Options.hs

{-# LANGUAGE DeriveGeneric #-}

{- |
Module      :  TLynx.Options
Description :  TLynx general options
Copyright   :  (c) Dominik Schrempf 2020
License     :  GPL-3.0-or-later

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

Creation date: Sat Sep  7 18:55:03 2019.

-}

module TLynx.Options
  ( Arguments(..)
  , CommandArguments(..)
  , parseArguments
  )
where

import           Options.Applicative

import           ELynx.Tools

import           TLynx.Coalesce.Options
import           TLynx.Compare.Options
import           TLynx.Connect.Options
import           TLynx.Distance.Options
import           TLynx.Examine.Options
import           TLynx.Shuffle.Options
import           TLynx.Simulate.Options
import           TLynx.Parsers                  ( newickHelp )

-- | The different TLynx commands and their arguments.
data CommandArguments =
  Coalesce CoalesceArguments
  | Compare CompareArguments
  | Connect ConnectArguments
  | Distance DistanceArguments
  | Examine ExamineArguments
  | Shuffle ShuffleArguments
  | Simulate SimulateArguments
  deriving (Eq, Show, Generic)

instance Reproducible CommandArguments where
  inFiles (Coalesce a) = inFiles a
  inFiles (Compare  a) = inFiles a
  inFiles (Connect  a) = inFiles a
  inFiles (Distance a) = inFiles a
  inFiles (Examine  a) = inFiles a
  inFiles (Shuffle  a) = inFiles a
  inFiles (Simulate a) = inFiles a

  outSuffixes (Coalesce a) = outSuffixes a
  outSuffixes (Compare  a) = outSuffixes a
  outSuffixes (Connect  a) = outSuffixes a
  outSuffixes (Distance a) = outSuffixes a
  outSuffixes (Examine  a) = outSuffixes a
  outSuffixes (Shuffle  a) = outSuffixes a
  outSuffixes (Simulate a) = outSuffixes a

  getSeed (Coalesce a) = getSeed a
  getSeed (Compare  a) = getSeed a
  getSeed (Connect  a) = getSeed a
  getSeed (Distance a) = getSeed a
  getSeed (Examine  a) = getSeed a
  getSeed (Shuffle  a) = getSeed a
  getSeed (Simulate a) = getSeed a

  setSeed (Coalesce a) = Coalesce . setSeed a
  setSeed (Compare  a) = Compare . setSeed a
  setSeed (Connect  a) = Connect . setSeed a
  setSeed (Distance a) = Distance . setSeed a
  setSeed (Examine  a) = Examine . setSeed a
  setSeed (Shuffle  a) = Shuffle . setSeed a
  setSeed (Simulate a) = Simulate . setSeed a

  parser  = commandArguments

  cmdName = "tlynx"

  cmdDsc  = ["Compare, examine, and simulate phylogenetic trees."]

  cmdFtr  = "Available tree file formats:" : indent newickHelp
    where indent = map ("  " ++)

instance FromJSON CommandArguments

instance ToJSON CommandArguments

coalesceCommand :: Mod CommandFields CommandArguments
coalesceCommand = createCommandReproducible Coalesce

compareCommand :: Mod CommandFields CommandArguments
compareCommand = createCommandReproducible Compare

connectCommand :: Mod CommandFields CommandArguments
connectCommand = createCommandReproducible Connect

distanceCommand :: Mod CommandFields CommandArguments
distanceCommand = createCommandReproducible Distance

examineCommand :: Mod CommandFields CommandArguments
examineCommand = createCommandReproducible Examine

shuffleCommand :: Mod CommandFields CommandArguments
shuffleCommand = createCommandReproducible Shuffle

simulateCommand :: Mod CommandFields CommandArguments
simulateCommand = createCommandReproducible Simulate

commandArguments :: Parser CommandArguments
commandArguments =
  hsubparser
    $  coalesceCommand
    <> compareCommand
    <> connectCommand
    <> distanceCommand
    <> examineCommand
    <> shuffleCommand
    <> simulateCommand