Bio::Location::NarrowestCoordPolicy - class implementing

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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

SYNOPSIS

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See Bio::Location::CoordinatePolicyI

DESCRIPTION

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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).

FEEDBACK

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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
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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 the web:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Hilmar Lapp, Jason Stajich

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Email <hlapp-at-gmx.net>, <jason@bioperl.org>

APPENDIX

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

start

  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.

end

  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.
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::Location::NarrowestCoordPolicy
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Hilmar Lapp <hlapp@gmx.net>
#          and Jason Stajich <jason@bioperl.org>
#
# Copyright Hilmar Lapp, Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code


# Let the code begin...


package Bio::Location::NarrowestCoordPolicy;
use strict;


use base qw(Bio::Root::Root Bio::Location::CoordinatePolicyI);

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;
}


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;