diff --git a/Biobase/Types/Accession.hs b/Biobase/Types/Accession.hs new file mode 100644 --- /dev/null +++ b/Biobase/Types/Accession.hs @@ -0,0 +1,88 @@ + +module Biobase.Types.Accession where + +import Data.Aeson +import Data.Binary +import Data.Hashable (Hashable) +import Data.Ix (Ix) +import Data.Serialize +import Data.Serialize.Text +import Data.String +import Data.Stringable +import Data.Text.Binary +import Data.Text (Text) +import GHC.Generics (Generic) + + + +-- * 'Accession' with phantom types. +-- +-- +-- +-- +-- +-- + +-- | The accession number is a unique identifier in bioinformatics. +-- +-- Depending on the source, accession numbers follow different alphanumeric +-- formats! While letters-than-numbers is quite common, swissprot uses +-- a mix. Hence, we just use a text string as accession. +-- +-- A phantom type is provided to enable type safety annotations. Helper +-- functions provide smart construction from the @Accession@ tagged generic +-- type. + +newtype Accession t = Accession { _getAccession :: Text } + deriving (Eq,Ord,Read,Show,Generic) + +accession :: Stringable s => s -> Accession t +accession = Accession . toText +{-# Inline accession #-} + +tagAccession :: Accession f -> Accession t +tagAccession = Accession . _getAccession +{-# Inline tagAccession #-} + +instance IsString (Accession t) where + fromString = accession + {-# Inline fromString #-} + +instance Binary (Accession t) +instance FromJSON (Accession t) +instance Hashable (Accession t) +instance Serialize (Accession t) +instance ToJSON (Accession t) + +-- ** NCBI phantom types + +-- | nucleotide sequence + +data Nucleotide + +-- | protein sequence + +data Protein + +-- ** Rfam phantom types +-- +-- The format is RFxxxxx, PFxxxxx, or CLxxxxx. + +-- | Tag as being a clan. + +data Clan + +-- | Tag as being a Pfam model. + +data Pfam + +-- | Tag as being an Rfam model. Used for Stockholm and CM files. + +data Rfam + + + +-- | Species have an accession number, too. + +data Species + diff --git a/Biobase/Types/Convert.hs b/Biobase/Types/Convert.hs deleted file mode 100644 --- a/Biobase/Types/Convert.hs +++ /dev/null @@ -1,36 +0,0 @@ -{-# LANGUAGE MultiParamTypeClasses #-} - --- | Provides a converting function between different types. Most useful --- conversions are instanced here. - -module Biobase.Types.Convert where - -import Biobase.Types.Ring -import Biobase.Types.Energy -import Biobase.Types.Score -import Biobase.Types.Partition - - - --- | How to convert between different values. - -class Convert a b c where - convert :: a -> b -> c - - - --- | From (Gibbs free) energy to partition function values. --- --- TODO temperature is running around here: move to some library later on - -newtype Kelvin = Kelvin {unKelvin :: Double} - -constR = undefined - -instance Convert Kelvin Energy Partition where - convert (Kelvin k) (Energy a) = Partition . exp $ (fromIntegral $ negate a) / (constR * k) - --- | From log-odd scores to partition function. - --- instance Convert Temperature Score Partition where --- convert (Score a) = Partition . exp $ (fromIntegral $ neg a) / (constR * constT) diff --git a/Biobase/Types/Energy.hs b/Biobase/Types/Energy.hs --- a/Biobase/Types/Energy.hs +++ b/Biobase/Types/Energy.hs @@ -1,51 +1,74 @@ -{-# LANGUAGE StandaloneDeriving #-} -{-# LANGUAGE MultiParamTypeClasses #-} -{-# LANGUAGE GeneralizedNewtypeDeriving #-} +-- | Different types of energies and conversion between. +-- +-- TODO enthalpy +-- TODO entropy + module Biobase.Types.Energy where -import qualified Data.Vector.Unboxed as VU -import qualified Data.Vector.Generic as VG -import qualified Data.Vector.Generic.Mutable as VGM -import Data.Primitive.Types +import Data.Aeson (FromJSON, ToJSON) +import Data.Binary (Binary) +import Data.Default +import Data.Hashable +import Data.Serialize (Serialize) +import Data.Vector.Unboxed.Deriving +import GHC.Generics -import Biobase.Types.Ring +import Biobase.Types.NumericalExtremes --- | Some default instances. Left out the Num one, so that you have to --- explicitly instanciate if you want to go around the Ring structure. +-- | Gibbs free energy change. +-- +-- For RNA structure, the change in energy from the unfolded structure to +-- the given structure. +-- +-- In units of @kcal / mol@. +-- +-- TODO shall we phantom-type the actual units? -newtype Energy = Energy {unEnergy :: Int} - deriving (Show, Read, Eq, Ord) +newtype DeltaGibbs = DG { getDG :: Double } + deriving (Eq,Ord,Num,Fractional,Read,Show,Generic) --- | Ring operations over Energy values. +derivingUnbox "DeltaGibbs" + [t| DeltaGibbs -> Double |] [| getDG |] [| DG |] -instance Ring Energy where - (Energy a) .+. (Energy b) = Energy $ a `min` b - {-# INLINE (.+.) #-} - (Energy a) .*. (Energy b) = Energy $ a + b - {-# INLINE (.*.) #-} - (Energy a) .^. k = Energy $ a * k - {-# INLINE (.^.) #-} - (Energy a) .^^. k = Energy . round $ fromIntegral a * k - {-# INLINE (.^^.) #-} - neg (Energy a) = Energy $ negate a - {-# INLINE neg #-} - one = Energy 0 - {-# INLINE one #-} - zero = Energy 10000000 - {-# INLINE zero #-} - isZero (Energy a) = a >= 1000000 - {-# INLINE isZero #-} +instance Hashable DeltaGibbs +instance Binary DeltaGibbs +instance Serialize DeltaGibbs +instance FromJSON DeltaGibbs +instance ToJSON DeltaGibbs +deriving instance NumericalExtremes DeltaGibbs +deriving instance NumericalEpsilon DeltaGibbs +instance Default DeltaGibbs where + def = extremelyLarge + {-# Inline def #-} --- * Vector instances. -deriving instance VGM.MVector VU.MVector Energy -deriving instance VG.Vector VU.Vector Energy -deriving instance VU.Unbox Energy -deriving instance Prim Energy + +-- | @round $ DeltaGibbs / 100@. + +newtype DeltaDekaGibbs = DekaG { getDekaG :: Int } + deriving (Eq,Ord,Num,Read,Show,Generic) + + + +derivingUnbox "DeltaDekaGibbs" + [t| DeltaDekaGibbs -> Int |] [| getDekaG |] [| DekaG |] + +instance Hashable DeltaDekaGibbs +instance Binary DeltaDekaGibbs +instance Serialize DeltaDekaGibbs +instance FromJSON DeltaDekaGibbs +instance ToJSON DeltaDekaGibbs + +deriving instance NumericalExtremes DeltaDekaGibbs + +instance Default DeltaDekaGibbs where + def = extremelyLarge + {-# Inline def #-} + diff --git a/Biobase/Types/Index.hs b/Biobase/Types/Index.hs new file mode 100644 --- /dev/null +++ b/Biobase/Types/Index.hs @@ -0,0 +1,96 @@ + +-- | Biological sequence data is oftentimes indexed either @0-@ or +-- @1-@based. The @Index@ type developed provides static guarantees that +-- there is no confusion what index is in use. +-- +-- This module does not export the ctor @Index@. If you want to (unsafely) +-- use it, import @Biobase.Types.Index.Type@ directly. Use @fromInt0@ to +-- make clear that you count from 0 and transform to an @Index t@. I.e. +-- @fromInt0 0 :: Index 1@ yields the lowest 1-base index. + +module Biobase.Types.Index + ( module Biobase.Types.Index + , getIndex + , index + , maybeIndex + , Index + ) where + +import Data.Proxy +import GHC.TypeLits +import Text.Printf + +import Biobase.Types.Index.Type + + + +-- | Uses 'index' to guarantee that the 'Index' is ok. + +checkIndex :: forall t . KnownNat t => Index t -> Index t +checkIndex i@(Index z) + | z >= 0 = i + | otherwise = error $ printf "%d < Index %d\n" (z+n) n + where n :: Int = fromIntegral $ natVal (Proxy :: Proxy t) +{-# Inline checkIndex #-} + +-- | Re-Index an index of type @Index n@ as @Index m@. This is always safe, +-- as @0 :: Index 0@ gives @1 :: Index 1@ for example. I.e. valid indices +-- become valid indices. + +reIndex :: forall n m . (KnownNat n, KnownNat m) => Index n -> Index m +reIndex (Index i) = Index $ i - n + m + where n = fromIntegral $ natVal (Proxy :: Proxy n) + m = fromIntegral $ natVal (Proxy :: Proxy m) +{-# Inline reIndex #-} + +-- | Helper function that allows @addition@ of an 'Index' and an 'Int', +-- with the 'Int' on the right. + +(+.) :: forall t . KnownNat t => Index t -> Int -> Index t +(+.) i n = checkIndex $ unsafePlus i n +{-# Inline (+.) #-} + +-- | Unsafe plus. + +unsafePlus :: forall t . KnownNat t => Index t -> Int -> Index t +unsafePlus i n = Index $ getIndex i + n +{-# Inline unsafePlus #-} + +-- | Helper function that allows @subtraction@ of an 'Index' and an 'Int', +-- with the 'Int' on the right. + +(-.) :: forall t . KnownNat t => Index t -> Int -> Index t +(-.) i n = checkIndex $ unsafeMinus i n +{-# Inline (-.) #-} + +-- | Unsafe minus. + +unsafeMinus :: forall t . KnownNat t => Index t -> Int -> Index t +unsafeMinus i n = Index $ getIndex i - n +{-# Inline unsafeMinus #-} + +-- | Return the index as an @Int@-style index that is zero-based. + +toInt0 :: forall t . KnownNat t => Index t -> Int +toInt0 = getIndex +{-# Inline toInt0 #-} + +-- | As an index from an @Int@-style zero-based one. +-- +-- TODO We might want to check that the argument is @[0..]@. + +fromInt0 :: forall t . KnownNat t => Int -> Index t +fromInt0 i + | i >= 0 = Index i + | otherwise = error "fromInt0 needs an Int >= 0" + where t = fromIntegral $ natVal (Proxy :: Proxy t) +{-# Inline fromInt0 #-} + +-- | Zero-based indices. + +type I0 = Index 0 + +-- | One-based indices. + +type I1 = Index 1 + diff --git a/Biobase/Types/Index/Type.hs b/Biobase/Types/Index/Type.hs new file mode 100644 --- /dev/null +++ b/Biobase/Types/Index/Type.hs @@ -0,0 +1,104 @@ + +module Biobase.Types.Index.Type where + +import Control.Applicative ((<$>)) +import Control.DeepSeq +import Data.Aeson +import Data.Binary +import Data.Hashable (Hashable) +import Data.Proxy +import Data.Serialize (Serialize) +import Data.Vector.Fusion.Stream.Monadic (flatten, Step(..)) +import Data.Vector.Fusion.Stream.Size +import Data.Vector.Unboxed.Deriving +import GHC.Generics +import GHC.TypeLits +import qualified Data.Ix as Ix +import Test.QuickCheck +import Text.Printf + +import Data.PrimitiveArray.Index.Class hiding (Index) +import qualified Data.PrimitiveArray.Index.Class as PA + + + +-- | A linear @Int@-based index type. + +newtype Index (t :: Nat) = Index { getIndex :: Int } + deriving (Show,Read,Eq,Ord,Generic,Ix.Ix) + +-- | Turn an 'Int' into an 'Index' safely. + +index :: forall t . KnownNat t => Int -> Index t +index i = maybe (error $ printf "%d < Index %d\n" i n) id $ maybeIndex i + where n = natVal (Proxy :: Proxy t) +{-# Inline index #-} + +-- | Produce 'Just' and 'Index' or 'Nothing'. + +maybeIndex :: forall t . KnownNat t => Int -> Maybe (Index t) +maybeIndex i + | i >= n = Just . Index $ i - n + | otherwise = Nothing + where n = fromIntegral $ natVal (Proxy :: Proxy t) +{-# Inline maybeIndex #-} + +instance KnownNat t => Num (Index t) where + Index a + Index b = error "not implemented, use (+.)" -- index $ a + b + Index a - Index b = error "not implemented, use (-.)" -- index $ a - b + Index a * Index b = error "not implemented" -- index $ a * b + negate = error "Indices are