#
# BioPerl module for Bio::LocationI
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# 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::LocationI - Abstract interface of a Location on a Sequence
=head1 SYNOPSIS
# get a LocationI somehow
printf( "start = %d, end = %d, strand = %s, seq_id = %s\n",
$location->start, $location->end, $location->strand,
$location->seq_id);
print "location str is ", $location->to_FTstring(), "\n";
=head1 DESCRIPTION
This Interface defines the methods for a Bio::LocationI, an object
which encapsulates a location on a biological sequence. Locations
need not be attached to actual sequences as they are stand alone
objects. LocationI objects are used by L<Bio::SeqFeatureI> objects to
manage and represent locations for a Sequence Feature.
=head1 FEEDBACK
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. 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
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-at-bioperl-dot-org
=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::LocationI;
use strict;
use Carp;
use base qw(Bio::RangeI);
=head2 location_type
Title : location_type
Usage : my $location_type = $location->location_type();
Function: Get location type encoded as text
Returns : string ('EXACT', 'WITHIN', 'IN-BETWEEN')
Args : none
=cut
sub location_type {
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 start
Title : start
Usage : $start = $location->start();
Function: Get the start coordinate of this location as defined by
the currently active coordinate computation policy. In
simple cases, this will return the same number as
min_start() and max_start(), in more ambiguous cases like
fuzzy locations the number may be equal to one or neither
of both.
We override this here from RangeI in order to delegate
'get' to a L<Bio::Location::CoordinatePolicy> implementing
object. Implementing classes may also wish to provide
'set' functionality, in which case they *must* override
this method. The implementation provided here will throw
an exception if called with arguments.
Returns : A positive integer value.
Args : none
See L<Bio::Location::CoordinatePolicy> for more information
=cut
sub start {
my ($self,@args) = @_;
# throw if @args means that we don't support updating information
# in the interface but will delegate to the coordinate policy object
# for interpreting the 'start' value
$self->throw_not_implemented if @args;
return $self->coordinate_policy()->start($self);
}
=head2 end
Title : end
Usage : $end = $location->end();
Function: Get the end coordinate of this location as defined by the
currently active coordinate computation policy. In simple
cases, this will return the same number as min_end() and
max_end(), in more ambiguous cases like fuzzy locations
the number may be equal to one or neither of both.
We override this here from Bio::RangeI in order to delegate
'get' to a L<Bio::Location::CoordinatePolicy> implementing
object. Implementing classes may also wish to provide
'set' functionality, in which case they *must* override
this method. The implementation provided here will throw
an exception if called with arguments.
Returns : A positive integer value.
Args : none
See L<Bio::Location::CoordinatePolicy> and L<Bio::RangeI> for more
information
=cut
sub end {
my ($self,@args) = @_;
# throw if @args means that we don't support updating information
# in the interface but will delegate to the coordinate policy object
# for interpreting the 'end' value
$self->throw_not_implemented if @args;
return $self->coordinate_policy()->end($self);
}
=head2 min_start
Title : min_start
Usage : my $minstart = $location->min_start();
Function: Get minimum starting point of feature.
Note that an implementation must not call start() in this method.
Returns : integer or undef if no minimum starting point.
Args : none
=cut
sub min_start {
my($self) = @_;
$self->throw_not_implemented();
}
=head2 max_start
Title : max_start
Usage : my $maxstart = $location->max_start();
Function: Get maximum starting point of feature.
Note that an implementation must not call start() in this method
unless start() is overridden such as not to delegate to the
coordinate computation policy object.
Returns : integer or undef if no maximum starting point.
Args : none
=cut
sub max_start {
my($self) = @_;
$self->throw_not_implemented();
}
=head2 start_pos_type
Title : start_pos_type
Usage : my $start_pos_type = $location->start_pos_type();
Function: Get start position type encoded as text
Known valid values are 'BEFORE' (<5..100), 'AFTER' (>5..100),
'EXACT' (5..100), 'WITHIN' ((5.10)..100), 'BETWEEN', (5^6), with
their meaning best explained by their GenBank/EMBL location string
encoding in brackets.
Returns : string ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args : none
=cut
sub start_pos_type {
my($self) = @_;
$self->throw_not_implemented();
}
=head2 flip_strand
Title : flip_strand
Usage : $location->flip_strand();
Function: Flip-flop a strand to the opposite
Returns : None
Args : None
=cut
sub flip_strand {
my $self= shift;
$self->strand($self->strand * -1);
}
=head2 min_end
Title : min_end
Usage : my $minend = $location->min_end();
Function: Get minimum ending point of feature.
