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14 non-PAUSE users.

Christopher Fields
and 1 contributors


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.


    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 );


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.


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AUTHOR - Chad Matsalla

Email bioinformatics1@dieselwurks.com


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


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 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.


 Title   : distance($new_distance)
 Usage   : $position->distance(new_distance) _or_
 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