Raw content of Bio::Coordinate::Pair # $Id: Pair.pm,v 1.9.2.1 2003/02/20 05:11:45 heikki Exp $ # # bioperl module for Bio::Coordinate::Pair # # 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::Pair - Continuous match between two coordinate sets =head1 SYNOPSIS use Bio::Location::Simple; use Bio::Coordinate::Pair; my $match1 = Bio::Location::Simple->new (-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 ); my $match2 = Bio::Location::Simple->new (-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 ); my $pair = Bio::Coordinate::Pair->new(-in => $match1, -out => $match2 ); # location to match $pos = Bio::Location::Simple->new (-start => 25, -end => 25, -strand=> -1 ); # results are in a Bio::Coordinate::Result # they can be Matches and Gaps; are Bio::LocationIs $res = $pair->map($pos); $res->isa('Bio::Coordinate::Result'); $res->each_match == 1; $res->each_gap == 0; $res->each_Location == 1; $res->match->start == 5; $res->match->end == 5; $res->match->strand == -1; $res->match->seq_id eq 'peptide'; =head1 DESCRIPTION This class represents a one continuous match between two coordinate systems represented by Bio::Location::Simple objects. The relationship is directed and reversible. It implements methods to ensure internal consistency, and map continuous and split locations from one coordinate system to another. The map() method returns Bio::Coordinate::Results with Bio::Coordinate::Result::Gaps. The calling code have to deal (process or ignore) them. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists =head2 Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki@ebi.ac.uk Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom =head1 CONTRIBUTORS Additional contributors names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Coordinate::Pair; use vars qw(@ISA ); use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Root::Root; use Bio::Coordinate::MapperI; use Bio::Coordinate::Result; use Bio::Coordinate::Result::Match; use Bio::Coordinate::Result::Gap; @ISA = qw(Bio::Root::Root Bio::Coordinate::MapperI); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my($in, $out) = $self->_rearrange([qw(IN OUT )], @args); $in && $self->in($in); $out && $self->out($out); return $self; # success - we hope! } =head2 in Title : in Usage : $obj->in('peptide'); Function: Set and read the input coordinate system. Example : Returns : value of input system Args : new value (optional), Bio::LocationI =cut sub in { my ($self,$value) = @_; if( defined $value) { $self->throw("Not a valid input Bio::Location [$value] ") unless $value->isa('Bio::LocationI'); $self->{'_in'} = $value; } return $self->{'_in'}; } =head2 out Title : out Usage : $obj->out('peptide'); Function: Set and read the output coordinate system. Example : Returns : value of output system Args : new value (optional), Bio::LocationI =cut sub out { my ($self,$value) = @_; if( defined $value) { $self->throw("Not a valid output coordinate Bio::Location [$value] ") unless $value->isa('Bio::LocationI'); $self->{'_out'} = $value; } return $self->{'_out'}; } =head2 swap Title : swap Usage : $obj->swap; Function: Swap the direction of mapping; input <-> output Example : Returns : 1 Args : =cut sub swap { my ($self) = @_; ($self->{'_in'}, $self->{'_out'}) = ($self->{'_out'}, $self->{'_in'}); return 1; } =head2 strand Title : strand Usage : $obj->strand; Function: Get strand value for the pair Example : Returns : ( 1 | 0 | -1 ) Args : =cut sub strand { my ($self) = @_; $self->warn("Outgoing coordinates are not defined") unless $self->out; $self->warn("Incoming coordinates are not defined") unless $self->in; return $self->in->strand * $self->out->strand; } =head2 test Title : test Usage : $obj->test; Function: test that both components are of the same length Example : Returns : ( 1 | undef ) Args : =cut sub test { my ($self) = @_; $self->warn("Outgoing coordinates are not defined") unless $self->out; $self->warn("Incoming coordinates are not defined") unless $self->in; 1 if $self->in->end - $self->in->start == $self->out->end - $self->out->start; } =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 Bio::LocationI in the output coordinate system or undef Args : Bio::LocationI object =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 $self->out; if ($value->isa("Bio::Location::SplitLocationI")) { my $result = new Bio::Coordinate::Result; my $split = new Bio::Location::Split(-seq_id=>$self->out->seq_id); 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 = new Bio::Coordinate::Result; my $offset = $self->in->start - $self->out->start; my $start = $value->start - $offset; my $end = $value->end - $offset; my $match = Bio::Location::Simple->new; $match->location_type($value->location_type); $match->strand($self->strand); #within # |-------------------------| # |-| if ($start >= $self->out->start and $end <= $self->out->end) { $match->seq_id($self->out->seq_id); $result->seq_id($self->out->seq_id); if ($self->strand == 1) { $match->start($start); $match->end($end); } else { $match->start($self->out->end - $end + $self->out->start); $match->end($self->out->end - $start + $self->out->start); } if ($value->strand) { $match->strand($match->strand * $value->strand); $result->strand($match->strand); } bless $match, 'Bio::Coordinate::Result::Match'; $result->add_sub_Location($match); } #out # |-------------------------| # |-| or |-| elsif ( ($end < $self->out->start or $start > $self->out->end ) or #insertions just outside the range need special settings ($value->location_type eq 'IN-BETWEEN' and ($end = $self->out->start or $start = $self->out->end))) { $match->seq_id($self->in->seq_id); $result->seq_id($self->in->seq_id); $match->start($value->start); $match->end($value->end); $match->strand($value->strand); bless $match, 'Bio::Coordinate::Result::Gap'; $result->add_sub_Location($match); } #partial I # |-------------------------| # |-----| elsif ($start < $self->out->start and $end <= $self->out->end ) { $result->seq_id($self->out->seq_id); if ($value->strand) { $match->strand($match->strand * $value->strand); $result->strand($match->strand); } my $gap = Bio::Location::Simple->new; $gap->start($value->start); $gap->end($self->in->start - 1); $gap->strand($value->strand); $gap->seq_id($self->in->seq_id); bless $gap, 'Bio::Coordinate::Result::Gap'; $result->add_sub_Location($gap); # match $match->seq_id($self->out->seq_id); if ($self->strand == 1) { $match->start($self->out->start); $match->end($end); } else { $match->start($self->out->end - $end + $self->out->start); $match->end($self->out->end); } bless $match, 'Bio::Coordinate::Result::Match'; $result->add_sub_Location($match); } #partial II # |-------------------------| # |------| elsif ($start >= $self->out->start and $end > $self->out->end ) { $match->seq_id($self->out->seq_id); $result->seq_id($self->out->seq_id); if ($value->strand) { $match->strand($match->strand * $value->strand); $result->strand($match->strand); } if ($self->strand == 1) { $match->start($start); $match->end($self->out->end); } else { $match->start($self->out->start); $match->end($self->out->end - $start + $self->out->start); } bless $match, 'Bio::Coordinate::Result::Match'; $result->add_sub_Location($match); my $gap = Bio::Location::Simple->new; $gap->start($self->in->end + 1); $gap->end($value->end); $gap->strand($value->strand); $gap->seq_id($self->in->seq_id); bless $gap, 'Bio::Coordinate::Result::Gap'; $result->add_sub_Location($gap); } #enveloping # |-------------------------| # |---------------------------------| elsif ($start < $self->out->start and $end > $self->out->end ) { $result->seq_id($self->out->seq_id); if ($value->strand) { $match->strand($match->strand * $value->strand); $result->strand($match->strand); } # gap1 my $gap1 = Bio::Location::Simple->new; $gap1->start($value->start); $gap1->end($self->in->start - 1); $gap1->strand($value->strand); $gap1->seq_id($self->in->seq_id); bless $gap1, 'Bio::Coordinate::Result::Gap'; $result->add_sub_Location($gap1); # match $match->seq_id($self->out->seq_id); $match->start($self->out->start); $match->end($self->out->end); bless $match, 'Bio::Coordinate::Result::Match'; $result->add_sub_Location($match); # gap2 my $gap2 = Bio::Location::Simple->new; $gap2->start($self->in->end + 1); $gap2->end($value->end); $gap2->strand($value->strand); $gap2->seq_id($self->in->seq_id); bless $gap2, 'Bio::Coordinate::Result::Gap'; $result->add_sub_Location($gap2); } else { $self->throw("Should not be here!"); } return $result; } 1;