Test.hs

module Bio.GFF3.Test (tests)
    where

import Control.Monad
import Control.Monad.Error
import qualified Data.ByteString.Lazy.Char8 as LBS
import Data.Char
import Test.QuickCheck

import Bio.GFF3.Escape
import qualified Bio.GFF3.Feature as F
import Bio.Location.Strand
import Bio.Sequence.SeqData
import Bio.Util.TestBase

tests :: [Test]
tests = [ T "%-escape inversion"            test_Escape_invert
        , T "%-escape completeness"         test_Escape_completeness

        , T "GFF3 parse inversion"          test_GFF3_unparseParse
        ]

instance Arbitrary LBS.ByteString where
    arbitrary = liftM LBS.pack $ arbitrary

-- Bio.GFF3.Escape

test_Escape_invert :: [Char] -> LBS.ByteString -> Bool
test_Escape_invert escchrs str = let escstr = escapeAllOf ('%':escchrs) str
                                     unescstr :: Either String LBS.ByteString
                                     unescstr = unEscapeByteString escstr
                                 in unescstr == Right str

test_Escape_completeness :: [Char] -> LBS.ByteString -> Bool
test_Escape_completeness escchrs str
    = let allescchrs = ('%':escchrs)
          nescchrs = length $ LBS.findIndices (flip elem allescchrs) str          
      in (length $ LBS.elemIndices '%' $ escapeAllOf allescchrs str) == nescchrs

-- Bio.GFF3.Feature

instance Arbitrary F.GFFAttr where
    arbitrary = liftM2 F.GFFAttr arbitrary (sized vector)

instance Arbitrary Strand where
    arbitrary = elements [Fwd, RevCompl]

instance Arbitrary F.Feature where
    arbitrary = do seqid <- arbitrary
                   source <- arbitrary
                   stype <- arbitrary
                   seq5 <- genNonNegOffset
                   len <- genPositiveOffset
                   score <- return Nothing -- Tricky to ask strict equality in a Double
                   strand <- arbitrary
                   phase <- oneof [return Nothing, liftM (Just . fromIntegral) $ choose ((0::Int),2)]
                   attrs <- sized vector
                   return $ F.Feature seqid source stype seq5 (seq5 + len - 1) score strand phase attrs

test_GFF3_unparseParse :: F.Feature -> Bool
test_GFF3_unparseParse f = let fline = F.unparse f
                               f' :: Either String F.Feature
                               f' = F.parse fline
                           in f' == Right f