package Bio::Coordinate::ExtrapolatingPair;
use utf8;
use strict;
use warnings;
use Bio::Root::Root;
use Bio::LocationI;
use parent qw(Bio::Coordinate::Pair);
# ABSTRACT: Continuous match between two coordinate sets.
# AUTHOR: Heikki Lehvaslaiho <heikki@bioperl.org>
# OWNER: Heikki Lehvaslaiho
# LICENSE: Perl_5
=head1 SYNOPSIS
use Bio::Location::Simple;
use Bio::Coordinate::ExtrapolatingPair;
$match1 = Bio::Location::Simple->new
(-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
$match2 = Bio::Location::Simple->new
(-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 );
$pair = Bio::Coordinate::ExtrapolatingPair->
new(-in => $match1,
-out => $match2,
-strict => 1
);
$pos = Bio::Location::Simple->new
(-start => 40, -end => 60, -strand=> 1 );
$res = $pair->map($pos);
$res->start eq 20;
$res->end eq 20;
=head1 DESCRIPTION
This class represents a one continuous match between two coordinate
systems represented by Bio::Location::Simple objects. The relationship
is directed and reversible. It implements methods to ensure internal
consistency, and map continuous and split locations from one
coordinate system to another.
This class is an elaboration of Bio::Coordinate::Pair. The map
function returns only matches which is the mode needed most of
tehtime. By default the matching regions between coordinate systems
are boundless, so that you can say e.g. that gene starts from here in
the chromosomal coordinate system and extends indefinetely in both
directions. If you want to define the matching regions exactly, you
can do that and set strict() to true.
=cut
=head2 new
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my($strict) =
$self->_rearrange([qw(STRICT
)],
@args);
$strict && $self->strict($strict);
return $self;
}
=head2 strict
Title : strict
Usage : $obj->strict(1);
Function: Set and read the strictness of the coordinate system.
Example :
Returns : value of input system
Args : boolean
=cut
sub strict {
my ($self,$value) = @_;
if( defined $value) {
$self->{'_strict'} = 1 if $value;
}
return $self->{'_strict'};
}
=head2 map
Title : map
Usage : $newpos = $obj->map($loc);
Function: Map the location from the input coordinate system
to a new value in the output coordinate system.
In extrapolating coodinate system there is no location zero.
Locations are...
Example :
Returns : new location in the output coordinate system or undef
Args : Bio::Location::Simple
=cut
sub map {
my ($self,$value) = @_;
$self->throw("Need to pass me a value.")
unless defined $value;
$self->throw("I need a Bio::Location, not [$value]")
unless $value->isa('Bio::LocationI');
$self->throw("Input coordinate system not set")
unless $self->in;
$self->throw("Output coordinate system not set")
unless $self->out;
my $match;
if ($value->isa("Bio::Location::SplitLocationI")) {
my $split = Bio::Coordinate::Result->new(-seq_id=>$self->out->seq_id);
foreach my $loc ( sort { $a->start <=> $b->start }
$value->sub_Location ) {
$match = $self->_map($loc);
$split->add_sub_Location($match) if $match;
}
$split->each_Location ? (return $split) : return ;
} else {
return $self->_map($value);
}
}
=head2 _map
Title : _map
Usage : $newpos = $obj->_map($simpleloc);
Function: Internal method that does the actual mapping. Called
multiple times by map() if the location to be mapped is a
split location
Example :
Returns : new location in the output coordinate system or undef
Args : Bio::Location::Simple
=cut
sub _map {
my ($self,$value) = @_;
my ($offset, $start, $end);
if ($self->strand == -1) {
$offset = $self->in->end + $self->out->start;
$start = $offset - $value->end;
$end = $offset - $value->start ;
} else { # undef, 0 or 1
$offset = $self->in->start - $self->out->start;
$start = $value->start - $offset;
$end = $value->end - $offset;
}
# strict prevents matches outside stated range
if ($self->strict) {
return if $start < 0 and $end < 0;
return if $start > $self->out->end;
$start = 1 if $start < 0;
$end = $self->out->end if $end > $self->out->end;
}
my $match = Bio::Location::Simple->
new(-start => $start,
-end => $end,
-strand => $self->strand,
-seq_id => $self->out->seq_id,
-location_type => $value->location_type
);
$match->strand($match->strand * $value->strand) if $value->strand;
bless $match, 'Bio::Coordinate::Result::Match';
return $match;
}
1;