Bio::Map::MappableI(3pm)				User Contributed Perl Documentation				  Bio::Map::MappableI(3pm)

NAME

       Bio::Map::MappableI - An object that can be placed in a map

SYNOPSIS

	   # do not use this module directly
	   # See Bio::Map::Mappable for an example of
	   # implementation.

DESCRIPTION

       This object handles the generic notion of an element placed on a (linear) Map. A Mappable can have multiple positions in multiple maps,
       such as is the case of Restriction enzyme cut sites on sequence maps. For exact information about a mappable's position in a map one must
       query the associate PositionI objects which are accessible through the get_positions() method.

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason@bioperl.org

CONTRIBUTORS

       Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein      lstein@cshl.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 Mappables 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 Mappables and other entities, so are
	implemented at the interface level

   add_position
	Title	: add_position
	Usage	: $mappable->add_position($position);
	Function: Add a position to this mappable (defining where on which map it is).
	Returns : n/a
	Args	: L<Bio::Map::PositionI> object

   get_positions
	Title	: get_positions
	Usage	: my @positions = $mappable->get_positions();
	Function: Get all the Positions of this Mappable (sorted).
	Returns : Array of L<Bio::Map::PositionI> objects
	Args	: none for all, OR
		  L<Bio::Map::MapI> object for positions on the given map, AND/OR some
		  other true value to avoid sorting

   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	: $mappable->purge_positions();
	Function: Remove positions from this mappable.
	Returns : n/a
	Args	: none to remove all positions, OR
		  L<Bio::Map::PositionI> object to remove just that Position, OR
			  L<Bio::Map::MapI> object to remove only those positions on the given
			  map

   known_maps
	Title	: known_maps
	Usage	: my @maps = $marker->known_maps()
	Function: Returns the maps that this mappable is found on
	Returns : Array of L<Bio::Map::MapI> objects
	Args	: none

   MappableI-specific methods
   name
	Title	: name
	Usage	: my $name = $marker->name();
		  $marker->name($new_name);
	Function: Get/Set the name for this Mappable.
	Returns : A scalar representing the current name of this Mappable
	Args	: none to get
		  string to set

   id
	Title	: id
	Usage	: my $id = $marker->id();
		  $marker->id($new_id);
	Function: Get/Set the id for this Mappable.
	Returns : A scalar representing the current id of this Mappable
	Args	: none to get
		  string to set

   in_map
	Title	: in_map
	Usage	: if ($marker->in_map($map)) {...}
	Function: Tests if this mappable is found on a specific map
	Returns : boolean
	Args	: L<Bio::Map::MapI>

RangeI-related Methods
       They throw an error if start and end are not defined in the Positions of the Mappables supplied.

   equals
	Title	: equals
	Usage	: if ($mappable->equals($other_mappable)) {...}
		  my @equal_positions = $mappable->equals($other_mappable);
	Function: Finds the positions in this mappable that are equal to any
		  comparison positions.
	Returns : array of L<Bio::Map::PositionI> objects
	Args	: arg #1 = L<Bio::Map::MappableI> OR L<Bio::Map::PositionI> to compare
			   this one to (mandatory)
		  arg #2 = optionally, the key => value pairs below
			  -map => Bio::Map::MapI	   : optionally a Map to only consider
							     positions on the given map
			  -relative => Bio::Map::RelativeI : optionally a Relative to ask if
												 the Positions equal in terms of
												 their relative position to the
												 thing described by that Relative

   overlaps
	Title	: overlaps
	Usage	: if ($mappable->overlaps($other_mappable)) {...}
		  my @overlapping_positions = $mappable->overlaps($other_mappable);
	Function: Finds the positions in this mappable that overlap with any
		  comparison positions.
	Returns : array of L<Bio::Map::PositionI> objects
	Args	: arg #1 = L<Bio::Map::MappableI> OR L<Bio::Map::PositionI> to compare
			   this one to (mandatory)
		  arg #2 = optionally, the key => value pairs below
			  -map => Bio::Map::MapI	   : optionally a Map to only consider
							     positions on the given map
			  -relative => Bio::Map::RelativeI : optionally a Relative to ask if
						     the Positions overlap in terms of
						     their relative position to the
						     thing described by that Relative

   contains
	Title	: contains
	Usage	: if ($mappable->contains($other_mappable)) {...}
		  my @container_positions = $mappable->contains($other_mappable);
	Function: Finds the positions in this mappable that contain any comparison
		  positions.
	Returns : array of L<Bio::Map::PositionI> objects
	Args	: arg #1 = L<Bio::Map::MappableI> OR L<Bio::Map::PositionI> to compare
			   this one to (mandatory)
		  arg #2 = optionally, the key => value pairs below
			  -map => Bio::Map::MapI	   : optionally a Map to only consider
							     positions on the given map
			  -relative => Bio::Map::RelativeI : optionally a Relative to ask if
						     the Positions contains in terms of
						     their relative position to the
						     thing described by that Relative

   intersection
	Title	: intersection
	Usage	: my $position = $mappable->intersection($other_mappable);
		  my $position = Bio::Map::Mappable->intersection(@mappables);
	Function: Make the position that is at the intersection of all positions of all
		  supplied mappables.
	Returns : L<Bio::Map::PositionI> object or undef (if not all positions overlap)
	Args	: arg #1 = L<Bio::Map::MappableI> OR L<Bio::Map::PositionI> to	compare
			   this one to, or an array ref of such objects (mandatory)
		  arg #2 = optionally, the key => value pairs below
			  -map => Bio::Map::MapI	   : optionally a Map to only consider
							     positions on the given map
			  -relative => Bio::Map::RelativeI : optionally a Relative to to ask
												 how the Positions intersect in
												 terms of their relative position
												 to the thing described by that
												 Relative

   union
	Title	: union
	Usage	: my $position = $mappable->union($other_mappable);
		  my $position = Bio::Map::Mappable->union(@mappables);
	Function: Make the minimal position that contains all of the positions of all
		  supplied mappables.
	Returns : L<Bio::Map::PositionI> object or undef (if not all positions overlap)
	Args	: arg #1 = L<Bio::Map::MappableI> OR L<Bio::Map::PositionI> to	compare
			   this one to, or an array ref of such objects (mandatory)
		  arg #2 = optionally, the key => value pairs below
			  -map => Bio::Map::MapI	   : optionally a Map to only consider
							     positions on the given map
			  -relative => Bio::Map::RelativeI : optionally a Relative to to ask
												 if the union of the Positions in
												 terms of their relative position
												 to the thing described by that
												 Relative

perl v5.14.2							    2012-03-02						  Bio::Map::MappableI(3pm)