#
# BioPerl module for Bio::Map::Position
#
# 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::Position - A single position of a Marker, or the range over which
that marker lies, in a Map
=head1 SYNOPSIS
use Bio::Map::Position;
my $position = Bio::Map::Position->new(-map => $map,
-element => $marker,
-value => 100
);
my $position_with_range = Bio::Map::Position->new(-map => $map,
-element => $marker,
-start => 100,
-length => 10
);
=head1 DESCRIPTION
This object is an implementation of the PositionI interface that
handles the specific values of a position. This allows a map element
(e.g. Marker) to have multiple positions within a map and still be
treated as a single entity.
This handles the concept of a relative map in which the order of
elements and the distance between them is known, but does not
directly handle the case when distances are unknown - in that case
arbitrary values must be assigned for position values.
No units are assumed here - units are handled by context of which Map
a position is placed in or the subclass of this Position.
=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://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
=head1 CONTRIBUTORS
Lincoln Stein, lstein@cshl.org
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
Chad Matsalla, bioinformatics1@dieselwurks.com
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::Position;
use strict;
use Scalar::Util qw(looks_like_number);
use Bio::Map::Relative;
use base qw(Bio::Root::Root Bio::Map::PositionI);
=head2 new
Title : new
Usage : my $obj = Bio::Map::Position->new();
Function: Builds a new Bio::Map::Position object
Returns : Bio::Map::Position
Args : -map => Bio::Map::MapI object
-element => Bio::Map::MappableI object
-relative => Bio::Map::RelativeI object
* If this position has no range, or if a single value can describe
the range *
-value => scalar : something that describes the single
point position or range of this
Position, most likely an int
* Or if this position has a range, at least two of *
-start => int : value of the start co-ordinate
-end => int : value of the end co-ordinate
-length => int : length of the range
=cut
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($map, $marker, $element, $value, $start, $end, $length, $relative) =
$self->_rearrange([qw( MAP
MARKER
ELEMENT
VALUE
START
END
LENGTH
RELATIVE
)], @args);
my $do_range = defined($start) || defined($end);
if ($value && $do_range) {
$self->warn("-value and (-start|-end|-length) are mutually exclusive, ignoring value");
$value = undef;
}
$map && $self->map($map);
$marker && $self->element($marker); # backwards compatibility
$element && $self->element($element);
$relative && $self->relative($relative);
defined($value) && $self->value($value);
if ($do_range) {
defined($start) && $self->start($start);
defined($end) && $self->end($end);
if ($length) {
if (defined($start) && ! defined($end)) {
$self->end($start + $length - 1);
}
elsif (! defined($start)) {
$self->start($end - $length + 1);
}
}
defined($self->end) || $self->end($start);
}
return $self;
}
=head2 relative
Title : relative
Usage : my $relative = $position->relative();
$position->relative($relative);
Function: Get/set the thing this Position's coordinates (numerical(), start(),
end()) are relative to, as described by a Relative object.
Returns : Bio::Map::RelativeI (default is one describing "relative to the
start of the Position's map")
Args : none to get, OR
Bio::Map::RelativeI to set
=cut
sub relative {
my ($self, $relative) = @_;
if ($relative) {
$self->throw("Must supply an object") unless ref($relative);
$self->throw("This is [$relative], not a Bio::Map::RelativeI") unless $relative->isa('Bio::Map::RelativeI');
$self->{_relative_not_implicit} = 1;
$self->{_relative} = $relative;
}
return $self->{_relative} || $self->absolute_relative;
}
=head2 absolute
Title : absolute
Usage : my $absolute = $position->absolute();
$position->absolute($absolute);
Function: Get/set how this Position's co-ordinates (numerical(), start(),
end()) are reported. When absolute is off, co-ordinates are
relative to the thing described by relative(). Ie. the value
returned by start() will be the same as the value you set start()
to. When absolute is on, co-ordinates are converted to be relative
to the start of the map.
So if relative() currently points to a Relative object describing
"relative to another position which is 100 bp from the start of
the map", this Position's start() had been set to 50 and absolute()
returns 1, $position->start() will return 150. If absolute() returns
0 in the same situation, $position->start() would return 50.
Returns : boolean (default 0)
Args : none to get, OR
boolean to set
=cut
sub absolute {
my $self = shift;
if (@_) { $self->{_absolute} = shift }
return $self->{_absolute} || 0;
}
=head2 value
Title : value
Usage : my $pos = $position->value;
Function: Get/Set the value for this postion
Returns : scalar, value
Args : [optional] new value to set
=cut
sub value {
my ($self, $value) = @_;
if (defined $value) {
$self->{'_value'} = $value;
$self->start($self->numeric) unless defined($self->start);
$self->end($self->numeric) unless defined($self->end);
}
return $self->{'_value'};
}
=head2 numeric
Title : numeric
Usage : my $num = $position->numeric;
Function: Read-only method that is guaranteed to return a numeric
representation of the start of this position.
Returns : scalar numeric
Args : none to get the co-ordinate normally (see absolute() method), OR
Bio::Map::RelativeI to get the co-ordinate converted to be
relative to what this Relative describes.
