Align ToDo




==============

	
	- speed up getCost
	- test code

	Basic PairwiseAligner:
		- have preprocess cost matrix for DNA data
		- deal with terminal gaps with lower cost
		- give it access to a user-supplied cost matrix
		- GUI for costs
		- preferences
		

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Travis: 
	- pickCosts is no longer used to set the basic costs.  That is now done by getDefaultCosts in AlignUtil
	
	- I've changed the code so that it copes with amino acid data (it didn't before).  e.g., alphabetLength
	is now passed along; the substitution matrix produced by getDefaultCosts is now
	of a size appropriate to the data
	
	- Ambiguity codes are now dealt with.  This requires different storage in the int[] A and int[]B.
	The values in these arrays NO LONGER correspond to the A=0, C=1, G=2, T=3.  Instead, the values
	here are simply int representations of the lower 32 bits of the state set.  
	e.g., the following state sets will have the following integer values:
		A = 1
		C = 2
		G = 4
		T = 8
		A or G = 5
		
	This requires that when two values are compared, a method is now used to calculate the subsitution cost.  
	This function is  AlignUtil.getCost(subs,a,b,alphabetLength), and it figures out the ambiguity cost.
	We should make this faster for DNA data by having a pre-processed subs matrix that is
	16x16, but I just haven't managed to do that yet.
	
	- I commented out your "score is" logging as it was taking too long!
	
	- some of the modules I wrote (e.g., AlignMatch)  now use PairwiseAligner rather than a module.