A general tutorial and feature overview can be found in the PROMPT Case Studies section.
If you issue is not covered here, please feel free to contact us or write to the PROMPT community mailing list.

PROMPT Reference

Schmidt, T. and Frishman, D. (2006) PROMPT: A protein mapping and comparison tool. BMC Bioinformatics, 7(1),331.


Advanced questions:

How to script? top

The complete functionality of PROMPT can be automated and used in own applications, client-server architectures (e.g. web servers) and (distributed) processing pipelines. The first and simplest possibility is to use the Beanshell language. This is a super set of Java allowing light-weight and straight forward scripting in addition to full syntax-conform Java. All existing Java classes (e.g. Web Services like Axis) can be used in Beanshell code.

PROMPT "writes" the programs for you:

click to enlarge

Within PROMPT's graphical user interface (GUI), you can find -next to the Infos and Messages field- the Beanshell Macro tab.

Here PROMPT records all actions that are performed within the GUI directly as Beanshell commands.

This is very convenient as you do not need to look up any details about classes or method names. Simply do it once in the GUI and let PROMPT log the script code. With the right-mouse click at the Beanshell tab you can save the recorded commands to a file and execute the workflow at any time.

All Beanshell scripts (or complete JAVA source code) can be executed by the PROMPT framework by a varity of ways:

How to use PROMPT's Java API directly? top

Simply include the prompt_complete.jar (download page) in your classpath and use the classes and methods in your Java program as any other classes. One practical approach is to let the PROMPT GUI log the actions and then extend the Beanshell script to full Java syntax.

How to set the R path (in my own scripts or applications)? top

In all cases in which PROMPT uses R as statistical calculation engine or as visualisation backend the path and name of the R executable is expected to be set in the Java-System Property rproject.rexe. This System property as well as all other configuration settings of the PROMPT framework can be set by a multitude of ways:

How to install additional R packages? top

The fancy scatter plot used in PROMPT needs an additional R package. Here you can find install instructions.

How to extend the classpath within Beanshell scripts dynamically? top

The conservative way to set the classpath is during the java run call (e.g. java -classpath /home/users/...). However you can also extend the classpath dynamically within Beanshell scripts. Example:

// includes the additional thtest.jar in c:\test
import *;
//automatically maps all class names and methods so that no additional imports should be necessary

More information can be found in the Beanshell documentation .

How to hack PROMPT? top

The PROMPT framework consists of multiple modules that are basically seperated into three layers: input, engine and visualisation. As most classes are independet from each other "global" settings are accomplished via Java's System Properties. A list of all hidden parameters is given here.


Thorsten Schmidt
Hochschule Emden/Leer
Faculty of Technology
Constantiaplatz 4, 26723 Emden, Germany

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