=cut
sub numeric {
my ($self, $value) = @_;
my $num = $self->{'_value'};
$self->throw("The value has not been set, can't convert to numeric") unless defined($num);
$self->throw("This value [$num] is not numeric") unless looks_like_number($num);
if (ref($value) && $value->isa('Bio::Map::RelativeI')) {
# get the value after co-ordinate conversion
my $raw = $num;
my ($abs_start, $rel_start) = $self->_relative_handler($value);
return $abs_start + $raw - $rel_start;
}
# get the value as per absolute
if ($self->{_relative_not_implicit} && $self->absolute) {
# this actually returns the start, but should be the same thing...
return $self->relative->absolute_conversion($self);
}
return $num;
}
=head2 start
Title : start
Usage : my $start = $position->start();
$position->start($start);
Function: Get/set the start co-ordinate of this position.
Returns : the start of this position
Args : scalar numeric to set, OR
none to get the co-ordinate normally (see absolute() method), OR
Bio::Map::RelativeI to get the co-ordinate converted to be
relative to what this Relative describes.
=cut
sub start {
my ($self, $value) = @_;
if (defined $value) {
if (ref($value) && $value->isa('Bio::Map::RelativeI')) {
# get the value after co-ordinate conversion
my $raw = $self->{start};
defined $raw || return;
my ($abs_start, $rel_start) = $self->_relative_handler($value);
return $abs_start + $raw - $rel_start;
}
else {
# set the value
$self->throw("This is [$value], not a number") unless looks_like_number($value);
$self->{start} = $value;
$self->value($value) unless defined($self->value);
}
}
# get the value as per absolute
if ($self->{_relative_not_implicit} && $self->absolute) {
return $self->relative->absolute_conversion($self);
}
return defined($self->{start}) ? $self->{start} : return;
}
=head2 end
Title : end
Usage : my $end = $position->end();
$position->end($end);
Function: Get/set the end co-ordinate of this position.
Returns : the end of this position
Args : scalar numeric to set, OR
none to get the co-ordinate normally (see absolute() method), OR
Bio::Map::RelativeI to get the co-ordinate converted to be
relative to what this Relative describes.
=cut
sub end {
my ($self, $value) = @_;
if (defined $value) {
if (ref($value) && $value->isa('Bio::Map::RelativeI')) {
# get the value after co-ordinate conversion
my $raw = $self->{end};
defined $raw || return;
my ($abs_start, $rel_start) = $self->_relative_handler($value);
return $abs_start + $raw - $rel_start;
}
else {
# set the value
$self->throw("This value [$value] is not numeric!") unless looks_like_number($value);
$self->{end} = $value;
}
}
# get the value as per absolute
if ($self->{_relative_not_implicit} && $self->absolute) {
my $raw = $self->{end} || return;
my $abs_start = $self->relative->absolute_conversion($self) || return;
return $abs_start + ($raw - $self->{start});
}
return defined($self->{end}) ? $self->{end} : return;
}
=head2 length
Title : length
Usage : $length = $position->length();
Function: Get/set the length of this position's range, changing the end() if
necessary. Getting and even setting the length will fail if both
start() and end() are not already defined.
Returns : the length of this range
Args : none to get, OR scalar numeric (>0) to set.
=cut
sub length {
my ($self, $length) = @_;
if ($length) {
$length > 0 || return;
my $existing_length = $self->length || return;
return $length if $existing_length == $length;
$self->end($self->{start} + $length - 1);
}
if (defined($self->start) && defined($self->end)) {
return $self->end - $self->start + 1;
}
return;
}
=head2 sortable
Title : sortable
Usage : my $num = $position->sortable();
Function: Read-only method that is guaranteed to return a value suitable
for correctly sorting this kind of position amongst other positions
of the same kind on the same map. Note that sorting different kinds
of position together is unlikely to give sane results.
Returns : numeric
Args : none
=cut
sub sortable {
my ($self, $given_map) = @_;
my $answer = $self->numeric($self->absolute_relative);
return $answer;
}
=head2 toString
Title : toString
Usage : print $position->toString(), "\n";
Function: stringifies this range
Returns : a string representation of the range of this Position
Args : optional Bio::Map::RelativeI to have the co-ordinates reported
relative to the thing described by that Relative
=cut
sub toString {
my ($self, $rel) = @_;
if (defined($self->start) && defined($self->end)) {
return $self->start($rel).'..'.$self->end($rel);
}
return '';
}
=head2 absolute_relative
Title : absolute_relative
Usage : my $rel = $position->absolute_relative();
Function: Get a relative describing the start of the map. This is useful for
supplying to the coordinate methods (start(), end() etc.) to get
the temporary effect of having set absolute(1).
Returns : Bio::Map::Relative
Args : none
=cut
sub absolute_relative {
return Bio::Map::Relative->new(-map => 0, -description => 'start of map');
}
# get our own absolute start and that of the thing we want as a frame of
# reference
sub _relative_handler {
my ($self, $value) = @_;
my $own_relative = $self->relative;
# if the requested relative position is the same as the actual
# relative, the current co-ordinate values are correct so shortcut
my ($own_type, $req_type) = ($own_relative->type, $value->type);
if ($own_type && $req_type && $own_type eq $req_type && $own_relative->$own_type eq $value->$req_type) {
return (0, 0);
}
my $abs_start = $own_relative->absolute_conversion($self);
my $rel_start = $value->absolute_conversion($self);
$self->throw("Unable to resolve co-ordinate because relative to something that ultimately isn't relative to the map start")
unless defined($abs_start) && defined($rel_start);
return ($abs_start, $rel_start);
}
1;