module SModel.Doublets where

import Bio.Alphabet
import SModel.ReversibleMarkov
import SModel.Nucleotides
import qualified Markov
import Markov (get_q, get_pi)

type DoubletAlphabet = Alphabet

foreign import bpcall "SModel:f2x4_frequencies" f2x4_frequencies_builtin :: DoubletAlphabet -> EVector Double -> EVector Double -> EVector Double
foreign import bpcall "SModel:singlet_to_doublet_rates" singlet_to_doublet_rates :: DoubletAlphabet -> Matrix Double -> Matrix Double -> Matrix Double

x2x2 a m1 m2 = reversible_markov a smap q pi where
    smap = simple_smap a
    q = singlet_to_doublet_rates a (get_q m1) (get_q m2)
    pi = f2x4_frequencies_builtin a (get_pi m1) (get_pi m2)

x2_sym a s = singlet_to_doublet_rates a s s
x2 a q = x2x2 a q q

foreign import bpcall "SModel:rna_16a_exchange" rna_stem_16a_exchange :: DoubletAlphabet -> Double -> Double -> Double -> Double -> Double -> Matrix Double

rna_stem_16a a aS aD b g e pi = gtr a (rna_stem_16a_exchange a aS aD b g e) pi

foreign import bpcall "SModel:" rna_editting_rates :: DoubletAlphabet -> Matrix Double -> EVector (EPair Int Int) -> Matrix Double
foreign import bpcall "SModel:" rna_editting_pi :: DoubletAlphabet -> EVector Double -> EVector (EPair Int Int) -> EVector Double

rna_editting a nuc_model edits = reversible_markov a smap q pi
    where smap = simple_smap a
          nuc_a = getNucleotides a
          q_nuc = get_q nuc_model
          pi_nuc = get_pi nuc_model
          q = rna_editting_rates a q_nuc edits'
          pi = rna_editting_pi a pi_nuc edits'
          edits' = list_to_vector [ c_pair (find_letter nuc_a i) (find_letter nuc_a j) | (i,j) <- edits]
