Raw content of Bio::Coordinate::Collection
<![CDATA[# $Id: Collection.pm,v 1.11.2.1 2003/02/20 05:11:45 heikki Exp $
#
# bioperl module for Bio::Coordinate::Collection
#
# Cared for by Heikki Lehvaslaiho <heikki@ebi.ac.uk>
#
# Copyright Heikki Lehvaslaiho
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Coordinate::Collection - Noncontinuous match between two coordinate sets
=head1 SYNOPSIS
# create Bio::Coordinate::Pairs or other Bio::Coordinate::MapperIs somehow
$pair1; $pair2;
# add them into a Collection
$collection = Bio::Coordinate::Collection->new;
$collection->add_mapper($pair1);
$collection->add_mapper($pair2);
# create a position and map it
$pos = Bio::Location::Simple->new (-start => 5, -end => 9 );
$res = $collection->map($pos);
$res->match->start == 1;
$res->match-> == 5;
# if mapping is many to one (*>1) or many-to-many (*>*)
# you have to give seq_id not get unrelevant entries
$pos = Bio::Location::Simple->new
(-start => 5, -end => 9 -seq_id=>'clone1');
=head1 DESCRIPTION
Generic, context neutral mapper to provide coordinate transforms
between two B<disjoint> coordinate systems. It brings into Bioperl the
functionality from Ewan Birney's Bio::EnsEMBL::Mapper ported into
current bioperl.
This class is aimed for representing mapping between whole chromosomes
and contigs, or between contigs and clones, or between sequencing
reads and assembly. The submaps are automatically sorted, so they can
be added in any order.
To map coordinates to the other direction, you have to swap() the
collection. Keeping track of the direction and ID restrictions
are left to the calling code.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing lists Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Heikki Lehvaslaiho
Email: heikki@ebi.ac.uk
Address:
EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom
=head1 CONTRIBUTORS
Ewan Birney, birney@ebi.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Coordinate::Collection;
use vars qw(@ISA );
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Root::Root;
use Bio::Coordinate::MapperI;
use Bio::Coordinate::Result;
use Bio::Coordinate::Result::Gap;
@ISA = qw(Bio::Root::Root Bio::Coordinate::MapperI);
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'_mappers'} = [];
my($in, $out, $strict, $mappers, $return_match) =
$self->_rearrange([qw(IN
OUT
STRICT
MAPPERS
RETURN_MATCH
)],
@args);
$in && $self->in($in);
$out && $self->out($out);
$mappers && $self->mappers($mappers);
$return_match && $self->return_match('return_match');
return $self; # success - we hope!
}
=head2 add_mapper
Title : add_mapper
Usage : $obj->add_mapper($mapper)
Function: Pushes one Bio::Coodinate::MapperI into the list of mappers.
Sets _is_sorted() to false.
Example :
Returns : 1 when succeeds, 0 for failure.
Args : mapper object
=cut
sub add_mapper {
my ($self,$value) = @_;
$self->throw("Is not a Bio::Coordinate::MapperI but a [$self]")
unless defined $value && $value->isa('Bio::Coordinate::MapperI');
# test pair range lengths
$self->warn("Coodinates in pair [". $value . ":" .
$value->in->seq_id . "/". $value->in->seq_id .
"] are not right.")
unless $value->test;
$self->_is_sorted(0);
push(@{$self->{'_mappers'}},$value);
}
=head2 mappers
Title : mappers
Usage : $obj->mappers();
Function: Returns or sets a list of mappers.
Example :
Returns : array of mappers
Args : array of mappers
=cut
sub mappers{
my ($self,@args) = @_;
if (@args) {
$self->throw("Is not a Bio::Coordinate::MapperI but a [$self]")
unless defined $args[0] && $args[0]->isa('Bio::Coordinate::MapperI');
push(@{$self->{'_mappers'}}, @args);
}
return @{$self->{'_mappers'}};
}
=head2 each_mapper
Title : each_mapper
Usage : $obj->each_mapper();
Function: Returns a list of mappers.
