Getting started

We recommend to use a software development environment (SDE) as for instance eclipse.

Basic Requirements

• Make sure that you have installed Java 1.6 or later.
• Download latest version of Jstacs.
• Include all jars (jstacs-<version>.jar and further potentially required jars from the lib directory of Jstacs) into your classpath:
  • Using a SDE, you have to add the jars to the Java build path by changing the properties of your project.
  • Using command line, you have to compile your program using: javac -cp <JARs> <YourClass>.java where <JARs> contains the path to all your jar-files.
• Run your program:
  • Using a SDE, running jobs depends on the SDE and is often linked with some button.
  • Using command line, you have to use java -cp <JARs> <YourClass>.

Additional Requirements

• If you want to use REnvironment, you must have a server with a running instance of R and Rserve.

• If you want to use UserTime, you must compile de_jstacs_utils_UserTime.c and you must set the library-path (-Djava.library.path) to the directory where the dynamic library resides. For details see the documentation of UserTime.

• Some parts of Jstacs require additional libraries. For instance, REnvironment requires RServe-<version>.jar or BioJavaAdapter requires biojava-live.jar and bytecode.jar. Such libraries can be found in the lib directory of the binary version of Jstacs.

• We use LaTeX to include formulas in our javadoc-comments. To render these as images, you need LaTeXlet.

First steps

For your first steps with Jstacs, we recommend to download the Recipes of the Jstacs Cookbook and start with compiling and running one of the simpler code examples, for instance the Creation of user-specfic alphabet. If you could compile and run this example successfully, you might want to have a look at the other Code examples and choose one of them as the starting point of your own application. If you want to extend Jstacs by your own model, classifier, or learning principle, we recommend to read the Jstacs Cookbook and use the API documentation for an overview of current implementation and abstract classes you could possibly make use of.