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bio::map::markeri(3pm) [debian man page]

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

NAME

       Bio::Map::MarkerI - Interface for basic marker functionality

SYNOPSIS

	   # do not use this module directly
	   # See Bio::Map::Marker for an example of
	   # implementation.

DESCRIPTION

       A Marker is a Bio::Map::Mappable with some properties particular to markers.  It also offers a number of convienience methods to make
       dealing with map elements easier.

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason@bioperl.org

CONTRIBUTORS

       Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein      lstein@cshl.org Jason Stajich	  jason@bioperl.org Chad Matsalla
       bioinformatics1@dieselwurks.com 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 _

   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.

   position
	Title	: position
	Usage	: my $position = $mappable->position();
			  $mappable->position($position);
	Function: Get/Set the Position of this Marker (where it is on which map),
		  purging all other positions before setting.
	Returns : L<Bio::Map::PositionI>
	Args	: Bio::Map::PositionI
		   OR
		  Bio::Map::MapI AND
		  scalar
		   OR
		  scalar, but only if the marker has a default map

   positions
	Title	: positions
	Usage	: $marker->positions([$pos1, $pos2, $pos3]);
	Function: Add multiple Bio::Map::PositionI to this marker
	Returns : n/a
	Args	: array ref of $map/value tuples or array ref of Bio::Map::PositionI

   default_map
	Title	: default_map
	Usage	: my $map = $marker->default_map();
	Function: Get/Set the default map for the marker.
	Returns : L<Bio::Map::MapI>
	Args	: [optional] new L<Bio::Map::MapI>

   in_map
	Title	: in_map
	Usage	: if ( $marker->in_map($map) ) {}
	Function: Tests if this marker is found on a specific map
	Returns : boolean
	Args	: a map unique id OR Bio::Map::MapI

perl v5.14.2							    2012-03-02						    Bio::Map::MarkerI(3pm)

Check Out this Related Man Page

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

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 positon 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://redmine.open-bio.org/projects/bioperl/

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

perl v5.14.2							    2012-03-02						 Bio::Map::CytoMarker(3pm)
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