The BIOJAVA interface in STRAP

BioJava is a set of modules and packages for biology, including sequence analysis, database access, and parsers for sequence files. Mark Schreiber maintains an excellent introduction, with many examples: BioJava Cookbook. An interface for BioJava is provided to allow authors of STRAP-plugins or -scripts to use the BioJava API. Vice-versa, BioJava projects can use the STRAP API.
Two classes are provided to convert objects between both tool-kits: One makes an GappedSequence object from a StrapProtein instance. The other class creates a StrapProtein object from a GappedSequence object. The sequence position specific features contained in the classes are also transformed.

Testing the STRAP-BioJava-interface

Plugins for STRAP can be created, started, and modified at runtime. A few demo-plugins are enclosed in STRAP to exemplify the usage of plugins. When STRAP is started there are several possibilities to get some protein files for testing into STRAP. In the menu Plugins of the toolbar is a menu item Start standard plugin ..... There you can select the BioJava example.

Comparing BioJava and the STRAP-API

Differences between BioJava and STRAP: