biohazard-1.1.0: bioinformatics support library

Safe HaskellNone
LanguageHaskell2010

Bio.Iteratee

Synopsis

Documentation

iGetString :: Int -> Iteratee ByteString m ByteString Source #

Collects a string of a given length. Don't use this for long strings, use takeStream instead.

iterLoop :: (Nullable s, Monad m) => (a -> Iteratee s m a) -> a -> Iteratee s m a Source #

Repeatedly apply an Iteratee to a value until end of stream. Returns the final value.

iLookAhead :: Monoid s => Iteratee s m a -> Iteratee s m a Source #

Run an Iteratee, collect the input. When it finishes, return the result along with *all* input. Effectively allows lookahead. Be careful, this will eat memory if the Iteratee doesn't return speedily.

protectTerm :: (Nullable s, MonadIO m) => Iteratee s m a -> Iteratee s m a Source #

Protects the terminal from binary junk. If i is an Iteratee that might write binary to stdout, then protectTerm i is the same Iteratee, but it will abort if stdout is a terminal device.

parMapChunksIO :: (MonadIO m, Nullable s) => Int -> (s -> IO t) -> Enumeratee s t m a Source #

Parallel map of an IO action over the elements of a stream

This Enumeratee applies an IO action to every chunk of the input stream. These IO actions are run asynchronously in a limited parallel way. Don't forget to evaluate

parRunIO :: MonadIO m => Int -> Enumeratee [IO a] a m b Source #

progressGen :: MonadIO m => (Int -> a -> String) -> Int -> (String -> IO ()) -> Enumeratee [a] [a] m b Source #

A general progress indicator that prints some message after a set number of records have passed through.

progressNum :: MonadIO m => String -> Int -> (String -> IO ()) -> Enumeratee [a] [a] m b Source #

A simple progress indicator that prints the number of records.

progressPos :: MonadIO m => (a -> (Refseq, Int)) -> String -> Refs -> Int -> (String -> IO ()) -> Enumeratee [a] [a] m b Source #

A simple progress indicator that prints a position every set number of passed records.

($==) :: Monad m => Enumerator' hdr input m (Iteratee output m result) -> Enumeratee input output m result -> Enumerator' hdr output m result infixl 1 Source #

Compose an Enumerator' with an Enumeratee, giving a new Enumerator'.

class Monad m => MonadIO (m :: * -> *) #

Monads in which IO computations may be embedded. Any monad built by applying a sequence of monad transformers to the IO monad will be an instance of this class.

Instances should satisfy the following laws, which state that liftIO is a transformer of monads:

