RootedSpec.hs

{-# LANGUAGE OverloadedStrings #-}

-- |
-- Module      :  ELynx.Data.Tree.RootedSpec
-- Description :  Unit tests for ELynx.Data.Tree.Rooted
-- Copyright   :  (c) Dominik Schrempf 2020
-- License     :  GPL-3.0-or-later
--
-- Maintainer  :  dominik.schrempf@gmail.com
-- Stability   :  unstable
-- Portability :  portable
--
-- Creation date: Mon May  6 14:04:05 2019.
module ELynx.Data.Tree.RootedSpec
  ( spec,
  )
where

import Data.ByteString.Lazy.Char8 (ByteString)
import qualified Data.ByteString.Lazy.Char8 as L
import Data.Maybe
import ELynx.Data.Tree
import ELynx.Import.Tree.Newick
import ELynx.Tools
import Test.Hspec

node :: Int -> Tree () Int
node n = Node () n []

smallTree :: Tree () Int
smallTree = Node () 0 [node 1, node 2]

smallSubTree :: Tree () Int
smallSubTree = Node () 0 [node 1]

smallSubTreePruned :: Tree () Int
smallSubTreePruned = node 1

sampleTreeBS :: ByteString
sampleTreeBS =
  L.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);"

largeTree :: Tree Phylo ByteString
largeTree = parseByteStringWith "Sample newick byte string" (newick Standard) sampleTreeBS

subSampleLargeTree :: Tree Phylo ByteString
subSampleLargeTree = fromJust $ dropLeavesWith ((/= 'P') . L.head) largeTree

spec :: Spec
spec = do
  describe "prune" $ do
    it "leaves a normal tree untouched" $
      prune largeTree `shouldBe` largeTree
    it "correctly prunes a small example" $
      prune smallSubTree `shouldBe` smallSubTreePruned
    it "leaves height constant for Measurable trees" $ do
      let t' =
            either error id $
              phyloToLengthTree subSampleLargeTree
      height (prune t') `shouldBe` height t'
  describe "dropLeavesWith" $ do
    it "returns the same tree if no leaves satisfy predicate" $
      dropLeavesWith (const False) smallTree `shouldBe` Just smallTree
    it "returns nothing if all leaves satisfy predicate" $
      dropLeavesWith (const True) smallTree `shouldBe` Nothing
    it "returns the correct subtree for a small example" $
      dropLeavesWith (== 2) smallTree `shouldBe` Just smallSubTree

-- TODO: intersect.