Example :
Returns : list of mappers
Args : none
=cut
sub each_mapper{
my ($self) = @_;
return @{$self->{'_mappers'}};
}
=head2 swap
Title : swap
Usage : $obj->swap;
Function: Swap the direction of mapping;input <-> output
Example :
Returns : 1
Args :
=cut
sub swap {
my ($self) = @_;
use Data::Dumper;
$self->sort unless $self->_is_sorted;
map {$_->swap;} @{$self->{'_mappers'}};
($self->{'_in_ids'}, $self->{'_out_ids'}) =
($self->{'_out_ids'}, $self->{'_in_ids'});
1;
}
=head2 test
Title : test
Usage : $obj->test;
Function: test that both components of all pairs are of the same length.
Ran automatically.
Example :
Returns : boolean
Args :
=cut
sub test {
my ($self) = @_;
my $res = 1;
foreach my $mapper ($self->each_mapper) {
$self->warn("Coodinates in pair [". $mapper . ":" .
$mapper->in->seq_id . "/". $mapper->in->seq_id .
"] are not right.") && ($res = 0)
unless $mapper->test;
}
$res;
}
=head2 map
Title : map
Usage : $newpos = $obj->map($pos);
Function: Map the location from the input coordinate system
to a new value in the output coordinate system.
Example :
Returns : new value in the output coordinate system
Args : integer
=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("No coordinate mappers!")
unless $self->each_mapper;
$self->sort unless $self->_is_sorted;
if ($value->isa("Bio::Location::SplitLocationI")) {
my $result = new Bio::Coordinate::Result;
foreach my $loc ( $value->sub_Location(1) ) {
my $res = $self->_map($loc);
map { $result->add_sub_Location($_) } $res->each_Location;
}
return $result;
} 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 $result = Bio::Coordinate::Result->new(-is_remote=>1);
IDMATCH: {
# bail out now we if are forcing the use of an ID
# and it is not in this collection
last IDMATCH if defined $value->seq_id &&
! $self->{'_in_ids'}->{$value->seq_id};
foreach my $pair ($self->each_mapper) {
# if we are limiting input to a certain ID
next if defined $value->seq_id && $value->seq_id ne $pair->in->seq_id;
# if we haven't even reached the start, move on
next if $pair->in->end < $value->start;
# if we have over run, break
last if $pair->in->start > $value->end;
my $subres = $pair->map($value);
$result->add_result($subres);
}
}
$result->seq_id($result->match->seq_id) if $result->match;
unless ($result->each_Location) {
#build one gap;
my $gap = Bio::Location::Simple->new(-start => $value->start,
-end => $value->end,
-strand => $value->strand,
-location_type => $value->location_type
);
$gap->seq_id($value->seq_id) if defined $value->seq_id;
bless $gap, 'Bio::Coordinate::Result::Gap';
$result->seq_id($value->seq_id) if defined $value->seq_id;
$result->add_sub_Location($gap);
}
return $result;
}
=head2 sort
Title : sort
Usage : $obj->sort;
Function: Sort function so that all mappings are sorted by
input coordinate start
Example :
Returns : 1
Args :
=cut
sub sort{
my ($self) = @_;
@{$self->{'_mappers'}} = map { $_->[0] }
sort { $a->[1] <=> $b->[1] }
map { [ $_, $_->in->start] }
@{$self->{'_mappers'}};
#create hashes for sequence ids
$self->{'_in_ids'} = ();
$self->{'_out_ids'} = ();
foreach ($self->each_mapper) {
$self->{'_in_ids'}->{$_->in->seq_id} = 1;
$self->{'_out_ids'}->{$_->out->seq_id} = 1;
}
$self->_is_sorted(1);
}
=head2 _is_sorted
Title : _is_sorted
Usage : $newpos = $obj->_is_sorted;
Function: toggle for whether the (internal) coodinate mapper data are sorted
Example :
Returns : boolean
Args : boolean
=cut
sub _is_sorted{
my ($self,$value) = @_;
$self->{'_is_sorted'} = 1 if defined $value && $value;
return $self->{'_is_sorted'};
}
1;
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