OpenAnyFile.hs

{-# LANGUAGE OverloadedStrings, CPP #-}

-- | Opening and reading a either normal or gzipped file in an efficient way -
-- either using strict 'ByteString' or mmap

module Bio.PDB.IO.OpenAnyFile(readFile, writeFile)

where

import Prelude hiding   (readFile, writeFile)
import System.Directory (doesFileExist, getPermissions, Permissions(..))
import System.IO.Error  (userError, IOError)
import System.IO        (withFile, IOMode(..))
-- if we have zlib:
import qualified Codec.Compression.GZip as GZip
import qualified Data.ByteString.Lazy   as BSL
import qualified Control.Exception      as Exc

-- if we have bzlib
--import qualified Codec.Compression.BZip as BZip

-- if we have MMap:
#ifdef HAVE_MMAP
import System.IO.Posix.MMap(unsafeMMapFile)
#endif

-- otherwise:
import qualified Data.ByteString.Char8 as BS

readFile fname = do r <- isReadable fname
                    if r
                      then
                        readFile' fname
                      else
                        throwNotFound fname

readFile' fname = do content <- simpleRead fname
                     let r = (let codec = getCodec fname content
                              in BS.concat $ BSL.toChunks $ codec $ BSL.fromChunks [content])
                     return r

throwNotFound :: String -> IO a
throwNotFound fname = ioError $ userError $ concat ["Cannot read ", show fname, "!"]

getCodec fname c | (".gz" `BS.isSuffixOf` BS.pack fname) ||
                   (".Z"  `BS.isSuffixOf` BS.pack fname) = GZip.decompressWith (gzipParams c)
--getCodec fname c | (".bz2" `BS.isSuffixOf` (BS.pack fname)) = BZip.decompressWith (bzipParams c) -- DOESN'T WORK!!!
getCodec fname c | otherwise                             = id

gzipParams c = GZip.DecompressParams GZip.defaultWindowBits (fromIntegral (BS.length c * 5))
#ifndef OLD_ZLIB
               Nothing
#endif
  -- Upper bound: compression rate never exceeded 4.7 for big test files.

--bzipParams c = BZip.DecompressParams BZip.DefaultMemoryLevel (fromIntegral (BS.length c * 7 + 4*1024*1024)) -- Upper bound: compression rate never exceeded 6.7 for big test files + 4MiB buffering.

isReadable fname = do exists <- doesFileExist fname
                      if exists
                        then do perms <- getPermissions fname
                                return $! readable perms 
                        else return False

#ifndef HAVE_MMAP
simpleRead fname = BS.readFile fname
#else
simpleRead fname = unsafeMMapFile fname `Exc.catch` \e -> do reportError (e :: IOError)
                                                             BS.readFile fname
  where
    reportError e = do putStrLn $ concat [show e, "while trying to mmap('", fname, "')"]
#endif

writeFile fname writer = do withFile fname WriteMode $ writer 
                            return ()