#
# BioPerl module for Bio::Map::MappableI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Map::MappableI - An object that can be placed in a map
=head1 SYNOPSIS
# do not use this module directly
# See Bio::Map::Mappable for an example of
# implementation.
=head1 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.
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
=head1 CONTRIBUTORS
Heikki Lehvaslaiho heikki-at-bioperl-dot-org
Lincoln Stein lstein@cshl.org
Sendu Bala bix@sendu.me.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Map::MappableI;
use strict;
use Bio::Map::PositionHandler;
use base qw(Bio::Map::EntityI Bio::AnnotatableI);
=head2 EntityI methods
These are fundamental to coordination of Mappables and other entities, so are
implemented at the interface level
=cut
=head2 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
=cut
sub get_position_handler {
my $self = shift;
unless (defined $self->{_eh}) {
my $ph = Bio::Map::PositionHandler->new(-self => $self);
$self->{_eh} = $ph;
$ph->register;
}
return $self->{_eh};
}
=head2 PositionHandlerI-related methods
These are fundamental to coordination of Mappables and other entities, so are
implemented at the interface level
=cut
=head2 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
=cut
sub add_position {
my $self = shift;
# actually, we allow multiple positions to be set at once
$self->get_position_handler->add_positions(@_);
}
=head2 get_positions
Title : get_positions
Usage : my @positions = $mappable->get_positions();
Function: Get all the Positions of this Mappable (sorted).
Returns : Array of L<Bio::Map::PositionI> objects
Args : none for all, OR
L<Bio::Map::MapI> object for positions on the given map, AND/OR some
other true value to avoid sorting
=cut
sub get_positions {
my ($self, $thing, $no_sort) = @_;
my $map;
if (ref($thing) && $thing->isa('Bio::Map::MapI')) {
$map = $thing;
}
else {
$no_sort = $thing;
}
my @positions = $self->get_position_handler->get_positions($map);
return @positions if @positions == 1;
unless ($no_sort) {
# don't do
# @positions = sort { $a->sortable <=> $b->sortable } @positions;
# directly since sortable() can result in the call of another sort
# routine and cause problems; pre-compute sortable values instead
# (which is also more efficient)
@positions = map { $_->[1] }
sort { $a->[0] <=> $b->[0] }
map { [$_->sortable, $_] }
@positions;
}
return @positions;
}
=head2 each_position
Title : each_position
Function: Synonym of the get_positions() method.
Status : deprecated, will be removed in next version
=cut
*each_position = \&get_positions;
=head2 purge_positions
Title : purge_positions
Usage : $mappable->purge_positions();
Function: Remove positions from this mappable.
Returns : n/a
Args : none to remove all positions, OR
L<Bio::Map::PositionI> object to remove just that Position, OR
L<Bio::Map::MapI> object to remove only those positions on the given
map
=cut
sub purge_positions {
my ($self, $thing) = @_;
$self->get_position_handler->purge_positions($thing);
}
=head2 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
=cut
sub known_maps {
my $self = shift;
return $self->get_position_handler->get_other_entities;
}
=head2 MappableI-specific methods
=cut
=head2 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
=cut
sub name {
my $self = shift;
$self->throw_not_implemented();
}
=head2 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
=cut
sub id {
my $self = shift;
$self->throw_not_implemented();
}
=head2 in_map
Title : in_map
Usage : if ($marker->in_map($map)) {...}
Function: Tests if this mappable is found on a specific map
Returns : boolean
Args : L<Bio::Map::MapI>
=cut
sub in_map {
my $self = shift;
$self->throw_not_implemented();
}
=head1 RangeI-related Methods
They throw an error if start and end are not defined in the Positions of the
Mappables supplied.
=cut
=head2 equals
Title : equals
Usage : if ($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
=cut
sub equals {
my $self = shift;
$self->throw_not_implemented();
}
=head2 overlaps
Title : overlaps
Usage : if ($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
=cut
sub overlaps {
my $self = shift;
$self->throw_not_implemented();
}
=head2 contains
Title : contains
Usage : if ($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
=cut
sub contains {
my $self = shift;
$self->throw_not_implemented();
}
=head2 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
=cut
sub intersection {
my $self = shift;
$self->throw_not_implemented();
}
=head2 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
=cut
sub union {
my $self = shift;
$self->throw_not_implemented();
}
1;