NAME

Bio::GMOD::Blast::Graph - display a graphical summary of a BLAST report

DESCRIPTION

This package provides methods for graphically displaying a BLAST search report.

METHODS

new

This is the constructor. It expects to be passed named arguments for the search outputfile, the file format (blast or fasta), the image file path, and image url. It can also accept an optional filehandle argument, which is the filehandle to which it will print its HTML output when "showGraph" is called. By default, prints to STDOUT.

Usage :

my $graph = Bio::GMOD::Blast::Graph->new(
    -outputfile => $blastOutputFile,
    -format     => 'blast',
    -dstDir     => $imageDir,
    -dstURL     => $imageUrl
    -fh         => \*STDOUT,
    );

showGraph

This method prints the map to stdout (web browser).

Usage:

$graph->showGraph;

getImageFile

This method returns the newly created image file name (with full path).

Usage:

my $imageFile = $graph->getImageFile;

hitNameArrayRef

This method returns the array ref for the hit names.

Usage:

my $hitArrayRef = $graph->hitNameArrayRef;

foreach my $hitName (@$hitArrayRef) {

   # do something useful here

}

AUTHORS

• Shuai Weng <shuai@genome.stanford.edu>

• John Slenk <jces@genome.stanford.edu>

• Robert Buels <rmb32@cornell.edu>

• Jonathan "Duke" Leto <jonathan@leto.net>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2011 by The Board of Trustees of Leland Stanford Junior University.

This is free software, licensed under:

The Artistic License 1.0