Ewan Birney

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 = new Bio::Map::OrderedPositionWithDistance(-positions => 1,
                        -distance => 22.3 );
        # the second marker in the sequence, 15.6 units from the fist one
    my $position2 = new Bio::Map::OrderedPositionWithDistance(-positions => 2,
                        -distance => 15.6 );
        # the third marker in the sequence, coincidental with the second
        # marker
    my $position3 = new Bio::Map::OrderedPositionWithDistance(-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/MailList.shtml  - About the mailing lists

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 email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

AUTHOR - Chad Matsalla

Email bioinformatics1@dieselwurks.com

CONTRIBUTORS

Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki@ebi.ac.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 = new Bio::Map::OrderedPositionWithDistance();
 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