Man pages sections > man3 > Bio::Map::CytoMarker

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

Bio::Map::CytoMarker(3pm) User Contributed Perl Documentation Bio::Map::CytoMarker(3pm)


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


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


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


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AUTHOR - Heikki Lehvaslaiho

Email heikki-at-bioperl-dot-org


Chad Matsalla Lincoln Stein Jason Stajich Sendu Bala


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

Bio::Map::MarkerI methods


 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

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


 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
2017-08-30 perl v5.26.0