May 16th, Monday

Begin work on the Proteins package. Able to reorganize HMM classifications.

[ticket: X]

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 Changes to be committed:
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	modified:   ContigIterator.pyc
	new file:   Proteins/DomainFamily.py
	new file:   Proteins/DomainFamily.pyc
	new file:   Proteins/HMMParser.py
	new file:   Proteins/HMMParser.pyc
	new file:   Proteins/ProteinRunner.py
	new file:   Proteins/__init__.py
	new file:   Proteins/__init__.pyc
	modified:   Runner.py
	modified:   SimilarityContigs.pyc
	modified:   TesterScript.py