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module SModel.MutSel where
import Data.Array
import Foreign.Vector
import SModel.ReversibleMarkov
import SModel.Codons
import SModel.Frequency -- for get_ordered_elements
import Bio.Alphabet
import qualified Markov
import Markov (getQ, getEqFreqs)
foreign import bpcall "SModel:" mut_sel_q :: Matrix Double -> EVector Double -> Matrix Double
foreign import bpcall "SModel:" mut_sel_pi :: EVector Double -> EVector Double -> EVector Double
mut_sel ws' m0@(Reversible (Markov a smap _ _)) = reversible $ markov a smap q pi where
q0 = getQ m0
pi0 = getEqFreqs m0
ws = toVector ws'
q = mut_sel_q q0 ws
pi = mut_sel_pi pi0 ws
mut_sel' w' q0 = mut_sel w q0 where
w = get_ordered_elements (getLetters a) w' "fitnesses"
a = getAlphabet q0
mut_sel_aa ws q@(Reversible (Markov codon_a _ _ _)) = mut_sel (aa_to_codon codon_a ws) q
mut_sel_aa' ws' q0 = mut_sel_aa ws q0 where
ws = get_ordered_elements (getLetters amino_alphabet) ws' "fitnesses"
codon_alphabet = getAlphabet q0
amino_alphabet = getAminoAcids codon_alphabet
fMutSel codon_a codon_w omega nuc_model = nuc_model & x3 codon_a & dNdS omega & mut_sel codon_w
fMutSel' codon_a codon_ws' omega nuc_model = fMutSel codon_a codon_ws omega nuc_model
where codon_ws = get_ordered_elements (getLetters codon_a) codon_ws' "fitnesses"
aa_to_codon codon_a xs = [xs_array!aa | codon <- codons, let aa = translate codon_a codon]
where xs_array = listArray' xs
codons = take n_letters [0..]
n_letters = alphabetSize codon_a
-- \#1->let {w' = listAray' #1} in \#2 #3->fMutSel #0 codon_w #2 #3
-- The whole body of the function is let-floated up in round 2, and w' is eliminated.
fMutSel0 codon_a aa_w omega nuc_q = fMutSel codon_a codon_w omega nuc_q
where codon_w = aa_to_codon codon_a aa_w
fMutSel0' codon_a amino_ws' omega nuc_model = fMutSel0 codon_a amino_ws omega nuc_model
where amino_ws = get_ordered_elements (getLetters amino_a) amino_ws' "fitnesses"
amino_a = getAminoAcids codon_a
-- Issue: bad mixing on fMutSel model
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