{-# LANGUAGE CPP #-}

module Bio.GB
  ( module T
  , fromFile
  , toFile
  , fromText
  , toText
  , genBankP
  ) where

import           Bio.GB.Parser
import           Bio.GB.Type            as T
import           Bio.GB.Writer          (genBankToText)
import           Control.Monad.IO.Class (MonadIO, liftIO)
import           Data.Attoparsec.Text   (parseOnly)
import           Data.Bifunctor         (first)
import           Data.Text              (Text, pack)
import qualified Data.Text.IO           as TIO (readFile, writeFile)
#if !MIN_VERSION_base(4,13,0)
import           Control.Monad.Fail     (MonadFail(..))
import           Prelude                hiding (fail)
#endif

-- | Reads 'GenBankSequence' from givem file.
--
fromFile :: (MonadFail m, MonadIO m) => FilePath -> m GenBankSequence
fromFile :: FilePath -> m GenBankSequence
fromFile FilePath
f = IO Text -> m Text
forall (m :: * -> *) a. MonadIO m => IO a -> m a
liftIO (FilePath -> IO Text
TIO.readFile FilePath
f) m Text -> (Text -> m GenBankSequence) -> m GenBankSequence
forall (m :: * -> *) a b. Monad m => m a -> (a -> m b) -> m b
>>= (FilePath -> m GenBankSequence)
-> (GenBankSequence -> m GenBankSequence)
-> Either FilePath GenBankSequence
-> m GenBankSequence
forall a c b. (a -> c) -> (b -> c) -> Either a b -> c
either FilePath -> m GenBankSequence
forall (m :: * -> *) a. MonadFail m => FilePath -> m a
fail GenBankSequence -> m GenBankSequence
forall (f :: * -> *) a. Applicative f => a -> f a
pure (Either FilePath GenBankSequence -> m GenBankSequence)
-> (Text -> Either FilePath GenBankSequence)
-> Text
-> m GenBankSequence
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Parser GenBankSequence -> Text -> Either FilePath GenBankSequence
forall a. Parser a -> Text -> Either FilePath a
parseOnly Parser GenBankSequence
genBankP

-- | Writes 'GenBankSequence' to file.
--
toFile :: MonadIO m => GenBankSequence -> FilePath -> m ()
toFile :: GenBankSequence -> FilePath -> m ()
toFile GenBankSequence
s FilePath
f = IO () -> m ()
forall (m :: * -> *) a. MonadIO m => IO a -> m a
liftIO (IO () -> m ()) -> IO () -> m ()
forall a b. (a -> b) -> a -> b
$ FilePath -> Text -> IO ()
TIO.writeFile FilePath
f (Text -> IO ()) -> Text -> IO ()
forall a b. (a -> b) -> a -> b
$ GenBankSequence -> Text
genBankToText GenBankSequence
s

-- | Reads 'GenBankSequence' from 'Text'.
--
fromText :: Text -> Either Text GenBankSequence
fromText :: Text -> Either Text GenBankSequence
fromText = (FilePath -> Text)
-> Either FilePath GenBankSequence -> Either Text GenBankSequence
forall (p :: * -> * -> *) a b c.
Bifunctor p =>
(a -> b) -> p a c -> p b c
first FilePath -> Text
pack (Either FilePath GenBankSequence -> Either Text GenBankSequence)
-> (Text -> Either FilePath GenBankSequence)
-> Text
-> Either Text GenBankSequence
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Parser GenBankSequence -> Text -> Either FilePath GenBankSequence
forall a. Parser a -> Text -> Either FilePath a
parseOnly Parser GenBankSequence
genBankP

-- | Writes 'GenBankSequence' to 'Text'.
--
toText :: GenBankSequence -> Text
toText :: GenBankSequence -> Text
toText = GenBankSequence -> Text
genBankToText