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

NAME

       Bio::Map::CytoMarker - An object representing a marker.

SYNOPSIS

         $o_usat = Bio::Map::CytoMarker->new(-name=>'Chad Super Marker 2',
                                        -position => $pos);

DESCRIPTION

       This object handles markers with a position in a cytogenetic map known.  This marker will have a name and
       a position.

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

       Chad Matsalla      bioinformatics1@dieselwurks.com Lincoln Stein      lstein@cshl.org Jason Stajich
       jason@bioperl.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 _

   Bio::Map::MarkerI methods
   get_position_object
        Title   : get_position_class
        Usage   : my $position = $marker->get_position_object();
        Function: To get an object of the default Position class
                  for this Marker. Subclasses should redefine this method.
                  The Position returned needs to be a L<Bio::Map::PositionI> with
                          -element set to self.
        Returns : L<Bio::Map::PositionI>
        Args    : none for an 'empty' PositionI object, optionally
                  Bio::Map::MapI and value string to set the Position's -map and -value
                  attributes.

   Comparison methods
       The numeric values for cutogeneic loctions go from the p tip of chromosome 1, down to the q tip and
       similarly throgh consecutive chromosomes, through X and end the the q tip of X. See
       Bio::Map::CytoPosition::cytorange for more details.

   New methods
   get_chr
        Title   : get_chr
        Usage   : my $mychr = $marker->get_chr();
        Function: Read only method for the  chromosome string of the location.
                  A shortcut to $marker->position->chr().
        Returns : chromosome value
        Args    : [optional] new chromosome value