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module SModel.Frequency (module SModel.Frequency, Markov.plus_gwf_matrix, Markov.plus_f_matrix) where
-- Rename to SModel.Frequencies?
import Bio.Alphabet
import Foreign.Vector
import Data.Matrix
import qualified Markov
foreign import bpcall "SModel:average_frequency" builtin_average_frequency :: Matrix Double -> EVector Double
-- pi is [Double] here
uniform_frequencies a = Markov.uniform_frequencies $ alphabetSize a
uniform_frequencies_dict a = zip (getLetters a) (uniform_frequencies a)
-- pi is [(String,Double)] here
select_element key dict = case lookup key dict of Just value -> value
Nothing -> error $ "Can't find element " ++ show key ++ " in dictionary!"
select_elements keys dict = map (flip select_element dict) keys
get_ordered_elements xs xps plural = if length xs == length xps
then select_elements xs xps
else error $ "Expected "++show (length xs)++" "++plural
++" but got "++ show (length xps)++"!"
frequenciesFromDict a pi = get_ordered_elements (getLetters a) pi "frequencies"
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