natural numbers" + abs = id + signum = index . signum . getIndex + fromInteger = index . fromIntegral + {-# Inline fromInteger #-} + +instance NFData (Index t) where + rnf = rnf . getIndex + {-# Inline rnf #-} + +instance Binary (Index t) +instance Serialize (Index t) +instance ToJSON (Index t) +instance FromJSON (Index t) +instance Hashable (Index t) + +derivingUnbox "Index" + [t| forall t . Index t -> Int |] [| getIndex |] [| Index |] + +instance forall t . KnownNat t => PA.Index (Index t) where + linearIndex _ _ (Index z) = z + {-# INLINE linearIndex #-} + smallestLinearIndex (Index l) = error "still needed?" + {-# INLINE smallestLinearIndex #-} + largestLinearIndex (Index h) = h + {-# INLINE largestLinearIndex #-} + size (_) (Index h) = h + 1 + {-# INLINE size #-} + inBounds (_) (Index h) (Index x) = 0<=x && x<=h + {-# INLINE inBounds #-} + +instance IndexStream z => IndexStream (z:.Index t) where + streamUp (ls:.Index lf) (hs:.Index ht) = flatten mk step Unknown $ streamUp ls hs + where mk z = return (z,lf) + step (z,k) + | k > ht = return $ Done + | otherwise = return $ Yield (z:.Index k) (z,k+1) + {-# Inline [0] mk #-} + {-# Inline [0] step #-} + {-# Inline streamUp #-} + streamDown (ls:.Index lf) (hs:.Index ht) = flatten mk step Unknown $ streamDown ls hs + where mk z = return (z,ht) + step (z,k) + | k < lf = return $ Done + | otherwise = return $ Yield (z:.Index k) (z,k-1) + {-# Inline [0] mk #-} + {-# Inline [0] step #-} + {-# Inline streamDown #-} + +instance IndexStream (Index t) + +instance Arbitrary (Index t) where + arbitrary = Index <$> arbitrary + shrink (Index j) = map Index $ shrink j + diff --git a/Biobase/Types/NumericalExtremes.hs b/Biobase/Types/NumericalExtremes.hs new file mode 100644 --- /dev/null +++ b/Biobase/Types/NumericalExtremes.hs @@ -0,0 +1,80 @@ + +-- | For some values, we want to have different kind of extreme values. +-- Consider a @Double@ representing an energy. We want @near infinities@ +-- that do not lead to numeric problems. +-- +-- TODO benchmark different extremes and their interplay with algebraic +-- operations. +-- +-- TODO consider the @ieee754@ package + +module Biobase.Types.NumericalExtremes where + + + +-- | Very large and small numbers with some numerical safety to @1/0@ or +-- @maxBound@ (depending on if we are @Integral@ or @RealFloat@. +-- +-- We have: +-- +-- @maxFinite >= extremelyLarge >= veryLarge@ +-- +-- @veryLarge >= verySmall@ +-- +-- @verySmall >= extremelySmall >= minFinite@. +-- +-- TODO the small stuff should actually be around zero, but positive and go +-- into @NumericalEpsilon@. Here we should actually use other names. + +class NumericalExtremes x where + -- | Largest finite number + maxFinite :: x + -- | Smallest finite number + minFinite :: x + -- | Around @1/100@ of the largest finite number + veryLarge :: x + -- | Around @1/100@ of the smallest finite number + verySmall :: x + -- | Around @1/ 10@ of the largest finite number + extremelyLarge :: x + -- | Around @1/ 10@ of the smallest finite number + extremelySmall :: x + +-- | Small numbers. + +class NumericalEpsilon x where + -- | Smallest positive number @/= 0.0@. + epsilon :: x + + + +instance NumericalExtremes Int where + maxFinite = maxBound + minFinite = minBound + veryLarge = maxBound `div` 100 + verySmall = minBound `div` 100 + extremelyLarge = maxBound `div` 10 + extremelySmall = minBound `div` 10 + {-# Inline veryLarge #-} + {-# Inline verySmall #-} + {-# Inline extremelyLarge #-} + {-# Inline extremelySmall #-} + + + +instance NumericalExtremes Double where + maxFinite = 1.79e+308 + minFinite = -1.79e+308 + veryLarge = maxFinite / 100 + verySmall = minFinite / 100 + extremelyLarge = maxFinite / 10 + extremelySmall = minFinite / 10 + {-# Inline veryLarge #-} + {-# Inline verySmall #-} + {-# Inline extremelyLarge #-} + {-# Inline extremelySmall #-} + +instance NumericalEpsilon Double where + epsilon = 2.2e-16 + {-# Inline epsilon #-} + diff --git a/Biobase/Types/Odds.hs b/Biobase/Types/Odds.hs new file mode 100644 --- /dev/null +++ b/Biobase/Types/Odds.hs @@ -0,0 +1,36 @@ + +-- | Discretized log-odds. + +module Biobase.Types.Odds where + +import Control.DeepSeq (NFData(..)) +import Data.Aeson (FromJSON,ToJSON) +import Data.Binary (Binary) +import Data.Serialize (Serialize) +import Data.Vector.Unboxed.Deriving +import GHC.Generics (Generic) + + + +-- | Discretized log-odds. +-- +-- The BLOSUM matrices, for example, store data in discretized log-odds +-- form. +-- +-- TODO Might move up even higher into statistics modules. + +newtype DLO = DLO { getDLO :: Int } + deriving (Generic,Eq,Ord,Show,Read) + +derivingUnbox "DLO" + [t| DLO -> Int |] [| getDLO |] [| DLO |] + +instance Binary DLO +instance Serialize DLO +instance FromJSON DLO +instance ToJSON DLO + +instance NFData DLO where + rnf (DLO k) = rnf k + {-# Inline rnf #-} + diff --git a/Biobase/Types/Partition.hs b/Biobase/Types/Partition.hs deleted file mode 100644 --- a/Biobase/Types/Partition.hs +++ /dev/null @@ -1,84 +0,0 @@ - -{-# LANGUAGE ForeignFunctionInterface #-} -{-# LANGUAGE StandaloneDeriving #-} -{-# LANGUAGE MultiParamTypeClasses #-} -{-# LANGUAGE GeneralizedNewtypeDeriving #-} - -module Biobase.Types.Partition where - -import qualified Data.Vector.Unboxed as VU -import qualified Data.Vector.Generic as VG -import qualified Data.Vector.Generic.Mutable as VGM -import Data.Primitive.Types - -import Biobase.Types.Ring - - - --- | Some default instances. Left out the Num one, so that you have to --- explicitly instanciate if you want to go around the Ring structure. - -newtype Partition = Partition {unPartition' :: Double} - deriving (Show, Read, Eq, Ord) - --- | - -mkPartition :: Double -> Partition -mkPartition x - | x < 0 = error $ "mkPartition: prob <0: " ++ show x - | x > 1 = error $ "mkPartition: prob >1: " ++ show x - | otherwise = Partition $ log x - -unPartition :: Partition -> Double -unPartition (Partition x) = exp x - - --- | Ring operations over Partition values. - -instance Ring Partition where - (Partition a) .+. (Partition b) = Partition $ logSum a b - {-# INLINE (.+.) #-} - (Partition a) .*. (Partition b) = Partition $ a + b - {-# INLINE (.*.) #-} - (Partition a) .^. k = Partition $ a * fromIntegral k - {-# INLINE (.^.) #-} - (Partition a) .^^. k = error ".^^. not defined for Partition" -- Partition $ a ^^ k - {-# INLINE (.^^.) #-} - neg (Partition a) = error $ "negate partition? " ++ show a -- Partition $ negate a - {-# INLINE neg #-} - one = Partition 1 - {-# INLINE one #-} - zero = Partition 0 - {-# INLINE zero #-} - isZero (Partition a) = a == 0 -- TODO use some epsilon? - {-# INLINE isZero #-} - -logSum :: Double -> Double -> Double -logSum a b - | a>b = f a b - | otherwise = f b a - where - f x y = x + log1p (exp $ y - x) - {-# INLINE f #-} -{-# INLINE logSum #-} - - - --- * Vector (and Prim) instances. - -deriving instance VGM.MVector VU.MVector Partition -deriving instance VG.Vector VU.Vector Partition -deriving instance VU.Unbox Partition -deriving instance Prim Partition - - - --- * math.h function for log/exp on pm1 are /much/ more efficient (what is --- haskell doing?) - -foreign import ccall unsafe "math.h log1p" - log1p :: Double -> Double - -foreign import ccall unsafe "math.h expm1" - expm1 :: Double -> Double - diff --git a/Biobase/Types/Ring.hs b/Biobase/Types/Ring.hs deleted file mode 100644 --- a/Biobase/Types/Ring.hs +++ /dev/null @@ -1,22 +0,0 @@ - --- | Algebraic ring structure. Very similar to others found throughout hackage. --- --- TODO maybe use on of the already-written packages? - -module Biobase.Types.Ring where - - - --- | Define the basic operations on a ring. - -class (Eq a, Ord a) => Ring a where - (.