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Bio::Map::CytoMap.3pm

NAME

Bio::Map::CytoMap - A Bio::MapI compliant map implementation handling cytogenic bands

SYNOPSIS

     use Bio::Map::CytoMap;
     my $map = Bio::Map::CytoMap->new(-name => 'human1',
                                       -species => $human);
     foreach my $marker ( @markers ) { # get a list of markers somewhere
         $map->add_element($marker);
     }
 
 

DESCRIPTION

This is the simple implementation of cytogenetic maps based on Bio::Map::MapI. It handles the essential storage of name, species, type, and units as well as in memory representation of the elements of a map.

For CytoMaps type is hard coded to be 'cytogeneticmap' and units are set to '' but can be set to something else.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Heikki Lehvaslaiho

Email heikki-at-bioperl-dot-org

CONTRIBUTORS

Jason Stajich jason@bioperl.org Lincoln Stein lstein@cshl.org Sendu Bala bix@sendu.me.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

  Title   : new
  Usage   : my $obj = Bio::Map::CytoMap->new();
  Function: Builds a new Bio::Map::CytoMap object
  Returns : Bio::Map::CytoMap
  Args    : -name    => name of map (string)
            -species => species for this map (Bio::Species) [optional]
            -elements=> elements to initialize with
                        (arrayref of Bio::Map::MappableI objects) [optional]
 
            -uid     => Unique Id
 
 

type

  Title   : type
  Usage   : my $type = $map->type
  Function: Get hard-coded Map type
  Returns : String coding Map type (always 'cyto')
  Args    : none
 
 

length

  Title   : length
  Usage   : my $length = $map->length();
  Function: Retrieves the length of the map,
  Returns : 0 since length is not calculatable for cytogenetic maps
  Args    : none