Minimal complete definition

liftIO

Instances
MonadIO IO

Since: base-4.9.0.0

Instance details

Defined in Control.Monad.IO.Class

Methods

liftIO :: IO a -> IO a #

MonadIO Q 
Instance details

Defined in Language.Haskell.TH.Syntax

Methods

liftIO :: IO a -> Q a #

MonadIO m => MonadIO (MaybeT m) 
Instance details

Defined in Control.Monad.Trans.Maybe

Methods

liftIO :: IO a -> MaybeT m a #

MonadIO m => MonadIO (ListT m) 
Instance details

Defined in Control.Monad.Trans.List

Methods

liftIO :: IO a -> ListT m a #

MonadIO m => MonadIO (ExceptT e m) 
Instance details

Defined in Control.Monad.Trans.Except

Methods

liftIO :: IO a -> ExceptT e m a #

MonadIO m => MonadIO (IdentityT m) 
Instance details

Defined in Control.Monad.Trans.Identity

Methods

liftIO :: IO a -> IdentityT m a #

(Error e, MonadIO m) => MonadIO (ErrorT e m) 
Instance details

Defined in Control.Monad.Trans.Error

Methods

liftIO :: IO a -> ErrorT e m a #

MonadIO m => MonadIO (StateT s m) 
Instance details

Defined in Control.Monad.Trans.State.Lazy

Methods

liftIO :: IO a -> StateT s m a #

MonadIO m => MonadIO (StateT s m) 
Instance details

Defined in Control.Monad.Trans.State.Strict

Methods

liftIO :: IO a -> StateT s m a #

(Monoid w, MonadIO m) => MonadIO (WriterT w m) 
Instance details

Defined in Control.Monad.Trans.Writer.Lazy

Methods

liftIO :: IO a -> WriterT w m a #

(Monoid w, MonadIO m) => MonadIO (WriterT w m) 
Instance details

Defined in Control.Monad.Trans.Writer.Strict

Methods

liftIO :: IO a -> WriterT w m a #

(Monoid w, Functor m, MonadIO m) => MonadIO (AccumT w m) 
Instance details

Defined in Control.Monad.Trans.Accum

Methods

liftIO :: IO a -> AccumT w m a #

MonadIO m => MonadIO (SelectT r m) 
Instance details

Defined in Control.Monad.Trans.Select

Methods

liftIO :: IO a -> SelectT r m a #

(MonadIO m, Nullable s, NullPoint s) => MonadIO (Iteratee s m) # 
Instance details

Defined in Bio.Iteratee.Base

Methods

liftIO :: IO a -> Iteratee s m a #

MonadIO m => MonadIO (ContT r m) 
Instance details

Defined in Control.Monad.Trans.Cont

Methods

liftIO :: IO a -> ContT r m a #

MonadIO m => MonadIO (ReaderT r m) 
Instance details

Defined in Control.Monad.Trans.Reader

Methods

liftIO :: IO a -> ReaderT r m a #

(Monoid w, MonadIO m) => MonadIO (RWST r w s m) 
Instance details

Defined in Control.Monad.Trans.RWS.Lazy

Methods

liftIO :: IO a -> RWST r w s m a #

(Monoid w, MonadIO m) => MonadIO (RWST r w s m) 
Instance details

Defined in Control.Monad.Trans.RWS.Strict

Methods

liftIO :: IO a -> RWST r w s m a #

class MonadCatch m => MonadMask (m :: * -> *) #

A class for monads which provide for the ability to account for all possible exit points from a computation, and to mask asynchronous exceptions. Continuation-based monads are invalid instances of this class.

Instances should ensure that, in the following code:

fg = f `finally` g

The action g is called regardless of what occurs within f, including async exceptions. Some monads allow f to abort the computation via other effects than throwing an exception. For simplicity, we will consider aborting and throwing an exception to be two forms of "throwing an error".

If f and g both throw an error, the error thrown by fg depends on which errors we're talking about. In a monad transformer stack, the deeper layers override the effects of the inner layers; for example, ExceptT e1 (Except e2) a represents a value of type Either e2 (Either e1 a), so throwing both an e1 and an e2 will result in Left e2. If f and g both throw an error from the same layer, instances should ensure that the error from g wins.

Effects other than throwing an error are also overriden by the deeper layers. For example, StateT s Maybe a represents a value of type s -> Maybe (a, s), so if an error thrown from f causes this function to return Nothing, any changes to the state which f also performed will be erased. As a result, g will see the state as it was before f. Once g completes, f's error will be rethrown, so g' state changes will be erased as well. This is the normal interaction between effects in a monad transformer stack.

By contrast, lifted-base's version of finally always discards all of g's non-IO effects, and g never sees any of f's non-IO effects, regardless of the layer ordering and regardless of whether f throws an error. This is not the result of interacting effects, but a consequence of MonadBaseControl's approach.

Minimal complete definition

mask, uninterruptibleMask, generalBracket

Instances
MonadMask IO 
Instance details

Defined in Control.Monad.Catch

Methods

mask :: ((forall a. IO a -> IO a) -> IO b) -> IO b #

uninterruptibleMask :: ((forall a. IO a -> IO a) -> IO b) -> IO b #

generalBracket :: IO a -> (a -> ExitCase b -> IO c) -> (a -> IO b) -> IO (b, c) #

e ~ SomeException => MonadMask (Either e)

Since: exceptions-0.8.3

Instance details

Defined in Control.Monad.Catch

Methods

mask :: ((forall a. Either e a -> Either e a) -> Either e b) -> Either e b #

uninterruptibleMask :: ((forall a. Either e a -> Either e a) -> Either e b) -> Either e b #

generalBracket :: Either e a -> (a -> ExitCase b -> Either e c) -> (a -> Either e b) -> Either e (b, c) #

MonadMask m => MonadMask (MaybeT m)

