/ 
bioperl-1.4
/ Bio::Map::Position

NAME

Bio::Map::Position - A single position of a Marker in a Map

SYNOPSIS

    use Bio::Map::Position;
    my $position = new Bio::Map::Position(-map => $map, 
					  -marker => $marker
					  -value => 100
					  );

DESCRIPTION

This object is an implementation of the PositionI interface that handles the specific values of a position. This allows an element (e.g. Marker) to have multiple positions within a map and still be treated as a single entity.

This does not directly handle the concept of a relative map in which no known exact positions exist but markers are just ordered relative to one another - in that case arbitrary values must be assigned for position values.

No units are assumed here - units are handled by context of which Map a position is placed in or the subclass of this Position.

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://bugzilla.bioperl.org/

AUTHOR - Jason Stajich

Email jason@bioperl.org

Describe contact details here

CONTRIBUTORS

Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki@ebi.ac.uk Chad Matsalla, bioinformatics1@dieselwurks.com

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::Position();
Function: Builds a new Bio::Map::Position object 
Returns : Bio::Map::Position
Args    : -map     a <Bio::Map::MapI> object
          -marker  a <Bio::Map::MarkerI> object
          -value   string or number

map

Title   : map
Usage   : my $id = map->$map;
Function: Get/Set the map the position is in.
Returns : L<Bio::Map::MapI>
Args    : [optional] new L<Bio::Map::MapI>

marker

Title   : marker
Usage   : my $id = marker->$marker;
Function: Get/Set the marker the position is in.
Returns : L<Bio::Map::MarkerI>
Args    : [optional] new L<Bio::Map::MarkerI>

value

Title   : value
Usage   : my $pos = $position->value;
Function: Get/Set the value for this postion
Returns : scalar, value
Args    : [optional] new value to set

numeric

Title   : numeric
Usage   : my $num = $position->numeric;
Function: Read-only method that is guarantied to return a numeric 
          representation for this position. 
Returns : numeric (int or real) 
Args    : none