#
# BioPerl module for Bio::Location::Atomic
# 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::Atomic - Implementation of a Atomic Location on a Sequence
=head1 SYNOPSIS
use Bio::Location::Atomic;
my $location = Bio::Location::Atomic->new(-start => 1, -end => 100,
-strand => 1 );
if( $location->strand == -1 ) {
printf "complement(%d..%d)\n", $location->start, $location->end;
} else {
printf "%d..%d\n", $location->start, $location->end;
}
=head1 DESCRIPTION
This is an implementation of Bio::LocationI to manage simple location
information on a Sequence.
=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::Atomic;
use strict;
use Bio::Location::WidestCoordPolicy;
use base qw(Bio::Root::Root Bio::LocationI);
our $coord_policy = Bio::Location::WidestCoordPolicy->new();
sub new {
my ($class, @args) = @_;
$class = ref $class || $class;
my $self = {};
# This is for the case when we've done something like this
# get a 2 features from somewhere (like Bio::Tools::GFF)
# Do
# my $location = $f1->location->union($f2->location);
# We get an error without the following code which
# explictly loads the Bio::Location::Simple class
unless( $class->can('start') ) {
eval { Bio::Root::Root->_load_module($class) };
if ( $@ ) {
Bio::Root::Root->throw("$class cannot be found\nException $@");
}
}
bless $self,$class;
my ($v,$start,$end,$strand,$seqid) = $self->_rearrange([qw(VERBOSE
START
END
STRAND
SEQ_ID)],@args);
defined $v && $self->verbose($v);
defined $strand && $self->strand($strand);
defined $start && $self->start($start);
defined $end && $self->end($end);
if( defined $self->start && defined $self->end &&
$self->start > $self->end && $self->strand != -1 ) {
$self->warn("When building a location, start ($start) is expected to be less than end ($end), ".
"however it was not. Switching start and end and setting strand to -1");
$self->strand(-1);
my $e = $self->end;
my $s = $self->start;
$self->start($e);
$self->end($s);
}
$seqid && $self->seq_id($seqid);
return $self;
}
=head2 start
Title : start
Usage : $start = $loc->start();
Function: get/set the start of this range
Returns : the start of this range
Args : optionaly allows the start to be set
: using $loc->start($start)
=cut
sub start {
my ($self, $value) = @_;
$self->min_start($value) if( defined $value );
return $self->SUPER::start();
}
=head2 end
Title : end
Usage : $end = $loc->end();
Function: get/set the end of this range
Returns : the end of this range
Args : optionaly allows the end to be set
: using $loc->end($start)
=cut
sub end {
my ($self, $value) = @_;
$self->min_end($value) if( defined $value );
return $self->SUPER::end();
}
=head2 strand
Title : strand
Usage : $strand = $loc->strand();
Function: get/set the strand of this range
Returns : the strandidness (-1, 0, +1)
Args : optionaly allows the strand to be set
: using $loc->strand($strand)
=cut
sub strand {
my $self = shift;
if ( @_ ) {
my $value = shift;
if ( defined($value) ) {
if ( $value eq '+' ) { $value = 1; }
elsif ( $value eq '-' ) { $value = -1; }
elsif ( $value eq '.' ) { $value = 0; }
elsif ( $value != -1 && $value != 1 && $value != 0 ) {
$self->throw("$value is not a valid strand info");
}
$self->{'_strand'} = $value;
}
}
# do not pretend the strand has been set if in fact it wasn't
return $self->{'_strand'};
#return $self->{'_strand'} || 0;
}
=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 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, $seqid) = @_;
if( defined $seqid ) {
$self->{'_seqid'} = $seqid;
}
return $self->{'_seqid'};
}
=head2 length
Title : length
Usage : $len = $loc->length();
Function: get the length in the coordinate space this location spans
Example :
Returns : an integer
Args : none
=cut
sub length {
my ($self) = @_;
return abs($self->end() - $self->start()) + 1;
}
=head2 min_start
Title : min_start
Usage : my $minstart = $location->min_start();
Function: Get minimum starting location of feature startpoint
Returns : integer or undef if no minimum starting point.
Args : none
=cut
sub min_start {
my ($self,$value) = @_;
if(defined($value)) {
$self->{'_start'} = $value;
}
return $self->{'_start'};
}
=head2 max_start
Title : max_start
Usage : my $maxstart = $location->max_start();
Function: Get maximum starting location of feature startpoint.
