Bio::Map::OrderedPosition.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Map::OrderedPosition - 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.

SYNOPSIS

     use Bio::Map::OrderedPosition;
         # the first marker in the sequence
     my $position = Bio::Map::OrderedPosition->new(-order => 1,
                         -positions => [ [ $map, 22.3] ] );
         # the second marker in the sequence, 15.6 units from the fist one
     my $position2 = Bio::Map::OrderedPosition->new(-order => 2,
                         -positions => [ [ $map, 37.9] ] );
         # the third marker in the sequence, coincidental with the second
         # marker
     my $position3 = Bio::Map::OrderedPosition->new(-order => 3,
                         -posititions => [ [ $map, 37.9]] );
 
 

DESCRIPTION

This object is an implementation of the PositionI interface and the Position object handles the specific values of a position. OrderedPosition 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.

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/wiki/Mailing_lists  - About the mailing lists
 
 

Support

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 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 the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Chad Matsalla

Email bioinformatics1@dieselwurks.com

CONTRIBUTORS

Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Jason Stajich, jason@bioperl.org Sendu Bala, bix@sendu.me.uk

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 = Bio::Map::OrderedPosition->new();
  Function: Builds a new Bio::Map::OrderedPosition object 
  Returns : Bio::Map::OrderedPosition
  Args    : -order : The order of this position
 
 

order

  Title   : order
  Usage   : $o_position->order($new_order);
            my $order = $o_position->order();
  Function: Get/set the order position of this position in a map.
  Returns : int, the order of this position
  Args    : none to get, OR int to set
 
 

sortable

  Title   : sortable
  Usage   : my $num = $position->sortable();
  Function: Read-only method that is guaranteed to return a value suitable
            for correctly sorting this kind of position amongst other positions
            of the same kind on the same map. Note that sorting different kinds
            of position together is unlikely to give sane results.
  Returns : numeric
  Args    : none
 
 

equals

  Title   : equals
  Usage   : if ($mappable->equals($mapable2)) {...}
  Function: Test if a position is equal to another position.
  Returns : boolean
  Args    : Bio::Map::PositionI
 
 

less_than

  Title   : less_than
  Usage   : if ($mappable->less_than($m2)) {...}
  Function: Tests if a position is less than another position
            It is assumed that 2 positions are in the same map.
  Returns : boolean
  Args    : Bio::Map::PositionI
 
 

greater_than

  Title   : greater_than
  Usage   : if ($mappable->greater_than($m2)) {...}
  Function: Tests if position is greater than another position.
            It is assumed that 2 positions are in the same map.
  Returns : boolean
  Args    : Bio::Map::PositionI