#
# BioPerl module for Bio::Location::SplitLocationI
# 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::Location::SplitLocationI - Abstract interface of a Location on a Sequence
which has multiple locations (start/end points)
=head1 SYNOPSIS
# get a SplitLocationI somehow
print $splitlocation->start, "..", $splitlocation->end, "\n";
my @sublocs = $splitlocation->sub_Location();
my $count = 1;
# print the start/end points of the sub locations
foreach my $location ( sort { $a->start <=> $b->start } @sublocs ) {
printf "sub feature %d [%d..%d]\n", $location->start,$location->end;
$count++;
}
=head1 DESCRIPTION
This interface encapsulates the necessary methods for representing the
location of a sequence feature that has more that just a single
start/end pair. Some examples of this are the annotated exons in a
gene or the annotated CDS in a sequence file.
=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://redmine.open-bio.org/projects/bioperl/
=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::Location::SplitLocationI;
use strict;
use Carp;
use base qw(Bio::LocationI);
=head2 sub_Location
Title : sub_Location
Usage : @locations = $feat->sub_Location();
Function: Returns an array of LocationI objects
Returns : An array
Args : none
=cut
sub sub_Location {
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 splittype
Title : splittype
Usage : $splittype = $fuzzy->splittype();
Function: get/set the split splittype
Returns : the splittype of split feature (join, order)
Args : splittype to set
=cut
sub splittype {
my($self) = @_;
$self->throw_not_implemented();
}
=head2 is_single_sequence
Title : is_single_sequence
Usage : if($splitloc->is_single_sequence()) {
print "Location object $splitloc is split ".
"but only across a single sequence\n";
}
Function: Determine whether this location is split across a single or
multiple sequences.
Returns : TRUE if all sublocations lie on the same sequence as the root
location (feature), and FALSE otherwise.
Args : none
=cut
sub is_single_sequence {
my ($self) = @_;
$self->throw_not_implemented();
}
=head1 Bio::LocationI methods
Bio::LocationI inherited methods follow
=head2 min_start
Title : min_start
Usage : my $minstart = $location->min_start();
Function: Get minimum starting location of feature startpoint
Returns : integer or undef if no maximum starting point.
Args : none
=cut
=head2 max_start
Title : max_start
Usage : my $maxstart = $location->max_start();
Function: Get maximum starting location of feature startpoint
Returns : integer or undef if no maximum starting point.
Args : none
=cut
=head2 start_pos_type
Title : start_pos_type
Usage : my $start_pos_type = $location->start_pos_type();
Function: Get start position type (ie <,>, ^)
Returns : type of position coded as text
('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args : none
=cut
=head2 min_end
Title : min_end
Usage : my $minend = $location->min_end();
Function: Get minimum ending location of feature endpoint
Returns : integer or undef if no minimum ending point.
Args : none
=cut
=head2 max_end
Title : max_end
Usage : my $maxend = $location->max_end();
Function: Get maximum ending location of feature endpoint
Returns : integer or undef if no maximum ending point.
Args : none
=cut
=head2 end_pos_type
Title : end_pos_type
Usage : my $end_pos_type = $location->end_pos_type();
Function: Get end position type (ie <,>, ^)
Returns : type of position coded as text
('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args : none
=cut
=head2 seq_id
Title : seq_id
Usage : my $seqid = $location->seq_id();
Function: Get/Set seq_id that location refers to
Returns : seq_id
Args : [optional] seq_id value to set
=cut
=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 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 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 Bio::Location::CoordinatePolicyI implementing object.
Args : On set, a Bio::Location::CoordinatePolicyI implementing object.
=cut
=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
1;