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BioPerl-1.6.901
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Map::MappableI

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
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