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module SModel.Codons (module SModel.Codons) where
import Alphabet
import SModel.ReversibleMarkov
import SModel.Nucleotides
builtin m0 3 "m0" "SModel"
builtin f3x4_frequencies_builtin 4 "f3x4_frequencies" "SModel"
builtin singlet_to_triplet_rates 4 "singlet_to_triplet_rates" "SModel"
builtin dNdS_matrix 2 "dNdS_matrix" "SModel"
f3x4_frequencies a pi1 pi2 pi3 = let pi1' = list_to_vector pi1
pi2' = list_to_vector pi2
pi3' = list_to_vector pi3
in list_from_vector $ f3x4_frequencies_builtin a pi1' pi2' pi3'
f3x4'_frequencies a pi1 pi2 pi3 = zip (alphabet_letters a) (f3x4_frequencies a pi1' pi2' pi3')
where pi1' = get_ordered_elements nuc_letters pi1 "frequencies"
pi2' = get_ordered_elements nuc_letters pi2 "frequencies"
pi3' = get_ordered_elements nuc_letters pi3 "frequencies"
nuc_letters = alphabet_letters a_nuc
a_nuc = getNucleotides a
f1x4_frequencies a pi = f3x4_frequencies a pi pi pi
f1x4'_frequencies a pi = f3x4'_frequencies a pi pi pi
gy94_ext sym w pi a = gtr a (m0 a sym w) pi
gy94 k w pi a = gy94_ext sym w pi a where sym = hky85_sym k $ getNucleotides a
mg94_ext a w q = q & x3 a & dNdS w
mg94k a k pi w = hky85 k pi nuc_a & mg94_ext a w where nuc_a = getNucleotides a
mg94 a pi w = f81 pi nuc_a & mg94_ext a w where nuc_a = getNucleotides a
x3x3 a (ReversibleMarkov _ _ q_1 pi_1 _ _ _) (ReversibleMarkov _ _ q_2 pi_2 _ _ _) (ReversibleMarkov _ _ q_3 pi_3 _ _ _) =
let smap = simple_smap a
q = singlet_to_triplet_rates a q_1 q_2 q_3
pi = f3x4_frequencies_builtin a pi_1 pi_2 pi_3
in reversible_markov a smap q pi
x3_sym a s = singlet_to_triplet_rates a s s s
x3 a q = x3x3 a q q q
-- maybe this should be t*(q %*% dNdS_matrix) in order to avoid losing scaling factors? Probably this doesn't matter at the moment.
dNdS omega (ReversibleMarkov a s q pi l t r) = reversible_markov a s q2 pi where q2 = q %*% dNdS_matrix a omega
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