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
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AUTHOR - Jason Stajich
Email [email protected]CONTRIBUTORS
Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein [email protected] Sendu Bala [email protected]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