Summary

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

Package variables

Included modules

Inherit

Bio::Coordinate::Pair

Synopsis

  # to use
  use Bio::Coordinate::ExtrapolatingPair;

  $a  = Bio::Coordinate::ExtrapolatingPair->new();
  $b  = Bio::Coordinate::ExtrapolatingPair -> new ( -id => 3 );

Description

Class

Methods

Methods description

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

 Title   : map
 Usage   : $newpos = $obj->map(5);
 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 value in the output coordinate system
 Args    : integer

Methods code

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'};

}

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 $result = new Bio::Coordinate::Result;

   my ($offset, $start, $end);
   if ($self->strand == -1) {
       $start = -1 * ($value->end - $self->in->end  - 1);
       $end = -1* ($value->start - $self->in->end  - 1);
   } 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';
#   $result->add_Location($match);
   return $match;

}

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
  http://bio.perl.org/MailList.html             - About the mailing lists

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 _