Since: exceptions-0.10.0

Instance details

Defined in Control.Monad.Catch

Methods

mask :: ((forall a. MaybeT m a -> MaybeT m a) -> MaybeT m b) -> MaybeT m b #

uninterruptibleMask :: ((forall a. MaybeT m a -> MaybeT m a) -> MaybeT m b) -> MaybeT m b #

generalBracket :: MaybeT m a -> (a -> ExitCase b -> MaybeT m c) -> (a -> MaybeT m b) -> MaybeT m (b, c) #

MonadMask m => MonadMask (ExceptT e m)

Since: exceptions-0.9.0

Instance details

Defined in Control.Monad.Catch

Methods

mask :: ((forall a. ExceptT e m a -> ExceptT e m a) -> ExceptT e m b) -> ExceptT e m b #

uninterruptibleMask :: ((forall a. ExceptT e m a -> ExceptT e m a) -> ExceptT e m b) -> ExceptT e m b #

generalBracket :: ExceptT e m a -> (a -> ExitCase b -> ExceptT e m c) -> (a -> ExceptT e m b) -> ExceptT e m (b, c) #

MonadMask m => MonadMask (IdentityT m) 
Instance details

Defined in Control.Monad.Catch

Methods

mask :: ((forall a. IdentityT m a -> IdentityT m a) -> IdentityT m b) -> IdentityT m b #

uninterruptibleMask :: ((forall a. IdentityT m a -> IdentityT m a) -> IdentityT m b) -> IdentityT m b #

generalBracket :: IdentityT m a -> (a -> ExitCase b -> IdentityT m c) -> (a -> IdentityT m b) -> IdentityT m (b, c) #

(Error e, MonadMask m) => MonadMask (ErrorT e m) 
Instance details

Defined in Control.Monad.Catch

Methods

mask :: ((forall a. ErrorT e m a -> ErrorT e m a) -> ErrorT e m b) -> ErrorT e m b #

uninterruptibleMask :: ((forall a. ErrorT e m a -> ErrorT e m a) -> ErrorT e m b) -> ErrorT e m b #

generalBracket :: ErrorT e m a -> (a -> ExitCase b -> ErrorT e m c) -> (a -> ErrorT e m b) -> ErrorT e m (b, c) #

MonadMask m => MonadMask (StateT s m) 
Instance details

Defined in Control.Monad.Catch

Methods

mask :: ((forall a. StateT s m a -> StateT s m a) -> StateT s m b) -> StateT s m b #

uninterruptibleMask :: ((forall a. StateT s m a -> StateT s m a) -> StateT s m b) -> StateT s m b #

generalBracket :: StateT s m a -> (a -> ExitCase b -> StateT s m c) -> (a -> StateT s m b) -> StateT s m (b, c) #

MonadMask m => MonadMask (StateT s m) 
Instance details

Defined in Control.Monad.Catch

Methods

mask :: ((forall a. StateT s m a -> StateT s m a) -> StateT s m b) -> StateT s m b #

uninterruptibleMask :: ((forall a. StateT s m a -> StateT s m a) -> StateT s m b) -> StateT s m b #

generalBracket :: StateT s m a -> (a -> ExitCase b -> StateT s m c) -> (a -> StateT s m b) -> StateT s m (b, c) #

(MonadMask m, Monoid w) => MonadMask (WriterT w m) 
Instance details

Defined in Control.Monad.Catch

Methods

mask :: ((forall a. WriterT w m a -> WriterT w m a) -> WriterT w m b) -> WriterT w m b #

uninterruptibleMask :: ((forall a. WriterT w m a -> WriterT w m a) -> WriterT w m b) -> WriterT w m b #

generalBracket :: WriterT w m a -> (a -> ExitCase b -> WriterT w m c) -> (a -> WriterT w m b) -> WriterT w m (b, c) #

(MonadMask m, Monoid w) => MonadMask (WriterT w m) 
Instance details

Defined in Control.Monad.Catch

Methods

mask :: ((forall a. WriterT w m a -> WriterT w m a) -> WriterT w m b) -> WriterT w m b #

uninterruptibleMask :: ((forall a. WriterT w m a -> WriterT w m a) -> WriterT w m b) -> WriterT w m b #

generalBracket :: WriterT w m a -> (a -> ExitCase b -> WriterT w m c) -> (a -> WriterT w m b) -> WriterT w m (b, c) #

