module SModel.ReversibleMarkov (module SModel.ReversibleMarkov, module SModel.Frequency) where

import SModel.Frequency
import Bio.Alphabet
import Data.Matrix

builtin get_equilibrium_rate 4 "get_equilibrium_rate" "SModel"
builtin get_eigensystem 2 "get_eigensystem" "SModel"
builtin lExp 3 "lExp" "SModel"
builtin builtin_gtr_sym 2 "gtr_sym" "SModel"
builtin fixup_diagonal_rates 1 "fixup_diagonal_rates" "SModel"
builtin %*% 2 "elementwise_multiply" "SModel"

data ReversibleMarkov = ReversibleMarkov a b c d e f g

qExp (ReversibleMarkov a s q pi l t r) = lExp l pi t

get_q (ReversibleMarkov _ _ q _ _ t _) = scaleMatrix t q

get_pi (ReversibleMarkov _ _ _ pi _ _ _) = pi

simple_smap a = list_to_vector [0..(alphabetSize a)-1]

-- In theory we could take just (a,q) since we could compute smap from a (if states are simple) and pi from q.
reversible_markov a smap q pi = ReversibleMarkov a smap q2 pi (get_eigensystem q2 pi) 1.0 (get_equilibrium_rate a smap q2 pi) where q2 = fixup_diagonal_rates q

generic_equ n x = generic_gtr_sym (replicate n_elements x) n
    where n_elements = n*(n-1) `div` 2

equ a = generic_equ (alphabetSize a) 1.0

generic_gtr_sym exchange n = builtin_gtr_sym (list_to_vector exchange) n
gtr_sym exchange a = generic_gtr_sym exchange (alphabetSize a)

gtr a s pi = reversible_markov a (simple_smap a) (s %*% plus_f_matrix pi') pi' where pi' = list_to_vector pi

f81     pi a = gtr a (equ a) pi
jukes_cantor a = gtr a (equ a) (uniform_frequencies a)

gtr' s'    pi a = gtr a (gtr_sym' s'    a) (frequencies_from_dict a pi)

-- es' is a [(String,Double)] here
all_pairs l = [(x,y) | (x:ys) <- tails l, y <- ys]

letter_pair_names a = [l1++l2|(l1,l2) <- all_pairs (letters a)]

get_element_exchange []                 x y = error ("No exchangeability specified for '" ++ x ++ "'")
get_element_exchange ((key,value):rest) x y = if key == x || key == y then value else get_element_exchange rest x y

-- factor out code to get gtr exch list
-- maybe put ReversibleFrequency into this file.
-- clean up f1x4 and f3x4?
gtr_sym' es' a = gtr_sym es a where lpairs = all_pairs (letters a)
                                    es = if length lpairs == length es' then
                                             [get_element_exchange es' (l1++l2) (l2++l1)| (l1,l2) <- lpairs]
                                         else
                                             error "Expected "++show (length lpairs)++" exchangeabilities but got "++ show (length es')++"!"

plus_f   a s pi   = gtr a s pi
plus_fe  a s      = plus_f a s (uniform_frequencies a)
plus_gwf a s pi f = reversible_markov a (simple_smap a) (s %*% plus_gwf_matrix pi' f) pi' where pi' = list_to_vector pi
