Biobase.SElab.CM.Import

Parses text-based covariance-model descriptions.

Covariance model parsing.

Infernal 1.0 and 1.1 covariance model parser

parseHeader :: Parser CMVersion

lineParser :: Monad m => Parser b -> Pipe l ByteString o u m b

parseCM1x :: (Monad m, MonadIO m) => Conduit ByteString m CM

Top-level parser for Infernal 1.0 and 1.1 human-readable covariance models. Reads all lines first, then builds up the CM.

readBS :: Read c => ByteString -> c

readBitScore :: ByteString -> BitScore

readAccession :: Read a => ByteString -> a

parseHeaders :: Monad m => [ByteString] -> Pipe l ByteString o u m (Map ByteString ByteString)

Infernal 1.0 header parser. Greps all lines until the MODEL: line, then return lines to top-level parser. Parses three lines at once in case of FT- lines.

finishedHeader :: Maybe ByteString -> Bool

parseNodes :: Monad m => CMVersion -> [(NodeType, NodeID, [State])] -> Pipe ByteString ByteString o u m [(NodeType, NodeID, [State])]

parseStates :: Monad m => CMVersion -> NodeType -> NodeID -> [State] -> Pipe ByteString ByteString o u m [State]

parseState :: CMVersion -> NodeType -> NodeID -> ByteString -> State

isNode :: Maybe ByteString -> Maybe (NodeType, NodeID)

Determine if a line is a node line (Just). If yes, we'll get the node type as string and the node identifier, too.

fromFile :: FilePath -> IO [CM]

test :: IO ()