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module SModel.Doublets where
import Bio.Alphabet
import SModel.ReversibleMarkov
import SModel.Nucleotides
import qualified Markov
import Markov (getQ, getEqFreqs)
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 = simpleSMap a
q = singlet_to_doublet_rates a (getQ m1) (getQ m2)
pi = f2x4_frequencies_builtin a (getEqFreqs m1) (getEqFreqs 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
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