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module SModel.MixtureModels where
import Bio.Alphabet
import SModel.Simple
import SModel.Rate
import SModel.MixtureModel
import Tree
import Data.IntMap (IntMap)
import qualified Data.IntMap as IntMap
import qualified Data.Text as T
-- Currently we are weirdly duplicating the mixture probabilities for each component.
-- Probably the actual data-type is something like [(Double,\Int->a)] or [(Double,[a])] where all the [a] should have the same length.
-- This would be a branch-dependent mixture
data MixtureModels m = MixtureModels (IntMap Int) [Discrete m]
branch_categories (MixtureModels categories _) = categories
mmm branch_cats m = MixtureModels branch_cats [m]
instance HasAlphabet m => HasAlphabet (MixtureModels m) where
getAlphabet (MixtureModels _ (m:ms)) = getAlphabet m
instance (HasSMap m, HasAlphabet m, RateModel m, HasBranchLengths t, SimpleSModel t m) => SimpleSModel t (MixtureModels m) where
type instance IsReversible (MixtureModels m) = IsReversible m
branchTransitionP (SModelOnTree tree smodel@(MixtureModels branchCats mms)) b = branchTransitionP (SModelOnTree tree mx) b
where mx = scaleTo 1 $ mms!!(branchCats IntMap.! undirectedName b)
distribution (SModelOnTree tree (MixtureModels _ (m:ms))) = distribution (SModelOnTree tree m)
nBaseModels (SModelOnTree tree (MixtureModels _ (m:ms))) = nBaseModels (SModelOnTree tree m)
stateLetters (SModelOnTree tree (MixtureModels _ (m:ms))) = stateLetters (SModelOnTree tree m)
componentFrequencies (SModelOnTree tree (MixtureModels _ (m:ms))) = componentFrequencies (SModelOnTree tree m)
-- No Attribute
getForeground Nothing = 0
-- Attribute with no value
getForeground (Just Nothing) = 1
-- Attribute with value
getForeground (Just (Just text)) = read (T.unpack text) :: Int
foregroundBranches tree key = edgeAttributes tree (T.pack key) getForeground
-- OK, so if I change this from [Mixture Omega] to Mixture [Omega] or Mixture (\Int -> Omega), how do I apply the function modelFunc to all the omegas?
branchSite fs ws posP posW branchCats modelFunc = MixtureModels branchCats [bgMixture,fgMixture]
-- background omega distribution -- where the last omega is 1 (neutral)
where bgDist = mkDiscrete (ws ++ [1]) fs
-- accelerated omega distribution -- posW for all categories
accelDist = mkDiscrete (repeat posW) fs
-- background branches always use the background omega distribution
bgMixture = modelFunc <$> mix [1-posP, posP] [bgDist, bgDist]
-- foreground branches use the foreground omega distribution with probability posP
fgMixture = modelFunc <$> mix [1-posP, posP] [bgDist, accelDist]
branchSiteTest fs ws posP posW posSelection branchCats modelFunc = branchSite fs ws posP posW' branchCats modelFunc
where posW' = if (posSelection == 1) then posW else 1
-- A rate of 1 means that we do not rescale it.
instance RateModel m => RateModel (MixtureModels m) where
rate _ = 1
instance Scalable m => Scalable (MixtureModels m) where
scaleBy f (MixtureModels categories mixtures) = MixtureModels categories (scaleBy f <$> mixtures)
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