Note that an implementation must not call end() in this method
unless end() is overridden such as not to delegate to the
coordinate computation policy object.
Returns : integer or undef if no minimum ending point.
Args : none
=cut
sub min_end {
my($self) = @_;
$self->throw_not_implemented();
}
=head2 max_end
Title : max_end
Usage : my $maxend = $location->max_end();
Function: Get maximum ending point of feature.
Note that an implementation must not call end() in this method
unless end() is overridden such as not to delegate to the
coordinate computation policy object.
Returns : integer or undef if no maximum ending point.
Args : none
=cut
sub max_end {
my($self) = @_;
$self->throw_not_implemented();
}
=head2 end_pos_type
Title : end_pos_type
Usage : my $end_pos_type = $location->end_pos_type();
Function: Get end position encoded as text.
Known valid values are 'BEFORE' (5..<100), 'AFTER' (5..>100),
'EXACT' (5..100), 'WITHIN' (5..(90.100)), 'BETWEEN', (5^6), with
their meaning best explained by their GenBank/EMBL location string
encoding in brackets.
Returns : string ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args : none
=cut
sub end_pos_type {
my($self) = @_;
$self->throw_not_implemented();
}
=head2 seq_id
Title : seq_id
Usage : my $seqid = $location->seq_id();
Function: Get/Set seq_id that location refers to
Returns : seq_id (a string)
Args : [optional] seq_id value to set
=cut
sub seq_id {
my($self) = @_;
$self->throw_not_implemented();
}
=head2 is_remote
Title : is_remote
Usage : $is_remote_loc = $loc->is_remote()
Function: Whether or not a location is a remote location.
A location is said to be remote if it is on a different
'object' than the object which 'has' this
location. Typically, features on a sequence will sometimes
have a remote location, which means that the location of
the feature is on a different sequence than the one that is
attached to the feature. In such a case, $loc->seq_id will
be different from $feat->seq_id (usually they will be the
same).
While this may sound weird, it reflects the location of the
kind of AL445212.9:83662..166657 which can be found in GenBank/EMBL
feature tables.
Example :
Returns : TRUE if the location is a remote location, and FALSE otherwise
Args : Value to set to
=cut
sub is_remote{
shift->throw_not_implemented();
}
=head2 coordinate_policy
Title : coordinate_policy
Usage : $policy = $location->coordinate_policy();
$location->coordinate_policy($mypolicy); # set may not be possible
Function: Get the coordinate computing policy employed by this object.
See L<Bio::Location::CoordinatePolicyI> for documentation
about the policy object and its use.
The interface *does not* require implementing classes to
accept setting of a different policy. The implementation
provided here does, however, allow to do so.
Implementors of this interface are expected to initialize
every new instance with a
L<Bio::Location::CoordinatePolicyI> object. The
implementation provided here will return a default policy
object if none has been set yet. To change this default
policy object call this method as a class method with an
appropriate argument. Note that in this case only
subsequently created Location objects will be affected.
Returns : A L<Bio::Location::CoordinatePolicyI> implementing object.
Args : On set, a L<Bio::Location::CoordinatePolicyI> implementing object.
See L<Bio::Location::CoordinatePolicyI> for more information
=cut
sub coordinate_policy {
shift->throw_not_implemented();
}
=head2 to_FTstring
Title : to_FTstring
Usage : my $locstr = $location->to_FTstring()
Function: returns the FeatureTable string of this location
Returns : string
Args : none
=cut
sub to_FTstring {
my($self) = @_;
$self->throw_not_implemented();
}
=head2 each_Location
Title : each_Location
Usage : @locations = $locObject->each_Location($order);
Function: Conserved function call across Location:: modules - will
return an array containing the component Location(s) in
that object, regardless if the calling object is itself a
single location or one containing sublocations.
Returns : an array of Bio::LocationI implementing objects
Args : Optional sort order to be passed to sub_Location() for Splits
=cut
sub each_Location {
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 valid_Location
Title : valid_Location
Usage : if ($location->valid_location) {...};
Function: boolean method to determine whether location is considered valid
(has minimum requirements for a specific LocationI implementation)
Returns : Boolean value: true if location is valid, false otherwise
Args : none
=cut
sub valid_Location {
my ($self,@args) = @_;
$self->throw_not_implemented();
}
1;