Installing BioJava is relatively easy. The easiest solution is to use Netbeans and Maven to do this for you. If you have not done so already, make sure you have installed the Maven plugin.
Start a new maven project, using the "quick start" archetype. You should then be able to find the relevant code to place into the Maven POM file. Add this code to the main class, fix the imports and then run. If it works, you have completed a BioJava "hello world".
public static void main(String[] args) throws Throwable {
ProteinSequence seq = new ProteinSequence("MSTNPKPQRKTKRNTNRRPQDVKFPGG");
List list = new ArrayList();
list.add( seq );
FastaWriterHelper.writeProteinSequence( System.out, list );
}
The complete working class is the "zeroth" part of your assessment.