-- |
-- Module      :  ELynx.Simulate.MarkovProcessAlongTreeSpec
-- Copyright   :  (c) Dominik Schrempf 2021
-- License     :  GPL-3.0-or-later
--
-- Maintainer  :  dominik.schrempf@gmail.com
-- Stability   :  unstable
-- Portability :  portable
--
-- Creation date: Thu Jan 24 15:25:49 2019.
module ELynx.Simulate.MarkovProcessAlongTreeSpec
  ( spec,
  )
where

import Data.Tree
import ELynx.Data.MarkovProcess.Nucleotide
import qualified ELynx.Data.MarkovProcess.SubstitutionModel as S
import ELynx.Simulate.MarkovProcess
import ELynx.Simulate.MarkovProcessAlongTree
import System.Random.MWC
import Test.Hspec

-- sampleNewickText :: T.Text
-- sampleNewickText = T.pack "(Aeropyrum0:0.5478645225,(((((((((Arabidopsi:0.0701001024,Oryza_sati:0.0765988261):0.0309636193,Gymnosperm:0.0520325624):0.0338982245,Physcomitr:0.0768008916):0.0895714685,(Chlamydomo:0.1136227755,Dunaliella:0.1406347323):0.1117340620):0.0818876186,Rhodophyta:0.3405656487):0.0363527066,((((((Babesia_bo:0.1646969208,Theileria0:0.1519889486):0.1908081096,Plasmodium:0.3250696762):0.0637865908,(Toxoplasma:0.1153570425,Eimeria000:0.1671916078):0.0980136930):0.0518956330,Cryptospor:0.3175062809):0.1607708388,Ciliophora:0.5687502950):0.0624078848,(Phytophtho:0.2016424948,((Thalassios:0.1202730781,Phaeodacty:0.1290341329):0.1772775509,Phaeophyce:0.1989260715):0.0312359673):0.1154768302):0.0311952864):0.0149160316,(((((((((Candida_al:0.1027755272,Saccharomy:0.1190206560):0.1333487870,Neurospora:0.1977309079):0.0522926266,Schizosacc:0.2019603227):0.0567441011,(Cryptococc:0.1948614959,Ustilago_m:0.1564451295):0.0775729694):0.0323959951,Glomus_int:0.1573670796):0.0194701292,Chytridiom:0.2228415254):0.0384370601,Encephalit:1.4622174644):0.0416231688,(((Drosophila:0.2160627753,(Mammalians:0.1080484094,Tunicates0:0.1739253014):0.0289624371):0.0346633757,Hydrozoa00:0.2058137032):0.0480963050,Monosiga_b:0.3020637584):0.0654894239):0.0380915725,(Dictyostel:0.3453588998,Mastigamoe:0.3844779231):0.0478795653):0.0129578395):1.7592083381,((Archaeoglo:0.5402784445,Methanococ:0.4088567459):0.0993669265,Pyrococcus:0.4058713829):0.1734405968):0.2193511807,Pyrobaculu:0.7507718047):0.1646616482,Sulfolobus:0.5404967897);"

testTree :: Tree Double
testTree = Node 0.0 [Node 1.0 [], Node 1.0 []]

-- testStateTree :: Tree State
-- testStateTree = Node 0 [Node 3 [], Node 2 []]

nullTree :: Tree Double
nullTree = Node 0 []

nullStateTree :: Tree State
nullStateTree = fmap (const 2) nullTree

-- uniformStationaryDistribution :: Int -> Vector R
-- uniformStationaryDistribution n = fromList $ replicate n (1.0 / fromIntegral n)

spec :: Spec
spec = describe "simulateNSitesAlongTree" $ do
  it "simulates one site along an easy tree" $ do
    gen <- create
    tr <- simulate 1 d e nullTree gen
    fmap head tr `shouldBe` nullStateTree
  it "simulates some sites along a harder tree" $ do
    gen <- create
    tr <- simulate 10 d e testTree gen
    (length . rootLabel $ tr) `shouldBe` 10
  where
    d = S.stationaryDistribution jc
    e = S.exchangeabilityMatrix jc