Need to move other things that make up their own scoring schemes to the standard library functions

[mattb112885]

I just wrote library functions to take BLAST results and compute scores in a standard way - but I still have some separate implementations of these floating around in various functions. I need to clean these up (particularly, db_bidirectionalBestHits.py, blastResultsToDistanceMatrix.py ... others?). makeBlastScoreTable.py has already been cleaned up and the recent function for Cytoscape export already was written (recently) to do this properly.