Bio::Map OrderedPositionWithDistance
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Summary
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.
Package variables
No package variables defined.
Inherit
Bio::Map::Position
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.
Methods
newDescriptionCode
distanceDescriptionCode
Methods description
newcode    nextTop
 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)codeprevnextTop
 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 $new_distance
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  $self->{'_positions'} = [];
  my ($positions,$distance) = $self->_rearrange([qw(POSITIONS DISTANCE)], @args);
  if( ref($positions) =~ /array/i ) { 
      foreach my $p ( @$positions ) {
	  $self->add_position($p);
      }
  } else { 
      $self->add_position($positions);
  }
	$distance && $self->distance($distance);
	
  return $self;
}
distancedescriptionprevnextTop
sub distance {
        my ($self,$distance) = @_;
        if ($distance) {
           $self->{'_distance'} = $distance;
        }
        return $self->{'_distance'};
}


1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Chad MatsallaTop
Email bioinformatics1@dieselwurks.com
CONTRIBUTORSTop
Lincoln Stein, lstein@cshl.org
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _