BiobaseTypes 0.0.2.2 → 0.1.1.0

raw patch · 16 files changed

+739/−917 lines, 16 filesdep +BiobaseTypesdep +PrimitiveArraydep +QuickCheckdep ~basedep ~primitivedep ~vectorPVP ok

version bump matches the API change (PVP)

Dependencies added: BiobaseTypes, PrimitiveArray, QuickCheck, aeson, binary, cereal, cereal-text, data-default, deepseq, hashable, log-domain, stringable, test-framework, test-framework-quickcheck2, test-framework-th, text, text-binary, vector-binary-instances, vector-th-unbox

Dependency ranges changed: base, primitive, vector

API changes (from Hackage documentation)

Files

• Biobase/Types/Accession.hs +88/−0
• Biobase/Types/Convert.hs +0/−36
• Biobase/Types/Energy.hs +58/−35
• Biobase/Types/Index.hs +96/−0
• Biobase/Types/Index/Type.hs +104/−0
• Biobase/Types/NumericalExtremes.hs +80/−0
• Biobase/Types/Odds.hs +36/−0
• Biobase/Types/Partition.hs +0/−84
• Biobase/Types/Ring.hs +0/−22
• Biobase/Types/Score.hs +0/−48
• Biobase/Types/Strand.hs +111/−0
• BiobaseTypes.cabal +91/−23
• LICENSE +24/−669
• README.md +20/−0
• changelog.md +16/−0
• tests/properties.hs +15/−0

@@ -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.+--+-- <http://www.ncbi.nlm.nih.gov/Sequin/acc.html>+--+-- <http://www.uniprot.org/help/accession_numbers>+--+-- <http://en.wikipedia.org/wiki/Accession_number_%28bioinformatics%29>++-- | 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+

@@ -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)

@@ -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 #-}+

@@ -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+

@@ -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+

@@ -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 #-}+

@@ -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 #-}+

@@ -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-

@@ -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 .^^.

@@ -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

@@ -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: <http://en.wikipedia.org/wiki/Sense_%28molecular_biology%29>.++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<j = [Strand $ j-1]+    | otherwise = []+

@@ -1,37 +1,105 @@ name:           BiobaseTypes-version:        0.0.2.2-author:         Christian Hoener zu Siederdissen-maintainer:     choener@tbi.univie.ac.at-copyright:      Christian Hoener zu Siederdissen, 2010-category:       Bioinformatics-synopsis:       (deprecated) Ring class, with several instances.-license:        GPL-3+version:        0.1.1.0+author:         Christian Hoener zu Siederdissen, 2015+copyright:      Christian Hoener zu Siederdissen, 2015+homepage:       https://github.com/choener/BiobaseTypes+bug-reports:    https://github.com/choener/BiobaseTypes/issues+maintainer:     choener@bioinf.uni-leipzig.de+category:       Data Structures, Bioinformatics+license:        BSD3 license-file:   LICENSE build-type:     Simple stability:      experimental-cabal-version:  >= 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+

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@@ -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/  +

@@ -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+

@@ -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)+