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Summary

Bio::Location::AvWithinCoordPolicy - class implementing
Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise

Package variables

Included modules

Inherit

Bio::Location::WidestCoordPolicy

Synopsis

See Bio::Location::CoordinatePolicyI

Description

CoordinatePolicyI implementing objects are used by Bio::LocationI
implementing objects to determine integer-valued coordinates when
asked for it.
This class will compute the coordinates such that for fuzzy locations
of type WITHIN and BETWEEN the average of the two limits will be
returned, and for all other locations it will return the widest
possible range, but by using some common sense. This means that
e.g. locations like "<5..100" (start before position 5) will return 5
as start (returned values have to be positive integers).

Methods

Methods description

  Title   : end
  Usage   : $end = $policy->end($location);
  Function: Get the integer-valued end coordinate of the given location as
            computed by this computation policy.
  Returns : A positive integer number.
  Args    : A Bio::LocationI implementing object.

  Title   : start
  Usage   : $start = $policy->start($location);
  Function: Get the integer-valued start coordinate of the given location as
            computed by this computation policy.
  Returns : A positive integer number.
  Args    : A Bio::LocationI implementing object.

Methods code

sub end {

    my ($self,$loc) = @_;

    if(($loc->end_pos_type() eq 'WITHIN') ||
       ($loc->end_pos_type() eq 'BETWEEN')) {
	my ($min, $max) = ($loc->min_end(), $loc->max_end());
	return int(($min+$max)/2) if($min && $max);
    }
    return $self->SUPER::end($loc);
}

1;

}

sub new {

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

    return $self;

}

sub start {

    my ($self,$loc) = @_;

    if(($loc->start_pos_type() eq 'WITHIN') ||
       ($loc->start_pos_type() eq 'BETWEEN')) {
	my ($min, $max) = ($loc->min_start(), $loc->max_start());
	return int(($min+$max)/2) if($min && $max);
    }
    return $self->SUPER::start($loc);

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
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  bioperl-bugs@bio.perl.org
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The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _