 
JRONN version 3.1b usage 1 August 2011:
java -jar JRONN_JAR_NAME -i=inputfile <OPTIONS>

Where -i=input file 
	Input file can contain one or more FASTA formatted sequences.

All OPTIONS are optional
Supported OPTIONS are: 
	-o=output file
	-d=disorder value
	-f=V or H 
	-s=statistics file
	-n=number of threads to use
OPTION DETAILED DESCRIPTION:
	-o full path to the output file, if not specified 
	standard out is used

	-d the value of disorder, defaults to 0.5

	-f output format, V for vertical, where the letters 
	of the sequence and corresponding disorder values are 
	output in two column layout. H for horizontal, where the
	disorder values are provided under the letters of the 
	sequence. Letters and values separated by tabulation in
	this case. Defaults to V.

	-s the file name to write execution statistics to.

	-n the number of threads to use. Defaults to the number of 
	cores available on the computer. n=1 mean sequential 
	processing. Valid values are 1 < n < (2 x num_of_cores)
	Default value will give the best performance.
	
EXAMPLES: 

	Predict disorder values for sequences from input file /home/input.fasta
	output the results to the standard out. Use default disorder value
	and utilise all cpus available on the computer.

	java -jar JRONN.JAR -i=/home/input.fasta
	
	Predict disorder values for sequences from input file /home/input.fasta
	output the results in horizontal layout to the /home/jronn.out, collect 
	execution statistics to /home/jronn.stat.txt file and limit the number 
	of threads to two. 
	
	java -jar JRONN.JAR -i=/home/input.fasta -o=/home/jronn.out -d=0.6 -n=2 -f=H
	 
	The arguments can be provided in any order.

ABOUT THE PROGRAM: 	
	
	JRONN is a Java implementation of RONN. JRONN is based on RONN and uses the 
	same model data, therefore gives the same predictions. Main motivation 
	behind JRONN development was providing an implementation of RONN more 
	suitable to use by the automated analysis pipelines and web services.  
	
	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
	See also http://www.strubi.ox.ac.uk/RONN
	
	Author: Peter Troshin 
	email: to.petr AT gmail DOT com
	
	This is a free software which comes with no guarantees.
	JRONN is distributed under Apache Licence version 2. The full version of 
	licence	can be obtained from http://www.apache.org/licenses/LICENSE-2.0
	
