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

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

NAME

       Bio::Map::OrderedPositionWithDistance - Abstracts the notion of a member      of an ordered list of markers. Each marker is a certain
       distance      from the one in the ordered list before it.

SYNOPSIS

	   use Bio::Map::OrderedPositionWithDistance;
	       # the first marker in the sequence
	   my $position = Bio::Map::OrderedPositionWithDistance->new(-positions => 1,
			       -distance => 22.3 );
	       # the second marker in the sequence, 15.6 units from the fist one
	   my $position2 = Bio::Map::OrderedPositionWithDistance->new(-positions => 2,
			       -distance => 15.6 );
	       # the third marker in the sequence, coincidental with the second
	       # marker
	   my $position3 = Bio::Map::OrderedPositionWithDistance->new(-positions => 3,
			       -distance => 0 );

DESCRIPTION

       This object is an implementation of the PositionI interface and the Position object handles the specific values of a position.
       OrderedPositionWithDistance is intended to be slightly more specific then Position but only specific enough for a parser from the MarkerIO
       subsystem to create and then pass to a client application to bless into the proper type. For an example of how this is intended to work,
       see the Mapmaker.pm.

       No units are assumed here - units are handled by context of which Map a position is placed in.

       Se Bio::Map::Position for additional information.

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 - Chad Matsalla
       Email bioinformatics1@dieselwurks.com

CONTRIBUTORS

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

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::OrderedPositionWithDistance->new();
	Function: Builds a new Bio::Map::OrderedPositionWithDistance object
	Returns : Bio::Map::OrderedPositionWithDistance
	Args	: -positions  - Should be a single value representing the order
	       of this marker within the list of markers
	       -distance - The distance this marker is from the marker before it.
		       0 reflects coincidentality.

   distance($new_distance)
	Title	: distance($new_distance)
	Usage	: $position->distance(new_distance) _or_
	       $position->distance()
	Function: get/set the distance of this position from the previous marker
	Returns : A scalar representing the current distance for this position.
	Args	: If $new_distance is provided the distance of this Position will
	       be set to $new_distance

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