+.), (.*.) :: a -> a -> a - (.^.) :: a -> Int -> a - (.^^.) :: a -> Double -> a - neg :: a -> a - one, zero :: a - isZero :: a -> Bool -- ^ ==zero does not work well for min-plus - infixl 6 .+. - infixl 7 .*. - infixr 8 .^. - infixr 8 .^^. diff --git a/Biobase/Types/Score.hs b/Biobase/Types/Score.hs deleted file mode 100644 --- a/Biobase/Types/Score.hs +++ /dev/null @@ -1,48 +0,0 @@ - -{-# LANGUAGE StandaloneDeriving #-} -{-# LANGUAGE MultiParamTypeClasses #-} -{-# LANGUAGE GeneralizedNewtypeDeriving #-} - -module Biobase.Types.Score where - -import qualified Data.Vector.Unboxed as VU -import qualified Data.Vector.Generic as VG -import qualified Data.Vector.Generic.Mutable as VGM -import Data.Primitive.Types - -import Biobase.Types.Ring - - - --- | Some default instances. Left out the Num one, so that you have to --- explicitly instanciate if you want to go around the Ring structure. - -newtype Score = Score {unScore :: Int} - deriving (Show, Read, Eq, Ord) - - - --- | Ring operations over Score values. - -instance Ring Score where - (Score a) .+. (Score b) = Score $ a `min` b - {-# INLINE (.+.) #-} - (Score a) .*. (Score b) = Score $ a + b - {-# INLINE (.*.) #-} - neg (Score a) = Score $ negate a - {-# INLINE neg #-} - one = Score 0 - {-# INLINE one #-} - zero = Score 10000000 - {-# INLINE zero #-} - isZero (Score a) = a >= 1000000 - {-# INLINE isZero #-} - - - --- * Vector instances. - -deriving instance VGM.MVector VU.MVector Score -deriving instance VG.Vector VU.Vector Score -deriving instance VU.Unbox Score -deriving instance Prim Score diff --git a/Biobase/Types/Strand.hs b/Biobase/Types/Strand.hs new file mode 100644 --- /dev/null +++ b/Biobase/Types/Strand.hs @@ -0,0 +1,111 @@ + +-- | Strand information. A newtyped version, complete with serialization, +-- pattern synonyms, being a @PrimitiveArray@ index type, etc. +-- +-- TODO will be expanded to encode biological sense information more +-- clearly: . + +module Biobase.Types.Strand where + +import Control.DeepSeq +import Control.Monad (guard) +import Data.Aeson +import Data.Binary +import Data.Hashable (Hashable) +import Data.Serialize (Serialize) +import Data.Vector.Fusion.Stream.Monadic (flatten, Step(..)) +import Data.Vector.Fusion.Stream.Size +import Data.Vector.Unboxed.Deriving +import GHC.Generics +import Test.QuickCheck +import Text.Printf + +import Data.PrimitiveArray.Index.Class + + + +newtype Strand = Strand { getStrand :: Int } + deriving (Eq,Ord,Generic) + +instance Show Strand where + show P = "+" + show M = "-" + +instance Read Strand where + readsPrec _ xs = do + ([pm],s) <- lex xs + guard $ pm `elem` "+-PMpm" + return (go pm,s) + where go x | x `elem` "+Pp" = P + | x `elem` "-Mm" = M + +instance Bounded Strand where + minBound = P + maxBound = M + +instance Enum Strand where + succ P = M + succ M = error "succ M" + pred M = P + pred P = error "pred P" + toEnum i | i>=0 && i<=1 = Strand i + toEnum i = error $ "toEnum (Strand)" ++ show i + fromEnum = getStrand + +instance NFData Strand + +pattern P = Strand 0 +pattern M = Strand 1 + +pattern Sense = P +pattern AntiSense = M + +instance