Bio::Map::Position - A single position of a Marker in a Map
use Bio::Map::Position; my $position = new Bio::Map::Position(-map => $map, -marker => $marker -value => 100 );
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.
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Email jason@bioperl.org
Describe contact details here
Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki@ebi.ac.uk Chad Matsalla, bioinformatics1@dieselwurks.com
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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>
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>
Title : value Usage : my $pos = $position->value; Function: Get/Set the value for this postion Returns : scalar, value Args : [optional] new value to set
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
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.