Raw content of Bio::Coordinate::ExtrapolatingPair # $Id: ExtrapolatingPair.pm,v 2003/02/20 05:11:45 heikki Exp $ # # bioperl module for Bio::Coordinate::ExtrapolatingPair # # 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::ExtrapolatingPair - Continuous match between two coordinate sets =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; $res->end eq 20; =head1 DESCRIPTION This class represents a one continuous match between two coordinate systems represented by Bio::Location::Simple objects. The relationship is directed and reversible. It implements methods to ensure internal consistency, and map continuous and split locations from one coordinate system to another. This class is an elaboration of Bio::Coordoinate::Pair. The map function returns only matches which is the mode needed most of tehtime. By default the matching regions between coordinate systems are boundless, so that you can say e.g. that gene starts from here in the chromosomal coordinate system and extends indefinetely in both directions. If you want to define the matching regions exactly, you can do that and set strict() to true. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists =head2 Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki@ebi.ac.uk Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Coordinate::ExtrapolatingPair; use vars qw(@ISA ); use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Root::Root; use Bio::LocationI; use Bio::Coordinate::Pair; @ISA = qw(Bio::Coordinate::Pair); sub new { my($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 undef) ; } 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 undef if $start < 0 and $end < 0; return undef 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;