Thesis writeup section implementation UML Diagram.
Simulating on different input encodings, final encoding for the std
grammar mixture number M = 5.
PCA implemented for input encoding dimension reduction.
(1) Test different input representations all using Non-negative matrix
	factorisation or Principle Component Analysis for input encoding
	dimension reduction
	--> msa profile (created)
	--> msa + hyydrophobic moment profiles (created)
	--> single seq + msa profile (created)

(2) Different grammars, mixtures, and window sizes
	--> tied at mixture level not state level
	--> different mixture numbers (1,3)
	--> window sizes (15,19,31)

(3) PSICOV 
	--> contact map estimation
	--> look for significant local correlation as most people only search
		for non-local correlation for beta-strands
	--> data stored on server at /gluster/data/tmb_maps.tgz