Ah Fu & Peter

Implements "CompoundSet" interface to enable the definition of any symbol in XML file to represent amino acids and modified amino acids. Implemented the Command Prompt, test cases for it and prepared several examples for it.

Finish up the work on Command Prompt (CookBook) and move on to the final phase of the project, which is the implementation of JABAWS.

Usage of BioJava FASTA Reader or implementation of our own.