Bio/Map/CytoMarker.pm

   1 #
   2 # BioPerl module for Bio::Map::CytoMarker
   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::CytoMarker - An object representing a marker.
  17
  18 =head1 SYNOPSIS
  19
  20   $o_usat = Bio::Map::CytoMarker->new(-name=>'Chad Super Marker 2',
  21                                  -position => $pos);
  22
  23 =head1 DESCRIPTION
  24
  25 This object handles markers with a positon in a cytogenetic map known.
  26 This marker will have a name and a position.
  27
  28 =head1 FEEDBACK
  29
  30 =head2 Mailing Lists
  31
  32 User feedback is an integral part of the evolution of this and other
  33 Bioperl modules. Send your comments and suggestions preferably to the
  34 Bioperl mailing list.  Your participation is much appreciated.
  35
  36   bioperl-l@bioperl.org                  - General discussion
  37   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  38
  39 =head2 Support
  40
  41 Please direct usage questions or support issues to the mailing list:
  42
  43 I<bioperl-l@bioperl.org>
  44
  45 rather than to the module maintainer directly. Many experienced and
  46 reponsive experts will be able look at the problem and quickly
  47 address it. Please include a thorough description of the problem
  48 with code and data examples if at all possible.
  49
  50 =head2 Reporting Bugs
  51
  52 Report bugs to the Bioperl bug tracking system to help us keep track
  53 of the bugs and their resolution. Bug reports can be submitted via the
  54 web:
  55
  56   https://redmine.open-bio.org/projects/bioperl/
  57
  58 =head1 AUTHOR - Heikki Lehvaslaiho
  59
  60 Email heikki-at-bioperl-dot-org
  61
  62 =head1 CONTRIBUTORS
  63
  64 Chad Matsalla      bioinformatics1@dieselwurks.com
  65 Lincoln Stein      lstein@cshl.org
  66 Jason Stajich      jason@bioperl.org
  67 Sendu Bala         bix@sendu.me.uk
  68
  69 =head1 APPENDIX
  70
  71 The rest of the documentation details each of the object methods.
  72 Internal methods are usually preceded with a _
  73
  74 =cut
  75
  76 # Let the code begin...
  77
  78 package Bio::Map::CytoMarker;
  79 use strict;
  80 use Bio::Map::CytoPosition;
  81
  82 use base qw(Bio::Map::Marker);
  83
  84
  85 =head2 Bio::Map::MarkerI methods
  86
  87 =cut
  88
  89 =head2 get_position_object
  90
  91  Title   : get_position_class
  92  Usage   : my $position = $marker->get_position_object();
  93  Function: To get an object of the default Position class
  94            for this Marker. Subclasses should redefine this method.
  95            The Position returned needs to be a L<Bio::Map::PositionI> with
  96                    -element set to self.
  97  Returns : L<Bio::Map::PositionI>
  98  Args    : none for an 'empty' PositionI object, optionally
  99            Bio::Map::MapI and value string to set the Position's -map and -value
 100            attributes.
 101
 102 =cut
 103
 104 sub get_position_object {
 105    my ($self, $map, $value) = @_;
 106    $map ||= $self->default_map;
 107    if ($value) {
 108           $self->throw("Value better be scalar, not [$value]") unless ref($value) eq '';
 109    }
 110
 111    my $pos = Bio::Map::CytoPosition->new();
 112    $pos->map($map) if $map;
 113    $pos->value($value) if $value;
 114    $pos->element($self);
 115    return $pos;
 116 }
 117
 118
 119 =head2 Comparison methods
 120
 121 The numeric values for cutogeneic loctions go from the p tip of
 122 chromosome 1, down to the q tip and similarly throgh consecutive
 123 chromosomes, through X and end the the q tip of X. See
 124 L<Bio::Map::CytoPosition::cytorange> for more details.
 125
 126 =cut
 127
 128 =head2 New methods
 129
 130 =cut
 131
 132 =head2 get_chr
 133
 134  Title   : get_chr
 135  Usage   : my $mychr = $marker->get_chr();
 136  Function: Read only method for the  chromosome string of the location.
 137            A shortcut to $marker->position->chr().
 138  Returns : chromosome value
 139  Args    : [optional] new chromosome value
 140
 141 =cut
 142
 143 sub get_chr {
 144     my ($self) = @_;
 145     return unless $self->position;
 146     return $self->position->chr;
 147 }
 148
 149 1;
 150