-- | Mafft data.
--
-- NOTE: For the "-" strand, the start position is given by ("genome size" -
-- "start position" + "length")
--
-- TODO mafft blocks contain "i" parts which i haven't seen yet. These have to
-- be parsed, too.

module Biobase.DataSource.Mafft where

import qualified Data.ByteString.Lazy.Char8 as BS



-- | A complete Mafft file.

data Mafft = Mafft
  { comments :: [BS.ByteString]
  , blocks :: [Block]
  }
  deriving (Show)

-- | One Mafft block.
--
-- THERE is "a ", "i ", "s "

data Block = Block
  { alignment :: BS.ByteString
  , sequences :: [Sequence]
  }
  deriving (Show)

-- | Encodes one sequence entry.

data Sequence = Sequence
  { species :: BS.ByteString
  , start :: Int
  , length :: Int
  , strand :: PlusMinus
  , genomeSize :: Int
  , alignedSequence :: CompressedBS
  }
  deriving (Show)

newtype PlusMinus = PlusMinus Char
  deriving (Eq,Show)

newtype CompressedBS = CompressedBS BS.ByteString
  deriving (Eq,Show)