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Summary

Bio::Location::NarrowestCoordPolicy - class implementing
Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range

Package variables

Included modules

Inherit

Bio::Location::CoordinatePolicyI Bio::Root::Root

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 always the narrowest possible
range is returned, 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) = @_;

    # For performance reasons we don't check that it's indeed a Bio::LocationI
    # object. Hopefully, Location-object programmers are smart enough.
    my $pos = $loc->min_end();
    # if min is not defined or equals 0 we resort to max
    $pos = $loc->max_end() if(! $pos);
    return $pos;
}

1;

}

sub new {

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

    return $self;

}

sub start {

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

    # For performance reasons we don't check that it's indeed a Bio::LocationI
    # object. Hopefully, Location-object programmers are smart enough.
    my $pos = $loc->max_start();
    # if max is not defined or equals 0 we resort to min
    $pos = $loc->min_start() if(! $pos);
    return $pos;

}

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
of 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 hlapp@gmx.net, jason@bioperl.org

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