added clean thresholding
rename _do_... routines to _do_dna_...
removed alphabet dependence from _standardize_read() now only depends on null and gap symbols
removed alphabet dependence from _estimate_probabilities() now only depends on gap and null symbols
now _estimate_probabilities() really *is* independendent of symbols
reset various arrays in _calculate_diversity() because they were not getting reset if the routine was called multiple times between calls to the initialize() method
separated symbol frequency calculation from probability, variance and covariance calculations
final cleanup of _accumulate_symbol_frequencies()
fixed bug in copy of @frequency
fixed a multitude of bugs associated with properly generating the frequency
array from the _freq array