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module SModel.Likelihood where
import Tree
-- peeling for connected-CLVs
builtin peel_leaf_branch 4 "peel_leaf_branch" "SModel"
builtin alignment_index2 2 "alignment_index2" "SModel"
builtin alignment_index3 3 "alignment_index3" "SModel"
builtin peel_internal_branch 6 "peel_internal_branch" "SModel"
builtin calc_root_probability 7 "calc_root_probability" "SModel"
-- peeling for SEV
builtin bitmask_from_alignment 2 "bitmask_from_alignment" "Alignment"
builtin peel_leaf_branch_SEV 4 "peel_leaf_branch_SEV" "SModel"
builtin peel_internal_branch_SEV 4 "peel_internal_branch_SEV" "SModel"
builtin calc_root_probability_SEV 5 "calc_root_probability_SEV" "SModel"
builtin peel_likelihood_1 3 "peel_likelihood_1" "SModel"
builtin peel_likelihood_2 6 "peel_likelihood_2" "SModel"
cached_conditional_likelihoods t seqs counts as alpha ps f = let lc = mkArray (2*numBranches t) lcf
lcf b = let bb = b `mod` (numBranches t)
in case edgesBeforeEdge t b of
[] -> let n=sourceNode t b
in peel_leaf_branch (seqs!n) (counts!n) alpha (ps!bb)
[b1,b2] -> peel_internal_branch (lc!b1) (lc!b2) (as!b1) (as!b2) (ps!bb) f
in lc
peel_likelihood t cl as f root = let likelihoods = mkArray (numNodes t) peel_likelihood'
peel_likelihood' root = let branches_in = map (reverseEdge t) (edgesOutOfNode t root)in
case branches_in of [b1,b2,b3]-> calc_root_probability (cl!b1) (cl!b2) (cl!b3) (as!b1) (as!b2) (as!b3) f
in likelihoods!root
cached_conditional_likelihoods_SEV t seqs alpha ps f a =
let lc = mkArray (2*numBranches t) lcf
lcf b = let bb = b `mod` (numBranches t) in
case edgesBeforeEdge t b of [] -> peel_leaf_branch_SEV (seqs!sourceNode t b) alpha (ps!bb) (bitmask_from_alignment a $ sourceNode t b)
[b1,b2] -> peel_internal_branch_SEV (lc!b1) (lc!b2) (ps!bb) f
in lc
peel_likelihood_SEV t cl f root counts = let branches_in = map (reverseEdge t) (edgesOutOfNode t root) in
case branches_in of [b1,b2,b3]-> calc_root_probability_SEV (cl!b1) (cl!b2) (cl!b3) f counts
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