Options.hs

{-# LANGUAGE DeriveGeneric #-}

{- |
Module      :  TLynx.Connect.Options
Description :  Options for the connect subcommand
Copyright   :  (c) Dominik Schrempf 2020
License     :  GPL-3.0-or-later

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

Creation date: Thu Sep 19 15:02:21 2019.

-}

module TLynx.Connect.Options
  ( ConnectArguments(..)
  , connectArguments
  )
where

import           Options.Applicative

import           ELynx.Tools

import           TLynx.Parsers

-- | Arguments of connect command.
data ConnectArguments = ConnectArguments
  { nwFormat    :: NewickFormat
  , constraints :: Maybe FilePath
  , inFileA     :: FilePath
  , inFileB     :: FilePath }
  deriving (Eq, Show, Generic)

instance Reproducible ConnectArguments where
  inFiles a = [inFileA a, inFileB a]
  outSuffixes _ = [".out"]
  getSeed _ = Nothing
  setSeed a _ = a
  parser  = connectArguments
  cmdName = "connect"
  cmdDsc =
    [ "Connect two phylogenetic trees in all ways (possibly honoring constraints)."
    ]

instance FromJSON ConnectArguments

instance ToJSON ConnectArguments

-- | Parse arguments of connect command.
connectArguments :: Parser ConnectArguments
connectArguments =
  ConnectArguments <$> newickFormat <*> constraintsFile <*> fileA <*> fileB

constraintsFile :: Parser (Maybe FilePath)
constraintsFile =
  optional
    $  strOption
    $  metavar "CONSTRAINTS"
    <> short 'c'
    <> long "contraints"
    <> help "File containing one or more Newick trees to be used as constraints"

fileA :: Parser FilePath
fileA = strArgument $ metavar "TREE-FILE-A" <> help
  "File containing the first Newick tree"

fileB :: Parser FilePath
fileB = strArgument $ metavar "TREE-FILE-B" <> help
  "File containing the second Newick tree"