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 listsReporting 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
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 levelget_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 : nonePositionHandlerI-related methods
These are fundamental to coordination of Mappables and other entities, so are
implemented at the interface leveladd_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> objectget_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 sortingeach_position
Title : each_position
Function: Synonym of the get_positions() method.
Status : deprecated, will be removed in next versionpurge_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
mapknown_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 : noneMappableI-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 setid
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 setin_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 Relativeoverlaps
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 Relativecontains
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 Relativeintersection
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
Relativeunion
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