If you just want to send a BLAST query to the NCBI-blast engine and then parse the result back, you can look at some examples that have been posted on Biostar: e.g: How To Perform A Blast Search From A Java Application? . You don't need Biojava.

If you want to implement the BLAST algorithm from scratch : it's a great challenge and you would learn many things(I've always dreamed to write this code), but I can't imagine this as a simple school-project, as I guess it took some years to write the first C version. However, IMHO, the most comprehensive description of the blast algorithm is its page on wikipedia: http://en.wikipedia.org/wiki/BLAST

Good Luck

You can find the QBLAST example in biojava cookbook. This is an old method that enables linking with BLAST. You can also try NCBI URLAPI if you are hoping to implement a web app.