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:

https://github.com/bioperl/bioperl-live/issues

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

PositionHandlerI-related methods

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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq