- AUTHOR - Chad Matsalla
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
Lincoln Stein, email@example.com 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_ $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