{- |
Module      :  Main
Description :  Work with phylogenetic trees
Copyright   :  (c) Dominik Schrempf 2019
License     :  GPL-3

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

Creation date: Thu Sep  5 21:53:07 2019.

-}

module Main where

import           Control.Monad.Trans.Reader

import           Options

import           Compare.Compare
import           Connect.Connect
import           Distance.Distance
import           Examine.Examine
import           Shuffle.Shuffle
import           Simulate.Simulate

import           ELynx.Tools.Logger
import           ELynx.Tools.Options

main :: IO ()
main = do
  Arguments g c <- parseArguments
  let fn  = outFileBaseName g
      lvl = verbosity g
      lf  = (++ ".log") <$> fn
  case c of
    Distance a -> runReaderT (eLynxWrapper lvl lf distanceDescription $ distance fn) a
    Examine  a -> runReaderT (eLynxWrapper lvl lf examineDescription  $ examine fn) a
    Simulate a -> runReaderT (eLynxWrapper lvl lf simulateDescription $ simulate fn) a
    Compare  a -> runReaderT (eLynxWrapper lvl lf compareDescription $ compareCmd fn) a
    Connect  a -> runReaderT (eLynxWrapper lvl lf connectDescription $ connectCmd fn) a
    Shuffle  a -> runReaderT (eLynxWrapper lvl lf shuffleDescription $ shuffleCmd fn) a