bionic (3) Bio::Map::CytoMap.3pm.gz

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:

         https://github.com/bioperl/bioperl-live/issues

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