new PWM model
pwm --> pm & pwm & named_model
pcm, ppm
add tests for each_position w/o a block; refine error for PWM#score; remove #consensus from PM
IUPAC module
consensus formatter
iupac-->alphabet&iupac
make use of alphabet for PM|PWM
added validation errors to exceptions
background classes
fix Motif #==. rspec should --> expect for parser_spec
matrix parser spec; bioinform error classes extracted
PrettyMatrixFormatter extracted to a class
formatters converted into format FormatterClass.new(options).format_string(pm)
parsers classified (not finished)
added equality check for alphabets; PM-s should be on equal alphabets to be equal; fixed typo in word ComplemetaryAlphabet
less use of @matrix instance variable, use accessors instead
remove bad and unused feature PM#as_pcm,#as_pwm, #as_ppm
converters don't use #get_parameters
most data models don't use parameters