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module SModel.RNAEdit where
import Bio.Alphabet
import SModel.ReversibleMarkov
import SModel.Nucleotides
import qualified Markov
import Markov (getQ, getEqFreqs)
import Probability.Distribution.Mixture
import SModel.Doublets
type RNAEditAlphabet = Alphabet
foreign import bpcall "SModel:" rna_editting_rates :: RNAEditAlphabet -> Matrix Double -> EVector (EPair Int Int) -> Double -> Matrix Double
foreign import bpcall "SModel:" rna_editting_pi :: RNAEditAlphabet -> EVector Double -> EVector (EPair Int Int) -> EVector Double
siteEdit alphabet nucModel rnaRate edits = reversible $ markov alphabet smap q pi
where smap = simpleSMap alphabet
nucs = getNucleotides alphabet
qNuc = getQ nucModel
piNuc = getEqFreqs nucModel
q = rna_editting_rates alphabet qNuc edits' rnaRate
pi = rna_editting_pi alphabet piNuc edits'
edits' = toVector [ c_pair (findLetter nucs i) (findLetter nucs j) | (i,j) <- edits]
siteNone a nucModel rnaRate = siteEdit a nucModel rnaRate []
siteC2U a nucModel rnaRate = siteEdit a nucModel rnaRate [("C","U")] -- forward
siteU2C a nucModel rnaRate = siteEdit a nucModel rnaRate [("U","C")] -- reverse
both a nucModel rnaRate = [ siteNone a nucModel rnaRate,
siteC2U a nucModel rnaRate,
siteU2C a nucModel rnaRate]
bothMixture a nucModel rnaRate ps = mixture ps $ both a nucModel rnaRate
--rna_edit_both'' a nuc_model rnaRate sym =
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