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Summary

Bio::Coordinate::ExtrapolatingPair - Continuous match between two coordinate sets

Package variables

Included modules

Inherit

Bio::Coordinate::Pair

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;

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.

Methods

Methods description

 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

 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

 Title   : strict
 Usage   : $obj->strict(1);
 Function: Set and read the strictness of the coordinate system.
 Example :
 Returns : value of input system
 Args    : boolean

Methods code

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;

}

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);
   }

}

sub new {

    my($class,@args) = @_;
    my $self = $class->SUPER::new(@args);

    my($strict) =
	$self->_rearrange([qw(STRICT
			     )],
			 @args);

    $strict  && $self->strict($strict);
    return $self;

}

sub strict {

   my ($self,$value) = @_;
   if( defined $value) {
       $self->{'_strict'} = 1 if $value;
   }
   return $self->{'_strict'};

}

General documentation

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
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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/

Email: heikki@ebi.ac.uk
Address:

     EMBL Outstation, European Bioinformatics Institute
     Wellcome Trust Genome Campus, Hinxton
     Cambs. CB10 1SD, United Kingdom

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _