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SENDU / bioperl-1.5.2_004-RC / Bio / DB / GFF / Util / Binning.pm 

            

              
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=head1 NAME
Bio::DB::GFF::Util::Binning - binning utility for Bio::DB::GFF index
=head1 SYNOPSIS
 use Bio::DB::GFF::Util::Binning qw(bin bin_bot bin_top);
 my $tier = bin($start,$stop,$min);
=head1 DESCRIPTION
This is a utility module that exports the functions bin(), bin_bot()
and bin_top().  These functions translate a range on the genome into a
named bin that is used as an index in the Bio::DB::GFF schema.  The
index makes certain range retrieval queries much faster.
=head1 API
The remainder of the document describes the function calls.  No calls
are exported by default, but must be imported explicitly.
=over 4
=cut
package Bio::DB::GFF::Util::Binning;
use strict;
require Exporter;
use vars qw(@EXPORT @EXPORT_OK);
use base qw(Exporter);
@EXPORT_OK = qw(bin bin_bot bin_top);
@EXPORT = @EXPORT_OK;
use Bio::Root::Version;
=item $bin_name = bin($start,$stop,$bin_size)
Given a start, stop and bin size on the genome, translate this
location into a bin name.  In a list context, returns the bin tier
name and the position that the bin begins.
=cut
sub bin {
  my ($start,$stop,$min) = @_;
  my $tier = $min;
  my ($bin_start,$bin_end);
  while (1) {
    $bin_start = int $start/$tier;
    $bin_end   = int $stop/$tier;
    last if $bin_start == $bin_end;
    $tier *= 10;
  }
  return wantarray ? ($tier,$bin_start) : bin_name($tier,$bin_start);
}
=item $bottom = bin_bot($tier,$start)
Given a tier name and a range start position, returns the lower end of
the bin range.
=cut
sub bin_bot {
  my $tier = shift;
  my $pos  = shift;
  bin_name($tier,int($pos/$tier));
}
=item $top = bin_top($tier,$end)
Given a tier name and the end of a range, returns the upper end of the
bin range.
=cut
sub bin_top {
  my $tier = shift;
  my $pos  = shift;
  bin_name($tier,int($pos/$tier));  #  bin_name($tier,int($pos/$tier),+1);
}
sub bin_name {
  my ($tier, $int, $fudge) = @_;
  my $pos = abs($int) + ($fudge || 0);
  $pos    = 0 if $pos < 0;
  sprintf("%d.%06d",$tier, $pos);
}
sub log10 {
  my $i = shift;
  log($i)/log(10);
}
1;
=back
=head1 BUGS
None known yet.
=head1 SEE ALSO
L<Bio::DB::GFF>,
=head1 AUTHOR
Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
Copyright (c) 2001 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
=cut