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.