JEnsembl: JavaAPI to Ensembl Datasources Files

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Ensembl Savant PlugIn Demo
version 2.0.2
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This plug-in for the Savant Genome Browser (http://compbio.cs.toronto.edu/savant/index.html ref. below)
uses the prototype Java API for the Ensembl datasources, JEnsembl (http://jensembl.sourceforge.net/).

Its aim is to demonstrate the potential of a Ensmebl JavaAPI for development of Java tools
for Bioinformatics. This plug-in works on Windows and Linux, but may be buggy on Macs.
The plug-in jar includes all of the JEnsembl API dependencies bundled up including
the 3.0.3 release version of BioJava3core (http://www.biojava.org/wiki/BioJava3_project).
The plug-in Jar should be added to the plug-ins directory of Savant.

The plug-in provides a simple menu driven Swing interface to import any available plant, animal or
bacterial chromosome sequence currently available for any Species at Ensembl or EnsemblGenomes
(including the bacterial collections at Ensembl Genomes as well as the more 'typical' eukaryotic genomes).
The chromosome can be imported with or without its DNA Sequence, and decorated with gene annotations
from the Ensembl data sources.

The plug-in is built with the Savant jar (version 2.0.2)
using JEnsembl demo release 1.10.

[Note it does not use the sdk  development jar of savant as this is not insync with the release binaries.]

***NOTE: Release 2.0.2 of this plug-in will only work properly with Savant version 2.0.2 and not  earlier releases ***

Code use is covered by GPLv3 licence (attached) .

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   USAGE
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Usage is illustrated in SavantEnsemblPluginPresentation.pdf available at
http://sourceforge.net/projects/jensembl/files/Savant%20Plugin/SavantEnsemblPluginPresentation.pdf/download

Once the user selects a species/build - they can load any of the chromosomes or assemblies
available for that species: either as a bare coordinate skeleton or as the full sequence.
Obviously loading the full sequence is quite heavy weight/slow, but the fasta and savant
binary versions of the file are stored locally allowing faster future access. Currently the
Plugin/Savant cannot handle importing extremely large chromosomal sequences for display,
and these should only be imported as coordinates.

NOTE a few species in Ensembl don't have chromosome builds - and  an  error will be reported by the GUI....

Once a genome track is loaded (as coordinates or sequence) the genes mapped on that chromosome
can be fetched from from Ensembl (again through the JEnsembl API).
The coordinates are converted to a BED file and Savant binary, and again these files are dumped locally.

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LICENCE
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/**
 * Copyright (C) 2012 The Roslin Institute <contact andy.law@roslin.ed.ac.uk>
 *
 * This file is part of the Ensembl Java API demonstration project developed by the
 * Bioinformatics Group at The Roslin Institute, The Royal (Dick) School of
 * Veterinary Studies, University of Edinburgh.
 *
 * This is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License (version 3) as published by
 * the Free Software Foundation.
 *
 * This software is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * in this software distribution. If not, see <http://www.gnu.org/licenses/gpl-3.0.html/>.
 */

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Savant Reference
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Fiume,M., Williams,V., Brook,A. and Brudno,M. (2010)
Savant: genome browser for high-throughput sequencing data. Bioinformatics, 26, 1938-1944.