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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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.
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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_
$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