In this implementation this is exactly the same as min_start().
Returns : integer or undef if no maximum starting point.
Args : none
=cut
sub max_start {
my ($self,@args) = @_;
return $self->min_start(@args);
}
=head2 start_pos_type
Title : start_pos_type
Usage : my $start_pos_type = $location->start_pos_type();
Function: Get start position type (ie <,>, ^).
In this implementation this will always be 'EXACT'.
Returns : type of position coded as text
('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args : none
=cut
sub start_pos_type {
my($self) = @_;
return 'EXACT';
}
=head2 min_end
Title : min_end
Usage : my $minend = $location->min_end();
Function: Get minimum ending location of feature endpoint
Returns : integer or undef if no minimum ending point.
Args : none
=cut
sub min_end {
my($self,$value) = @_;
if(defined($value)) {
$self->{'_end'} = $value;
}
return $self->{'_end'};
}
=head2 max_end
Title : max_end
Usage : my $maxend = $location->max_end();
Function: Get maximum ending location of feature endpoint
In this implementation this is exactly the same as min_end().
Returns : integer or undef if no maximum ending point.
Args : none
=cut
sub max_end {
my($self,@args) = @_;
return $self->min_end(@args);
}
=head2 end_pos_type
Title : end_pos_type
Usage : my $end_pos_type = $location->end_pos_type();
Function: Get end position type (ie <,>, ^)
In this implementation this will always be 'EXACT'.
Returns : type of position coded as text
('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args : none
=cut
sub end_pos_type {
my($self) = @_;
return 'EXACT';
}
=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) = @_;
return 'EXACT';
}
=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 {
my $self = shift;
if( @_ ) {
my $value = shift;
$self->{'is_remote'} = $value;
}
return $self->{'is_remote'};
}
=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 - for
Simple locations, the return value is just itself.
Args :
=cut
sub each_Location {
my ($self) = @_;
return ($self);
}
=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) = @_;
if( $self->start == $self->end ) {
return $self->start;
}
my $str = $self->start . ".." . $self->end;
if( $self->strand == -1 ) {
$str = sprintf("complement(%s)", $str);
}
return $str;
}
=head2 valid_Location
Title : valid_Location
Usage : if ($location->valid_location) {...};
Function: boolean method to determine whether location is considered valid
(has minimum requirements for Simple implementation)
Returns : Boolean value: true if location is valid, false otherwise
Args : none
=cut
sub valid_Location {
my ($self) = @_;
return 1 if $self->{'_start'} && $self->{'_end'};
return 0;
}
=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 {
my ($self, $policy) = @_;
if(defined($policy)) {
if(! $policy->isa('Bio::Location::CoordinatePolicyI')) {
$self->throw("Object of class ".ref($policy)." does not implement".
" Bio::Location::CoordinatePolicyI");
}
if(ref($self)) {
$self->{'_coordpolicy'} = $policy;
} else {
# called as class method
$coord_policy = $policy;
}
}
return (ref($self) && exists($self->{'_coordpolicy'}) ?
$self->{'_coordpolicy'} : $coord_policy);
}
=head2 trunc
Title : trunc
Usage : $trunc_location = $location->trunc($start, $end, $relative_ori);
Function: To truncate a location and keep annotations and features
within the truncated segment intact.
This might do things differently where the truncation
splits the location in half.
CAVEAT : As yet, this is an untested and unannounced method. Use
with caution!
Returns : A L<Bio::Location::Atomic> object.
Args : The start and end position for the trunction, and the relative
orientation.
=cut
sub trunc {
my ($self,$start,$end,$relative_ori) = @_;
my $newstart = $self->start - $start+1;
my $newend = $self->end - $start+1;
my $newstrand = $relative_ori * $self->strand;
my $out;
if( $newstart < 1 || $newend > ($end-$start+1) ) {
$out = Bio::Location::Atomic->new();
$out->start($self->start);
$out->end($self->end);
$out->strand($self->strand);
$out->seq_id($self->seqid);
$out->is_remote(1);
} else {
$out = Bio::Location::Atomic->new();
$out->start($newstart);
$out->end($newend);
$out->strand($newstrand);
$out->seq_id();
}
return $out;
}
1;