Lucene-lite : A GBrowse GFF data adaptor
v. 1.1 2005/08/30  

SYNOPSIS
  # generate index this way
  bp_load_gff.pl --adaptor lucene --create \
     --dsn $HTDOCS/gbrowse/databases/yeast_lucene \
     $HTDOCS/gbrowse/sample_data/yeast_data.gff

  # Use with GBrowse with this conf/gbrowse.conf/yeast_lucene.conf
  db_adaptor    = Bio::DB::GFF
  db_args       = -adaptor lucene
      -dsn '$HTDOCS/gbrowse/databases/yeast_lucene'

 where $HTDOCS is full path to {Generic-Genome-Browser}/htdocs

INSTALLATION
  You need to have installed and tested GBrowse, version 1.63+ 
  Fetch this adaptor software from 
  ftp://ftp.eugenes.org/eugenes/gbrowse/lucene-gbrowse-lite.zip

  Unzip and place these in {Generic-Genome-Browser}/lib/java/ 
   lib/java/lucene.jar , LuceneIndexer.class, LuceneSearcher.class
   
  Place these either in {Generic-Genome-Browser}/lib/Bio/DB/GFF/Adaptor/
  or where you have installed others in BioPerl Bio/DB/GFF/Adaptor/ .
   lib/Bio/DB/GFF/Adaptor/lucene.pm , LuceneFasta.pm
   
  Make sure this lib is in your PERL path for bp_load_gff.pl
  See  PerlDoc in lucene.pm for more information.
  
DESCRIPTION
  This adaptor implements a Lucene-index version of Bio::DB::GFF.
  It is a simple example for replacing BerkeleyDB or MySQL with Lucene. It
  runs as fast or somewhat faster than the BerkeleyDB and MySQL
  adaptors.  It is easy to install and use.
  
  The indices generated are platform-independent, unlike BerkeleyDB.
  Thus GFF data, indices, the Lucene software can be copied and used
  without special installation, compiling, data-reindexing 
  among any computers with Java.

  As soon as I get updates from this test rolled into the
  Lucene package, that will superceed this in functionality.

  There is a simple socket server, LuceneSocket, as an option to
  replace  command-line invocation of Lucene.  Benchmarks
  show that it does not speed up use over the command-line invocation,
  so it is not recommended unless you have other needs (such as
  separating Gbrowse and Lucene applications among two servers). See
  the PerlDoc in lucene.pm for more information.
  
SEE ALSO
  ftp://ftp.eugenes.org/eugenes/gbrowse/ 
  has a set of Lucene indices of genomes for Worm, Yeast, Rice,
  and 9 Fruitfly species, along with Gbrowse configuration files. You
  should be able to copy these, add to Gbrowse the Lucene-lite and
  Lucegene adaptors, and display the genomes from your favorite
  server computer.

  Example servers with these data and comparisons to other
  GBrowse adapators (Chado-Pg, MySQL, BerkeleyDB) are here:
   http://server2.eugenes.org/gbrowse/  (Sun-Solaris-x64)
   http://server3.eugenes.org/gbrowse/  (Apple-MacOSX-ppc)
     
  http://www.gmod.org/lucegene/, http://lucene.apache.org/

AUTHORS
  Don Gilbert <gilbertd@indiana.edu>
  
  Adapted from Bio::DB::GFF::Adaptor::berkeleydb 
  of Vsevolod (Simon) Ilyushchenko >simonf@cshl.edu< 
  and Lincoln Stein >lstein@cshl.edu<