Reference

Bio::Map::OrderedPositionWithDistance(3pm)

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.

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Chad Matsalla

Email [email protected]

CONTRIBUTORS

Lincoln Stein, [email protected] 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

History