Binary Strand +instance Serialize Strand +instance ToJSON Strand +instance FromJSON Strand +instance Hashable Strand + +derivingUnbox "Strand" + [t| Strand -> Int |] [| getStrand |] [| Strand |] + +instance Index Strand where + linearIndex _ _ (Strand z) = z + {-# INLINE linearIndex #-} + smallestLinearIndex (Strand l) = error "still needed?" + {-# INLINE smallestLinearIndex #-} + largestLinearIndex (Strand h) = h + {-# INLINE largestLinearIndex #-} + size (_) (Strand h) = h + 1 + {-# INLINE size #-} + inBounds (_) (Strand h) (Strand x) = 0<=x && x<=h + {-# INLINE inBounds #-} + +instance IndexStream z => IndexStream (z:.Strand) where + streamUp (ls:.Strand lf) (hs:.Strand ht) = flatten mk step Unknown $ streamUp ls hs + where mk z = return (z,lf) + step (z,k) + | k > ht = return $ Done + | otherwise = return $ Yield (z:.Strand k) (z,k+1) + {-# Inline [0] mk #-} + {-# Inline [0] step #-} + {-# Inline streamUp #-} + streamDown (ls:.Strand lf) (hs:.Strand ht) = flatten mk step Unknown $ streamDown ls hs + where mk z = return (z,ht) + step (z,k) + | k < lf = return $ Done + | otherwise = return $ Yield (z:.Strand k) (z,k-1) + {-# Inline [0] mk #-} + {-# Inline [0] step #-} + {-# Inline streamDown #-} + +instance IndexStream Strand + +instance Arbitrary Strand where + arbitrary = do + b <- choose (0,1) + return $ Strand b + shrink (Strand j) + | 0= 1.4.0 +cabal-version: >= 1.10.0 +tested-with: GHC == 7.8.4, GHC == 7.10.1 +synopsis: Collection of types for bioinformatics description: - Provides an algebraic ring class and instances for Gibbs free - energy, partition function probabilities, and scores. - Conversion between different entities is provided by a convert - function. All entities are ready for the vector library. + Types used in a number of bioinformatics libraries. . - - Ignore everything except the Ring itself! + * linear indices + . + * energies + . + * numerics -library - build-depends: - base >=4 && <5, - vector >=0.7 && <0.8, - primitive >=0.3 && <0.4 +Extra-Source-Files: + README.md + changelog.md + + +library + build-depends: base >= 4.7 && < 4.9 + , aeson >= 0.8 && < 0.10 + , binary >= 0.7 && < 0.8 + , cereal >= 0.4 && < 0.5 + , cereal-text >= 0.1 && < 0.2 + , data-default >= 0.5 && < 0.6 + , deepseq >= 1.3 && < 1.5 + , hashable >= 1.2 && < 1.3 + , log-domain >= 0.10 && < 0.11 + , primitive >= 0.5 && < 0.7 + , PrimitiveArray >= 0.6.0 && < 0.6.2 + , QuickCheck >= 2.7 && < 2.9 + , stringable >= 0.1.3 && < 0.2 + , text >= 1.0 && < 1.3 + , text-binary >= 0.2 && < 0.3 + , vector >= 0.10 && < 0.11 + , vector-binary-instances >= 0.2 && < 0.3 + , vector-th-unbox >= 0.2 && < 0.3 exposed-modules: - Biobase.Types.Ring - Biobase.Types.Convert + Biobase.Types.Accession Biobase.Types.Energy - Biobase.Types.Partition - Biobase.Types.Score + Biobase.Types.Index + Biobase.Types.Index.Type + Biobase.Types.NumericalExtremes + Biobase.Types.Odds + Biobase.Types.Strand + default-language: + Haskell2010 + default-extensions: BangPatterns + , DataKinds + , DeriveGeneric + , FlexibleInstances + , GeneralizedNewtypeDeriving + , KindSignatures + , MultiParamTypeClasses + , PatternSynonyms + , ScopedTypeVariables + , StandaloneDeriving + , TemplateHaskell + , TypeFamilies + , TypeOperators + ghc-options: + -O2 -funbox-strict-fields + + +test-suite properties + type: + exitcode-stdio-1.0 + main-is: + properties.hs ghc-options: - -O2 + -threaded -rtsopts -with-rtsopts=-N + hs-source-dirs: + tests + default-language: + Haskell2010 + default-extensions: ScopedTypeVariables + , TemplateHaskell + build-depends: base + , BiobaseTypes + , QuickCheck + , test-framework >= 0.8 && < 0.9 + , test-framework-quickcheck2 >= 0.3 && < 0.4 + , test-framework-th >= 0.2 && < 0.3 + + + +source-repository head + type: git + location: git://github.com/choener/BiobaseTypes + diff --git a/LICENSE b/LICENSE --- a/LICENSE +++ b/LICENSE @@ -1,675 +1,30 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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If not, see . - -Also add information on how to contact you by electronic and paper mail. +Copyright Christian Hoener zu Siederdissen 2015 - If the program does terminal interaction, make it output a short -notice like this when it starts in an interactive mode: +All rights reserved. - Copyright (C) - This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. - This is free software, and you are welcome to redistribute it - under certain conditions; type `show c' for details. +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: -The hypothetical commands `show w' and `show c' should show the appropriate -parts of the General Public License. Of course, your program's commands -might be different; for a GUI interface, you would use an "about box". + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. - You should also get your employer (if you work as a programmer) or school, -if any, to sign a "copyright disclaimer" for the program, if necessary. -For more information on this, and how to apply and follow the GNU GPL, see -. + * Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following + disclaimer in the documentation and/or other materials provided + with the distribution. - The GNU General Public License does not permit incorporating your program -into proprietary programs. If your program is a subroutine library, you -may consider it more useful to permit linking proprietary applications with -the library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. But first, please read -. + * Neither the name of Christian Hoener zu Siederdissen nor the names of other + contributors may be used to endorse or promote products derived + from this software without specific prior written permission. +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/README.md b/README.md new file mode 100644 --- /dev/null +++ b/README.md @@ -0,0 +1,20 @@ +[![Build Status](https://travis-ci.org/choener/BiobaseTypes.svg?branch=master)](https://travis-ci.org/choener/BiobaseTypes) + +# BiobaseTypes + +A bunch of types in use in different modules: + +- numerical small and large numbers +- Gibbs free energy change +- phantom-typed linear indices: these encode the (rather annoying) habit of + computational biology of having both 0-based and 1-based data + + + +#### Contact + +Christian Hoener zu Siederdissen +Leipzig University, Leipzig, Germany +choener@bioinf.uni-leipzig.de +http://www.bioinf.uni-leipzig.de/~choener/ + diff --git a/changelog.md b/changelog.md new file mode 100644 --- /dev/null +++ b/changelog.md @@ -0,0 +1,16 @@ +0.1.1.0 +------- + +- added Biobase.Types.Odds module (from the BiobaseBlast package) + +0.1.0.0 +------- + +- re-introduced the types library for bioinformatics +- travis-ci integration + +0.0.x,y +------- + +- old variant; completely rewritten by now + diff --git a/tests/properties.hs b/tests/properties.hs new file mode 100644 --- /dev/null +++ b/tests/properties.hs @@ -0,0 +1,15 @@ + +module Main where + +import Test.Framework.Providers.QuickCheck2 +import Test.Framework.TH +import Test.QuickCheck.Modifiers +import Test.QuickCheck.Property + +import Biobase.Types.NumericalExtremes + + + +main :: IO () +main = $(defaultMainGenerator) +