MonadMask m => MonadMask (ReaderT r m) 
Instance details

Defined in Control.Monad.Catch

Methods

mask :: ((forall a. ReaderT r m a -> ReaderT r m a) -> ReaderT r m b) -> ReaderT r m b #

uninterruptibleMask :: ((forall a. ReaderT r m a -> ReaderT r m a) -> ReaderT r m b) -> ReaderT r m b #

generalBracket :: ReaderT r m a -> (a -> ExitCase b -> ReaderT r m c) -> (a -> ReaderT r m b) -> ReaderT r m (b, c) #

(MonadMask m, Monoid w) => MonadMask (RWST r w s m) 
Instance details

Defined in Control.Monad.Catch

Methods

mask :: ((forall a. RWST r w s m a -> RWST r w s m a) -> RWST r w s m b) -> RWST r w s m b #

uninterruptibleMask :: ((forall a. RWST r w s m a -> RWST r w s m a) -> RWST r w s m b) -> RWST r w s m b #

generalBracket :: RWST r w s m a -> (a -> ExitCase b -> RWST r w s m c) -> (a -> RWST r w s m b) -> RWST r w s m (b, c) #

(MonadMask m, Monoid w) => MonadMask (RWST r w s m) 
Instance details

Defined in Control.Monad.Catch

Methods

mask :: ((forall a. RWST r w s m a -> RWST r w s m a) -> RWST r w s m b) -> RWST r w s m b #

uninterruptibleMask :: ((forall a. RWST r w s m a -> RWST r w s m a) -> RWST r w s m b) -> RWST r w s m b #

generalBracket :: RWST r w s m a -> (a -> ExitCase b -> RWST r w s m c) -> (a -> RWST r w s m b) -> RWST r w s m (b, c) #

lift :: (MonadTrans t, Monad m) => m a -> t m a #

Lift a computation from the argument monad to the constructed monad.

liftIO :: MonadIO m => IO a -> m a #

Lift a computation from the IO monad.

stdin :: Handle #

A handle managing input from the Haskell program's standard input channel.

stdout :: Handle #

A handle managing output to the Haskell program's standard output channel.

stderr :: Handle #

A handle managing output to the Haskell program's standard error channel.

data Ordering' a Source #

Constructors

Less 
Equal a 
NotLess 

mergeSortStreams :: Monad m => (a -> a -> Ordering' a) -> Enumeratee [a] [a] (Iteratee [a] m) b Source #

type Enumerator' h eo m b = (h -> Iteratee eo m b) -> m (Iteratee eo m b) Source #

type Enumeratee' h ei eo m b = (h -> Iteratee eo m b) -> Iteratee ei m (Iteratee eo m b) Source #

mergeEnums' Source #

Arguments

:: (Nullable s2, Nullable s1, Monad m) 
=> Enumerator' hi s1 m a

inner enumerator

-> Enumerator' ho s2 (Iteratee s1 m) a

outer enumerator

-> (ho -> Enumeratee s2 s1 (Iteratee s1 m) a)

merging enumeratee

-> Enumerator' hi s1 m a 

Merge two Enumerator's into one. The header provided by the inner Enumerator' is passed to the output iterator, the header provided by the outer Enumerator' is passed to the merging iteratee

data QQ a Source #

Constructors

QQ !Int [a] [a] 

pushQ :: a -> QQ a -> QQ a Source #

popQ :: QQ a -> Maybe (a, QQ a) Source #

cancelAll :: MonadIO m => QQ (Async a) -> m () Source #

parserToIteratee :: Parser a -> Iteratee ByteString m a Source #

A function to convert attoparsec Parsers into Iteratees.

stream2vector :: (MonadIO m, Vector v a) => Iteratee [a] m (v a) Source #

Reads the whole stream into a Vector.

stream2vectorN :: (MonadIO m, Vector v a) => Int -> Iteratee [a] m (v a) Source #

Equivalent to joinI $ takeStream n $ stream2vector, but more efficient.

