Ewan Birney

NAME

Bio::Map::PositionI - Abstracts the notion of a position having a value in the context of a marker and a Map

SYNOPSIS

    # do not use directly

DESCRIPTION

This object stores one of the postions a that a mappable object (e.g. Marker) may have in a map (e.g. restriction enzymes or a SNP mapped to several chromosomes).

The method numeric() returns the position in a form that can be compared between other positions of the same type.

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://bioperl.org/bioperl-bugs/

AUTHOR - Jason Stajich

Email jason@bioperl.org

Describe contact details here

CONTRIBUTORS

Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki@ebi.ac.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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 position
 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 
           representation for this position that can be compared with others
 Returns : numeric (int, real or range)
 Args    : none