/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
/**<p>
* BioJava provide a module biojava-protein-disorder for prediction disordered regions
* from a protein sequence. Biojava-protein-disorder module for now contains one method
* for the prediction of disordered regions. This method is based on the Java
* implementation of RONN predictor.
* <p>
* This code has been originally developed for use with <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>.
* We call this code JRONN. JRONN is based on the C implementation of RONN algorithm and uses the same model data,
* therefore gives the same predictions. JRONN based on <a href="http://www.strubi.ox.ac.uk/RONN">RONN</a>
* version 3.1 which is still current in time of writing (August 2011).
* Main motivation behind JRONN development was providing an implementation of RONN more
* suitable to use by the automated analysis pipelines and web services.
* Robert Esnouf has kindly allowed us to explore the RONN code and share the results with the community.
* <p>
* Original version of RONN is described in Yang,Z.R., Thomson,R., McMeil,P. and Esnouf,R.M. (2005)
* RONN: the bio-basis function neural network technique applied to the detection of natively
* disordered regions in proteins. Bioinformatics 21: 3369-3376
* <p>
* Examples of use are provided below. For more information please refer to JronnExample testcases.
* @author Peter Troshin
*
* @version 1.0 January 2010
* @since 3.0.2
*/
package org.biojava.nbio.ronn;