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Bio::Map::MapI(3)     User Contributed Perl Documentation    Bio::Map::MapI(3)

NAME
       Bio::Map::MapI - Interface for describing Map objects in bioperl

SYNOPSIS
	   # get a MapI somehow
	   my $name   = $map->name();	  # string
	   my $length = $map->length();	  # integer
	   my $species= $map->species;	  # Bio::Species
	   my $type   = $map->type();	  # genetic/sts/rh/

DESCRIPTION
       This object describes the basic functionality of a Map in bioperl.
       Maps are anything from Genetic Map to Sequence Map to Assembly Map to
       Restriction Enzyme to FPC.

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 - Jason Stajich
       Email jason@bioperl.org

CONTRIBUTORS
       Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-
       dot-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 _

   EntityI methods
	These are fundamental to coordination of Maps and other entities, so are
	implemented at the interface level

   get_position_handler
	Title	: get_position_handler
	Usage	: my $position_handler = $entity->get_position_handler();
	Function: Gets a PositionHandlerI that $entity is registered with.
	Returns : Bio::Map::PositionHandlerI object
	Args	: none

   PositionHandlerI-related methods
	These are fundamental to coordination of Maps and other entities, so are
	implemented at the interface level

   get_positions
	Title	: get_positions
	Usage	: my @positions = $mappable->get_positions();
	Function: Get all the Positions on this Map (sorted).
	Returns : Array of L<Bio::Map::PositionI> objects
	Args	: none for all, OR
		  L<Bio::Map::MappableI> object for positions of the given Mappable

   each_position
	Title	: each_position
	Function: Synonym of the get_positions() method.
	Status	: deprecated, will be removed in next version

   purge_positions
	Title	: purge_positions
	Usage	: $map->purge_position();
	Function: Remove all positions from this map. Notifies the positions they are
		  no longer on this map.
	Returns : n/a
	Args	: none to remove all positions, OR
		  L<Bio::Map::PositionI> object to remove just that Position, OR
			  L<Bio::Map::MappableI> object to remove only those positions of the
		  given mappable

   get_elements
	Title	: get_elements
	Usage	: my @elements = $map->get_elements;
	Function: Retrieves all the elements on a map (unordered)
	Returns : Array of Map elements (L<Bio::Map::MappableI>)
	Args	: none

   each_element
	Title	: each_element
	Function: Synonym of the get_elements() method.
	Status	: deprecated, will be removed in the next version

   common_elements
	Title	: common_elements
	Usage	: my @common_elements = $map->common_elements(\@other_maps);
		  my @common_elements = Bio::Map::SimpleMap->common_elements(\@maps);
	Function: Find the elements that are common to multiple maps.
	Returns : array of Bio::Map::MappableI
	Args	: arg #1 = L<Bio::Map::MapI> to compare this one to, or an array ref
			   of such objects (mandatory)
		  arg #2 = optionally, one or more of the key => value pairs below
		  -min_num => int	 : the minimum number of input maps an element
					   must be found on before before returned
					   [default is 1]
		  -min_percent => number : as above, but the minimum percentage of
					   input maps [default is 100 - note that this
					   will effectively override all other options]
		  -require_self => 1|0	 : require that all output elements at least
					   be on the calling map [default is 1, has no
					   effect when the second usage form is used]
		  -required => \@maps	 : require that all output elements be on at
					   least all the maps supplied here

   MapI-specific methods
   species
	Title	: species
	Usage	: my $species = $map->species;
	Function: Get/Set Species for a map
	Returns : L<Bio::Species> object
	Args	: (optional) Bio::Species

   units
	Title	: units
	Usage	: $map->units('cM');
	Function: Get/Set units for a map
	Returns : units for a map
	Args	: units for a map (string)

   type
	Title	: type
	Usage	: my $type = $map->type
	Function: Get/Set Map type
	Returns : String coding map type
	Args	: (optional) string

   name
	Title	: name
	Usage	: my $name = $map->name
	Function: Get/Set Map name
	Returns : Map name
	Args	: (optional) string

   length
	Title	: length
	Usage	: my $length = $map->length();
	Function: Retrieves the length of the map.
		  It is possible for the length to be unknown for maps such as
		  Restriction Enzyme, will return 0 in that case
	Returns : integer representing length of map in current units
		  will return undef if length is not calculateable
	Args	: none

perl v5.14.1			  2011-07-22		     Bio::Map::MapI(3)
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