Safe Haskell	None
Language	Haskell2010

Biobase.Types.Bitscore

Description

Bit scores as used by different algorithms in bioinformatics, linguistics, and probably elsewhere.

Basically, the base-2 logarithm of the probability of the input given the model vs the probability of the input given the null model.

S = log_2 (P(seq|model) / P(seq|null))

Synopsis

Documentation

newtype Bitscore Source #

Bit score; behaves like a double (deriving Num). In particular, the algebraic operations behave as expected Bitscore a + Bitscore b == Bitscore (a+b).

Currently geared towards use as in Infernal and HMMER.

Infernal users guide, p.42: log-odds score in log_2 (aka bits).

Constructors

Bitscore
Fields getBitscore :: Double

Instances

Eq Bitscore Source #
Methods (==) :: Bitscore -> Bitscore -> Bool # (/=) :: Bitscore -> Bitscore -> Bool #
Fractional Bitscore Source #
Methods (/) :: Bitscore -> Bitscore -> Bitscore # recip :: Bitscore -> Bitscore # fromRational :: Rational -> Bitscore #
Num Bitscore Source #
Methods (+) :: Bitscore -> Bitscore -> Bitscore # (-) :: Bitscore -> Bitscore -> Bitscore # (*) :: Bitscore -> Bitscore -> Bitscore # negate :: Bitscore -> Bitscore # abs :: Bitscore -> Bitscore # signum :: Bitscore -> Bitscore # fromInteger :: Integer -> Bitscore #
Ord Bitscore Source #
Methods compare :: Bitscore -> Bitscore -> Ordering # (<) :: Bitscore -> Bitscore -> Bool # (<=) :: Bitscore -> Bitscore -> Bool # (>) :: Bitscore -> Bitscore -> Bool # (>=) :: Bitscore -> Bitscore -> Bool # max :: Bitscore -> Bitscore -> Bitscore # min :: Bitscore -> Bitscore -> Bitscore #
Read Bitscore Source #
Methods readsPrec :: Int -> ReadS Bitscore # readList :: ReadS [Bitscore] # readPrec :: ReadPrec Bitscore # readListPrec :: ReadPrec [Bitscore] #
Show Bitscore Source #
Methods showsPrec :: Int -> Bitscore -> ShowS # show :: Bitscore -> String # showList :: [Bitscore] -> ShowS #
Generic Bitscore Source #
Associated Types type Rep Bitscore :: * -> * # Methods from :: Bitscore -> Rep Bitscore x # to :: Rep Bitscore x -> Bitscore #
Hashable Bitscore Source #
Methods hashWithSalt :: Int -> Bitscore -> Int # hash :: Bitscore -> Int #
ToJSON Bitscore Source #
Methods toJSON :: Bitscore -> Value # toEncoding :: Bitscore -> Encoding # toJSONList :: [Bitscore] -> Value # toEncodingList :: [Bitscore] -> Encoding #
FromJSON Bitscore Source #
Methods parseJSON :: Value -> Parser Bitscore # parseJSONList :: Value -> Parser [Bitscore] #
Binary Bitscore Source #
Methods put :: Bitscore -> Put # get :: Get Bitscore # putList :: [Bitscore] -> Put #
Serialize Bitscore Source #
Methods put :: Putter Bitscore # get :: Get Bitscore #
Default Bitscore Source #	A default bitscore of "-infinity", but with `10-1` wiggle room. TODO Check out the different "defaults" Infernal uses
Methods def :: Bitscore #
NFData Bitscore Source #
Methods rnf :: Bitscore -> () #
Unbox Bitscore Source #

NumericalExtremes Bitscore Source #
Methods maxFinite :: Bitscore Source # minFinite :: Bitscore Source # maxExtreme :: Bitscore Source # minExtreme :: Bitscore Source # maxLarge :: Bitscore Source # minLarge :: Bitscore Source #
Vector Vector Bitscore Source #
Methods basicUnsafeFreeze :: PrimMonad m => Mutable Vector (PrimState m) Bitscore -> m (Vector Bitscore) # basicUnsafeThaw :: PrimMonad m => Vector Bitscore -> m (Mutable Vector (PrimState m) Bitscore) # basicLength :: Vector Bitscore -> Int # basicUnsafeSlice :: Int -> Int -> Vector Bitscore -> Vector Bitscore # basicUnsafeIndexM :: Monad m => Vector Bitscore -> Int -> m Bitscore # basicUnsafeCopy :: PrimMonad m => Mutable Vector (PrimState m) Bitscore -> Vector Bitscore -> m () # elemseq :: Vector Bitscore -> Bitscore -> b -> b #
MVector MVector Bitscore Source #
Methods basicLength :: MVector s Bitscore -> Int # basicUnsafeSlice :: Int -> Int -> MVector s Bitscore -> MVector s Bitscore # basicOverlaps :: MVector s Bitscore -> MVector s Bitscore -> Bool # basicUnsafeNew :: PrimMonad m => Int -> m (MVector (PrimState m) Bitscore) # basicInitialize :: PrimMonad m => MVector (PrimState m) Bitscore -> m () # basicUnsafeReplicate :: PrimMonad m => Int -> Bitscore -> m (MVector (PrimState m) Bitscore) # basicUnsafeRead :: PrimMonad m => MVector (PrimState m) Bitscore -> Int -> m Bitscore # basicUnsafeWrite :: PrimMonad m => MVector (PrimState m) Bitscore -> Int -> Bitscore -> m () # basicClear :: PrimMonad m => MVector (PrimState m) Bitscore -> m () # basicSet :: PrimMonad m => MVector (PrimState m) Bitscore -> Bitscore -> m () # basicUnsafeCopy :: PrimMonad m => MVector (PrimState m) Bitscore -> MVector (PrimState m) Bitscore -> m () # basicUnsafeMove :: PrimMonad m => MVector (PrimState m) Bitscore -> MVector (PrimState m) Bitscore -> m () # basicUnsafeGrow :: PrimMonad m => MVector (PrimState m) Bitscore -> Int -> m (MVector (PrimState m) Bitscore) #
type Rep Bitscore Source #
type Rep Bitscore = D1 (MetaData "Bitscore" "Biobase.Types.Bitscore" "BiobaseTypes-0.1.2.1-1LTYzU1e5OWItpBBqXiV1g" True) (C1 (MetaCons "Bitscore" PrefixI True) (S1 (MetaSel (Just Symbol "getBitscore") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Double)))
data Vector Bitscore Source #
data Vector Bitscore = V_Bitscore (Vector Double)
data MVector s Bitscore Source #
data MVector s Bitscore = MV_Bitscore (MVector s Double)

prob2Score :: Double -> Double -> Bitscore Source #

Given a null model and a probability, calculate the corresponding BitScore.

TODO x<=epsilon ?

score2Prob :: Double -> Bitscore -> Double Source #

Given a null model and a BitScore return the corresponding probability.