BioJava is a suite of libraries which is specifically designed for bioinformatics, described here:
BioJava: an Open-Source Framework for Bioinformatics
R.C.G. Holland; T. Down; M. Pocock; A. Prlić; D. Huen; K. James; S. Foisy; A. Dräger; A. Yates; M. Heuer; M.J. Schreiber Bioinformatics 2008; doi://10.1093/bioinformatics/btn397
Please read this paper.
We will be working through the BioJava tutorial. You will be assessed on how well you implement the examples that are given. Code will be submitted through subversion. This means that it will be accessible to everybody; the complete history and full timestamps will also be available. Please remember the university regulations on submission of coursework.
Installing BioJava is relatively easy. You should be able to find the jar files that you need to download for yourself; there are 5 or 6 of these. Download and put them somewhere safe on your machine.
Create a new project within Netbeans called "biojava". When the project has been created, click on "libraries" in the "Project" window, then "add jar/directory". You can now select your Jar files; the dialogue will allow you to select several files at the same time.