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

NAME

       Bio::Map::Position - A single position of a Marker, or the range over which
			    that marker lies, in a Map

SYNOPSIS

	   use Bio::Map::Position;
	   my $position = Bio::Map::Position->new(-map => $map,
						 -element => $marker,
						 -value => 100
						 );

	       my $position_with_range = Bio::Map::Position->new(-map => $map,
						 -element => $marker,
						 -start => 100,
						 -length => 10
						 );

DESCRIPTION

       This object is an implementation of the PositionI interface that handles the specific values of a position. This allows a map element (e.g.
       Marker) to have multiple positions within a map and still be treated as a single entity.

       This handles the concept of a relative map in which the order of elements and the distance between them is known, but does not directly
       handle the case when distances are unknown - in that case arbitrary values must be assigned for position values.

       No units are assumed here - units are handled by context of which Map a position is placed in or the subclass of this 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 - Jason Stajich
       Email jason@bioperl.org

CONTRIBUTORS

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

   new
	Title	: new
	Usage	: my $obj = Bio::Map::Position->new();
	Function: Builds a new Bio::Map::Position object
	Returns : Bio::Map::Position
	Args	: -map	    => Bio::Map::MapI object
		  -element  => Bio::Map::MappableI object
		  -relative => Bio::Map::RelativeI object

		  * If this position has no range, or if a single value can describe
		    the range *
		  -value => scalar	       : something that describes the single
						 point position or range of this
						 Position, most likely an int

		  * Or if this position has a range, at least two of *
		  -start => int 	       : value of the start co-ordinate
		  -end => int		       : value of the end co-ordinate
		  -length => int	       : length of the range

   relative
	 Title	 : relative
	 Usage	 : my $relative = $position->relative();
		   $position->relative($relative);
	 Function: Get/set the thing this Position's coordinates (numerical(), start(),
		   end()) are relative to, as described by a Relative object.
	 Returns : Bio::Map::RelativeI (default is one describing "relative to the
		   start of the Position's map")
	 Args	 : none to get, OR
		   Bio::Map::RelativeI to set

   absolute
	 Title	 : absolute
	 Usage	 : my $absolute = $position->absolute();
		   $position->absolute($absolute);
	 Function: Get/set how this Position's co-ordinates (numerical(), start(),
		   end()) are reported. When absolute is off, co-ordinates are
		   relative to the thing described by relative(). Ie. the value
		   returned by start() will be the same as the value you set start()
		   to. When absolute is on, co-ordinates are converted to be relative
		   to the start of the map.

		   So if relative() currently points to a Relative object describing
		   "relative to another position which is 100 bp from the start of
		   the map", this Position's start() had been set to 50 and absolute()
		   returns 1, $position->start() will return 150. If absolute() returns
		   0 in the same situation, $position->start() would return 50.

	 Returns : boolean (default 0)
	 Args	 : none to get, OR
		   boolean to set

   value
	Title	: value
	Usage	: my $pos = $position->value;
	Function: Get/Set the value for this postion
	Returns : scalar, value
	Args	: [optional] new value to set

   numeric
	Title	: numeric
	Usage	: my $num = $position->numeric;
	Function: Read-only method that is guaranteed to return a numeric
		  representation of the start of this position.
	Returns : scalar numeric
	Args	: none to get the co-ordinate normally (see absolute() method), OR
		  Bio::Map::RelativeI to get the co-ordinate converted to be
		  relative to what this Relative describes.

   start
	 Title	 : start
	 Usage	 : my $start = $position->start();
		   $position->start($start);
	 Function: Get/set the start co-ordinate of this position.
	 Returns : the start of this position
	 Args	 : scalar numeric to set, OR
		   none to get the co-ordinate normally (see absolute() method), OR
		   Bio::Map::RelativeI to get the co-ordinate converted to be
		   relative to what this Relative describes.

   end
	 Title	 : end
	 Usage	 : my $end = $position->end();
		   $position->end($end);
	 Function: Get/set the end co-ordinate of this position.
	 Returns : the end of this position
	 Args	 : scalar numeric to set, OR
		   none to get the co-ordinate normally (see absolute() method), OR
		   Bio::Map::RelativeI to get the co-ordinate converted to be
		   relative to what this Relative describes.

   length
	 Title	 : length
	 Usage	 : $length = $position->length();
	 Function: Get/set the length of this position's range, changing the end() if
		   necessary. Getting and even setting the length will fail if both
		   start() and end() are not already defined.
	 Returns : the length of this range
	 Args	 : none to get, OR scalar numeric (>0) to set.

   sortable
	Title	: sortable
	Usage	: my $num = $position->sortable();
	Function: Read-only method that is guaranteed to return a value suitable
		  for correctly sorting this kind of position amongst other positions
		  of the same kind on the same map. Note that sorting different kinds
		  of position together is unlikely to give sane results.
	Returns : numeric
	Args	: none

   toString
	 Title	 : toString
	 Usage	 : print $position->toString(), "
";
	 Function: stringifies this range
	 Returns : a string representation of the range of this Position
	 Args	 : optional Bio::Map::RelativeI to have the co-ordinates reported
		   relative to the thing described by that Relative

   absolute_relative
	Title	: absolute_relative
	Usage	: my $rel = $position->absolute_relative();
	Function: Get a relative describing the start of the map. This is useful for
		  supplying to the coordinate methods (start(), end() etc.) to get
		  the temporary effect of having set absolute(1).
	Returns : Bio::Map::Relative
	Args	: none

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