Provided by: libbio-perl-perl_1.6.901-2_all bug

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