NewickSpec.hs

{- |
Module      :  ELynx.Export.Tree.NewickSpec
Copyright   :  (c) Dominik Schrempf 2020
License     :  GPL-3.0-or-later

Maintainer  :  dominik.schrempf@gmail.com
Stability   :  unstable
Portability :  portable

Creation date: Wed Feb 13 11:01:53 2019.

-}

module ELynx.Export.Tree.NewickSpec
  ( spec
  )
where

import qualified Data.ByteString.Lazy.Char8    as L
import           Data.Tree
import           Test.Hspec
import           Test.QuickCheck         hiding ( label )
import           Test.QuickCheck.Instances.Containers
                                                ( )

import           ELynx.Data.Tree
import           ELynx.Data.Tree.PhyloTreeArbitraryInstance
                                                ( )
import           ELynx.Export.Tree.Newick
import           ELynx.Import.Tree.Newick
import           ELynx.Tools

samplePhyloByteStringTree :: Tree (PhyloLabel L.ByteString)
samplePhyloByteStringTree = parseByteStringWith "Sample newick byte string"
                                                (newick Standard)
                                                sampleNewickByteString1

sampleNewickByteString1 :: L.ByteString
sampleNewickByteString1 =
  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);"

prop_invariant :: Tree (PhyloLabel Int) -> Bool
prop_invariant t =
  parseByteStringWith "Sample newick byte string" (newick Standard) (toNewick t)
    ==
                   -- We have to convert Int to ByteString, but we cannot use
                   -- arbitrary instances with ByteStrings because many
                   -- characters are disallowed and break the Newick string.
       fmap (\l -> l { label = getName l }) t

spec :: Spec
spec = describe "parseByteStringWith newick $ toNewickPhyloByteString" $ do
  it "should be an invariant for a sample tree" $ do
    let bs = toNewick samplePhyloByteStringTree
    parseByteStringWith "Newick string converted from tree object"
                        (newick Standard)
                        bs
      `shouldBe` samplePhyloByteStringTree

  it "should be an invariant for a sample tree" $ property prop_invariant