1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
|
module SModel.BranchModel where
import qualified Markov
import Markov (CTMC(..))
import SModel.Simple
import SModel.Rate
import SModel.Frequency
import Bio.Alphabet
import Data.Matrix
import Tree
{-
This model is for PAML's branch-model, where every branch can have a different Q matrix
BUT they must all have the same equilibrium frequencies.
-}
-- Should this also take a tree?
-- Should we just have a bare function?
-- Should we have an IntMap?
data BranchMap a = BranchMap (Int -> a)
data BranchModel a = BranchModel Alphabet (EVector Int) (EVector Double) (BranchMap a)
instance Functor BranchMap where
fmap f (BranchMap g) = BranchMap (f . g)
instance Functor BranchModel where
fmap f (BranchModel a smap pi map) = BranchModel a smap pi (f <$> map)
instance HasAlphabet (BranchModel a) where
getAlphabet (BranchModel alphabet _ _ _) = alphabet
instance HasSMap (BranchModel a) where
getSMap (BranchModel _ smap _ _) = smap
instance (HasSMap m, HasBranchLengths t, CTMC m) => SimpleSModel t (BranchModel m) where
stateLetters (SModelOnTree tree model) = getSMap model
branchTransitionP (SModelOnTree tree model) b = [qExp $ scaleBy (branchLength tree b) (ratesForBranch b)]
where (BranchModel _ _ _ (BranchMap ratesForBranch)) = model
componentFrequencies (SModelOnTree _ (BranchModel _ _ pi _)) = [pi]
|
