Safe Haskell | None |
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Parses text-based covariance-model descriptions.
- parseHeader :: Parser CMVersion
- lineParser :: Monad m => Parser b -> Pipe l ByteString o u m b
- parseCM1x :: (Monad m, MonadIO m) => Conduit ByteString m 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)
- 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)
- fromFile :: FilePath -> IO [CM]
- test :: IO ()
Covariance model parsing.
Infernal 1.0 and 1.1 covariance model parser
lineParser :: Monad m => Parser b -> Pipe l ByteString o u m bSource
parseCM1x :: (Monad m, MonadIO m) => Conduit ByteString m CMSource
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 -> cSource
readAccession :: Read a => ByteString -> aSource
parseHeaders :: Monad m => [ByteString] -> Pipe l ByteString o u m (Map ByteString ByteString)Source
parseNodes :: Monad m => CMVersion -> [(NodeType, NodeID, [State])] -> Pipe ByteString ByteString o u m [(NodeType, NodeID, [State])]Source
parseStates :: Monad m => CMVersion -> NodeType -> NodeID -> [State] -> Pipe ByteString ByteString o u m [State]Source
parseState :: CMVersion -> NodeType -> NodeID -> ByteString -> StateSource