data Fd #

Instances
Bounded Fd 
Instance details

Defined in System.Posix.Types

Methods

minBound :: Fd #

maxBound :: Fd #

Enum Fd 
Instance details

Defined in System.Posix.Types

Methods

succ :: Fd -> Fd #

pred :: Fd -> Fd #

toEnum :: Int -> Fd #

fromEnum :: Fd -> Int #

enumFrom :: Fd -> [Fd] #

enumFromThen :: Fd -> Fd -> [Fd] #

enumFromTo :: Fd -> Fd -> [Fd] #

enumFromThenTo :: Fd -> Fd -> Fd -> [Fd] #

Eq Fd 
Instance details

Defined in System.Posix.Types

Methods

(==) :: Fd -> Fd -> Bool #

(/=) :: Fd -> Fd -> Bool #

Integral Fd 
Instance details

Defined in System.Posix.Types

Methods

quot :: Fd -> Fd -> Fd #

rem :: Fd -> Fd -> Fd #

div :: Fd -> Fd -> Fd #

mod :: Fd -> Fd -> Fd #

quotRem :: Fd -> Fd -> (Fd, Fd) #

divMod :: Fd -> Fd -> (Fd, Fd) #

toInteger :: Fd -> Integer #

Num Fd 
Instance details

Defined in System.Posix.Types

Methods

(+) :: Fd -> Fd -> Fd #

(-) :: Fd -> Fd -> Fd #

(*) :: Fd -> Fd -> Fd #

negate :: Fd -> Fd #

abs :: Fd -> Fd #

signum :: Fd -> Fd #

fromInteger :: Integer -> Fd #

Ord Fd 
Instance details

Defined in System.Posix.Types

Methods

compare :: Fd -> Fd -> Ordering #

(<) :: Fd -> Fd -> Bool #

(<=) :: Fd -> Fd -> Bool #

(>) :: Fd -> Fd -> Bool #

(>=) :: Fd -> Fd -> Bool #

max :: Fd -> Fd -> Fd #

min :: Fd -> Fd -> Fd #

Read Fd 
Instance details

Defined in System.Posix.Types

Real Fd 
Instance details

Defined in System.Posix.Types

Methods

toRational :: Fd -> Rational #

Show Fd 
Instance details

Defined in System.Posix.Types

Methods

showsPrec :: Int -> Fd -> ShowS #

show :: Fd -> String #

showList :: [Fd] -> ShowS #

Storable Fd 
Instance details

Defined in System.Posix.Types

Methods

sizeOf :: Fd -> Int #

alignment :: Fd -> Int #

peekElemOff :: Ptr Fd -> Int -> IO Fd #

pokeElemOff :: Ptr Fd -> Int -> Fd -> IO () #

peekByteOff :: Ptr b -> Int -> IO Fd #

pokeByteOff :: Ptr b -> Int -> Fd -> IO () #

peek :: Ptr Fd -> IO Fd #

poke :: Ptr Fd -> Fd -> IO () #

Bits Fd 
Instance details

Defined in System.Posix.Types

Methods

(.&.) :: Fd -> Fd -> Fd #

(.|.) :: Fd -> Fd -> Fd #

xor :: Fd -> Fd -> Fd #

complement :: Fd -> Fd #

shift :: Fd -> Int -> Fd #

rotate :: Fd -> Int -> Fd #

zeroBits :: Fd #

bit :: Int -> Fd #

setBit :: Fd -> Int -> Fd #

clearBit :: Fd -> Int -> Fd #

complementBit :: Fd -> Int -> Fd #

testBit :: Fd -> Int -> Bool #

bitSizeMaybe :: Fd -> Maybe Int #

bitSize :: Fd -> Int #

isSigned :: Fd -> Bool #

shiftL :: Fd -> Int -> Fd #

unsafeShiftL :: Fd -> Int -> Fd #

shiftR :: Fd -> Int -> Fd #

unsafeShiftR :: Fd -> Int -> Fd #

rotateL :: Fd -> Int -> Fd #

rotateR :: Fd -> Int -> Fd #

popCount :: Fd -> Int #

FiniteBits Fd 
Instance details

Defined in System.Posix.Types

Prim Fd 
Instance details

Defined in Data.Primitive.Types

withFileFd :: (MonadIO m, MonadMask m) => FilePath -> (Fd -> m a) -> m a Source #