Can I use the (protein disorder) predictor from the command line?

BioJava module biojava3-protein-disorder can be compiled into a single executable JAR file and run using java java -jar <jar_file_name> command. The jar file can be downloaded from the BioJava repository biojava3-protein-disorder-3.0.2-SNAPSHOT.jar

Alternatively if you want to integrate the predictor into your code you can use API functions to perform the calculations.

Options supported by the command line executable

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

    -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.

    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.