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    my $path = $self->option('basedir');
    return File::Spec->rel2abs($wig,$path);
}

1;

__END__

=head1 NAME

Bio::Graphics::Glyph::wiggle_box - A generic box glyph compatible with dense "wig"data

=head1 SYNOPSIS

  See <Bio::Graphics::Panel> and <Bio::Graphics::Glyph>.

=head1 DESCRIPTION

This glyph works like the regular 'box' glyph but takes value data in
Bio::Graphics::Wiggle file format:

 reference = chr1
 ChipCHIP Feature1 1..10000 wigfile=./test.wig;wigstart=0
 ChipCHIP Feature2 10001..20000 wigfile=./test.wig;wigstart=656
 ChipCHIP Feature3 25001..35000 wigfile=./test.wig;wigstart=1312

The "wigfile" attribute gives a relative or absolute pathname to a
Bio::Graphics::Wiggle format file. The optional "wigstart" option
gives the offset to the start of the data. If not specified, a linear
search will be used to find the data. The data consist of a packed
binary representation of the values in the feature, using a constant
step such as present in tiling array data.

This glyph is intended for dense, qualitative feature data.  Any score data
for each data point is only evaluated for true/false, when true, a box
of the specified bgcolor is drawn, when false, nothing is drawn.  No
data smoothing is used.

Two primary benefits of using this glyph (with wiggle data) are:

 1) For large, genome-wide data sets, the speed of panel rendering is 
    greatly improved.
 2) Large sets of related features can be rendered as a UCSC-style subtrack
    without the need for  aggregation or a GFF3 containment hierarchy. 

A disadvantage to this approach is that individual features will have no
attributes associated with them and will appear as anonymous blocks within
a sub-track. 

An example use for this glyph is annotated transcribed regions from microarray
experiments.  Such regions are identified based on raw microarray data but do 
not necessarily have a score associated with them.  In this case, using the 
wiggle_box glyph provides a graphical summary of an expression array experiment.

=head2 DATA

The wiggle data used for this glyph should be loaded using the 'BED' format in
order to allow features of variable width.  The fourth column should be a true
value, with numeric or ".".  An example is shown below:

 track type=wiggle_0 name="transfrags" description="D. melanogaster transcribed fragments 0-2hrs"
 2L      9309    9451    1
 2L      10697   11021   1
 2L      11101   11345   1
 2L      11410   11521   1
 2L      11771   12243   1
 2L      12314   12954   1
 2L      13516   15746   1
 2L      17033   17191   1
 2L      18232   18580   1
 2L      19860   19999   1

=head2 OPTIONS

This glyph accepts the standard generic option set.  It differs in that
the label and description and title/mouseover labels apply to the whole, 
panel-wide sub-track feature rather than to individual boxes.

See Bio::Graphics::Glyph::wiggle_xyplot for a description of the
wiggle-specific options and data formats.

=head1 BUGS

Please report them.

=head1 SEE ALSO

L<Bio::Graphics::Panel>,
L<Bio::Graphics::Glyph>,
L<Bio::Graphics::Glyph::arrow>,
L<Bio::Graphics::Glyph::cds>,
L<Bio::Graphics::Glyph::crossbox>,
L<Bio::Graphics::Glyph::diamond>,
L<Bio::Graphics::Glyph::dna>,
L<Bio::Graphics::Glyph::dot>,
L<Bio::Graphics::Glyph::ellipse>,
L<Bio::Graphics::Glyph::extending_arrow>,
L<Bio::Graphics::Glyph::generic>,
L<Bio::Graphics::Glyph::graded_segments>,
L<Bio::Graphics::Glyph::heterogeneous_segments>,
L<Bio::Graphics::Glyph::line>,
L<Bio::Graphics::Glyph::pinsertion>,
L<Bio::Graphics::Glyph::primers>,
L<Bio::Graphics::Glyph::rndrect>,
L<Bio::Graphics::Glyph::segments>,
L<Bio::Graphics::Glyph::ruler_arrow>,
L<Bio::Graphics::Glyph::toomany>,
L<Bio::Graphics::Glyph::transcript>,
L<Bio::Graphics::Glyph::transcript2>,
L<Bio::Graphics::Glyph::translation>,
L<Bio::Graphics::Glyph::allele_tower>,
L<Bio::DB::GFF>,
L<Bio::SeqI>,
L<Bio::SeqFeatureI>,
L<Bio::Das>,
L<GD>

=head1 AUTHOR

Sheldon McKay  E<lt>mckays@cshl.eduE<gt>.