On Jan 1, 2009 11:50pm, "Galchin, Vasili" <[email protected]> wrote:
> it is a bioinformatics standard .. . I am writing on this newsgroup in order
> to try to be objective to get a "correct" and elegant answer .. in any case I
> am helping on the bioinformatics code (you can see on Hackage). I am trying
> to finish the 2Bit file format code ... it seems to me that bioinformatics as
> an area is not clearly defined .... e.g. it is unclear to me whether "offset"
> is a marshalled/serialized concept or or unmarshalled/unserialized concept
> ..... this distinction is very important .... I will have to think about more
> myself!
>
>
> Regards, Vasili
>
Here's some code using Data.Binary to store data as offsets into a
byte array. I haven't tested it too much, so it may have bugs. Maybe
there's some inspiration in there.
-Antoine
>>>>
import Data.Binary
import Data.Binary.Get
import Data.Binary.Put
import Data.ByteString.Lazy (ByteString)
import qualified Data.ByteString.Lazy as B
data TestStruct = TestStruct
{ property1 :: ByteString
, property2 :: ByteString
, property3 :: ByteString
}
deriving Show
{-
The serialized format looks like (all big-endian):
* first offset into data block (Word32)
* second offset into data block (Word32)
* third offset into data block (Word32)
* length of bnary data block (Word32)
* binary data block (Arbitrary binary data)
-}
instance Binary TestStruct where
put struct =
let data1 = property1 struct
data2 = property2 struct
data3 = property3 struct
dataBlock = data1 `B.append` data2 `B.append` data3
offset1 = 0
offset2 = offset1 + B.length data1
offset3 = offset2 + B.length data2
in do
putWord32be $ fromIntegral offset1
putWord32be $ fromIntegral offset2
putWord32be $ fromIntegral offset3
putWord32be $ fromIntegral $ B.length dataBlock
putLazyByteString dataBlock
get = do
offset1 <- getWord32be
offset2 <- getWord32be
offset3 <- getWord32be
dataBlockLength <- getWord32be
dataBlock <- B.drop (fromIntegral offset1) `fmap`
getLazyByteString (fromIntegral dataBlockLength)
let (data1, rest1) =
B.splitAt (fromIntegral $ offset2 - offset1) dataBlock
(data2, rest2) =
B.splitAt (fromIntegral $ offset3 - offset2 - offset1) rest1
data3 = rest2
return $ TestStruct data1 data2 data3
<<<<<
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