cyto')
 113  Args    : none
 114
 115 =cut
 116
 117 sub type {
 118    return 'cyto';
 119 }
 120
 121 =head2 length
 122
 123  Title   : length
 124  Usage   : my $length = $map->length();
 125  Function: Retrieves the length of the map,
 126  Returns : 0 since length is not calculatable for cytogenetic maps
 127  Args    : none
 128
 129 =cut
 130
 131 sub length {
 132    return 0;
 133 }
 134
 135 1;