Bio::Map::MapI.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Map::MapI - Interface for describing Map objects in bioperl

SYNOPSIS

     # get a MapI somehow
     my $name   = $map->name();     # string
     my $length = $map->length();   # integer
     my $species= $map->species;    # Bio::Species
     my $type   = $map->type();     # genetic/sts/rh/
 
 

DESCRIPTION

This object describes the basic functionality of a Map in bioperl. Maps are anything from Genetic Map to Sequence Map to Assembly Map to Restriction Enzyme to FPC.

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 - Jason Stajich

Email jason@bioperl.org

CONTRIBUTORS

Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-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 _

EntityI methods

  These are fundamental to coordination of Maps and other entities, so are
  implemented at the interface level
 
 

get_position_handler

  Title   : get_position_handler
  Usage   : my $position_handler = $entity->get_position_handler();
  Function: Gets a PositionHandlerI that $entity is registered with.
  Returns : Bio::Map::PositionHandlerI object
  Args    : none
 
 
  These are fundamental to coordination of Maps and other entities, so are
  implemented at the interface level
 
 

get_positions

  Title   : get_positions
  Usage   : my @positions = $mappable->get_positions();
  Function: Get all the Positions on this Map (sorted).
  Returns : Array of L<Bio::Map::PositionI> objects
  Args    : none for all, OR
            L<Bio::Map::MappableI> object for positions of the given Mappable
 
 

each_position

  Title   : each_position
  Function: Synonym of the get_positions() method.
  Status  : deprecated, will be removed in next version
 
 

purge_positions

  Title   : purge_positions
  Usage   : $map->purge_position();
  Function: Remove all positions from this map. Notifies the positions they are
            no longer on this map.
  Returns : n/a
  Args    : none to remove all positions, OR
            L<Bio::Map::PositionI> object to remove just that Position, OR
                    L<Bio::Map::MappableI> object to remove only those positions of the
            given mappable
 
 

get_elements

  Title   : get_elements
  Usage   : my @elements = $map->get_elements;
  Function: Retrieves all the elements on a map (unordered)
  Returns : Array of Map elements (L<Bio::Map::MappableI>)
  Args    : none
 
 

each_element

  Title   : each_element
  Function: Synonym of the get_elements() method.
  Status  : deprecated, will be removed in the next version
 
 

common_elements

  Title   : common_elements
  Usage   : my @common_elements = $map->common_elements(\@other_maps);
            my @common_elements = Bio::Map::SimpleMap->common_elements(\@maps);
  Function: Find the elements that are common to multiple maps.
  Returns : array of Bio::Map::MappableI
  Args    : arg #1 = L<Bio::Map::MapI> to compare this one to, or an array ref
                     of such objects (mandatory)
            arg #2 = optionally, one or more of the key => value pairs below
            -min_num => int        : the minimum number of input maps an element
                                     must be found on before before returned
                                     [default is 1]
            -min_percent => number : as above, but the minimum percentage of
                                     input maps [default is 100 - note that this
                                     will effectively override all other options]
            -require_self => 1|0   : require that all output elements at least
                                     be on the calling map [default is 1, has no
                                     effect when the second usage form is used]
            -required => \@maps    : require that all output elements be on at
                                     least all the maps supplied here
 
 

MapI-specific methods

species

  Title   : species
  Usage   : my $species = $map->species;
  Function: Get/Set Species for a map
  Returns : L<Bio::Species> object
  Args    : (optional) Bio::Species
 
 

units

  Title   : units
  Usage   : $map->units('cM');
  Function: Get/Set units for a map
  Returns : units for a map
  Args    : units for a map (string)
 
 

type

  Title   : type
  Usage   : my $type = $map->type
  Function: Get/Set Map type
  Returns : String coding map type
  Args    : (optional) string
 
 

name

  Title   : name
  Usage   : my $name = $map->name
  Function: Get/Set Map name
  Returns : Map name
  Args    : (optional) string
 
 

length

  Title   : length
  Usage   : my $length = $map->length();
  Function: Retrieves the length of the map. 
            It is possible for the length to be unknown for maps such as
            Restriction Enzyme, will return 0 in that case
  Returns : integer representing length of map in current units
            will return undef if length is not calculateable
  Args    : none