{-# LANGUAGE DeriveGeneric #-}

{- |
Module      :  SLynx.Concatenate.Options
Description :  ELynxSeq argument parsing
Copyright   :  (c) Dominik Schrempf 2018
License     :  GPL-3.0-or-later

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

Creation date: Sun Oct  7 17:29:45 2018.

-}

module SLynx.Concatenate.Options
  ( ConcatenateArguments(..)
  , concatenateArguments
  )
where

import           Control.Applicative
import           Options.Applicative

import           SLynx.Tools

import           ELynx.Data.Alphabet.Alphabet
import           ELynx.Tools

-- | Arguments needed to concatenate multi sequence alignments.
data ConcatenateArguments = ConcatenateArguments
    { ccAlphabet :: Alphabet
    , ccInFiles  :: [FilePath] }
  deriving (Eq, Show, Generic)

instance Reproducible ConcatenateArguments where
  inFiles = ccInFiles
  outSuffixes _ = [".fasta"]
  getSeed _ = Nothing
  setSeed = const
  parser  = concatenateArguments
  cmdName = "concatenate"
  cmdDsc  = ["Concatenate sequences found in input files."]

instance FromJSON ConcatenateArguments

instance ToJSON ConcatenateArguments

-- | Command line parser.
concatenateArguments :: Parser ConcatenateArguments
concatenateArguments = ConcatenateArguments <$> alphabetOpt <*> some inFileArg

inFileArg :: Parser FilePath
inFileArg =
  strArgument $ metavar "INPUT-FILE" <> help "Read sequences from INPUT-FILE"