BiobaseXNA 0.10.0.0 → 0.11.0.0

raw patch · 20 files changed

+440/−1090 lines, 20 filesdep +BiobaseENAdep +data-defaultdep ~BiobaseTypesdep ~ForestStructuresdep ~PrimitiveArrayPVP ok

version bump matches the API change (PVP)

Dependencies added: BiobaseENA, data-default

Dependency ranges changed: BiobaseTypes, ForestStructures, PrimitiveArray, base, vector

API changes (from Hackage documentation)

Files

• Biobase/Primary/AA.hs +62/−48
• Biobase/Primary/Hashed.hs +6/−6
• Biobase/Primary/IUPAC.hs +27/−25
• Biobase/Primary/Letter.hs +80/−42
• Biobase/Primary/Nuc/Conversion.hs +14/−14
• Biobase/Primary/Nuc/DNA.hs +17/−19
• Biobase/Primary/Nuc/RNA.hs +32/−32
• Biobase/Primary/Nuc/XNA.hs +16/−16
• Biobase/Primary/Pretty.hs +4/−4
• Biobase/Primary/Trans.hs +45/−0
• Biobase/Primary/Unknown.hs +15/−20
• Biobase/Secondary.hs +3/−3
• Biobase/Secondary/Basepair.hs +8/−6
• Biobase/Secondary/Constraint.hs +0/−107
• Biobase/Secondary/Convert.hs +6/−4
• Biobase/Secondary/Isostericity.hs +3/−3
• Biobase/Secondary/Vienna.hs +18/−23
• BiobaseXNA.cabal +57/−49
• LICENSE +24/−669
• changelog.md +3/−0

@@ -1,7 +1,11 @@ --- | This module has the translation tables for the genetic code. We do--- have a symbol 'Undef' for undefined amino acids (say because of @N@s in--- the nucleotide code).+-- | This module has the translation tables for the genetic code.+--+-- In addition, @Any@ is included to denote that any amino acid is ok, and+-- @Unknown@ to denote unknown data.  We do have a symbol 'Undef' for undefined+-- amino acids, which denotes error condition.+--+-- TODO this nomenclature might change!  module Biobase.Primary.AA where @@ -14,7 +18,6 @@ import           Data.Tuple (swap) import           Data.Vector.Unboxed.Deriving import           GHC.Base (remInt,quotInt)-import qualified GHC.Exts as GHC import           GHC.Generics (Generic) import qualified Data.Bijection.HashMap as B import qualified Data.ByteString.Char8 as BS@@ -25,77 +28,83 @@ import qualified Data.Vector.Generic as VG import qualified Data.Vector.Generic.Mutable as VGM import qualified Data.Vector.Unboxed as VU+import qualified GHC.Exts as GHC +import           Biobase.Types.BioSequence+ import           Biobase.Primary.Letter   --- | Amino acid phantom type.--data AA--pattern  Stop = Letter  0 :: Letter AA-pattern     A = Letter  1 :: Letter AA-pattern     B = Letter  2 :: Letter AA-pattern     C = Letter  3 :: Letter AA-pattern     D = Letter  4 :: Letter AA-pattern     E = Letter  5 :: Letter AA-pattern     F = Letter  6 :: Letter AA-pattern     G = Letter  7 :: Letter AA-pattern     H = Letter  8 :: Letter AA-pattern     I = Letter  9 :: Letter AA-pattern     K = Letter 10 :: Letter AA-pattern     L = Letter 11 :: Letter AA-pattern     M = Letter 12 :: Letter AA-pattern     N = Letter 13 :: Letter AA-pattern     P = Letter 14 :: Letter AA-pattern     Q = Letter 15 :: Letter AA-pattern     R = Letter 16 :: Letter AA-pattern     S = Letter 17 :: Letter AA-pattern     T = Letter 18 :: Letter AA-pattern     V = Letter 19 :: Letter AA-pattern     W = Letter 20 :: Letter AA-pattern     X = Letter 21 :: Letter AA-pattern     Y = Letter 22 :: Letter AA-pattern     Z = Letter 23 :: Letter AA-pattern Undef = Letter 24 :: Letter AA-+pattern  Stop   = Letter  0 ∷ Letter AA n+pattern     A   = Letter  1 ∷ Letter AA n+pattern     B   = Letter  2 ∷ Letter AA n+pattern     C   = Letter  3 ∷ Letter AA n+pattern     D   = Letter  4 ∷ Letter AA n+pattern     E   = Letter  5 ∷ Letter AA n+pattern     F   = Letter  6 ∷ Letter AA n+pattern     G   = Letter  7 ∷ Letter AA n+pattern     H   = Letter  8 ∷ Letter AA n+pattern     I   = Letter  9 ∷ Letter AA n+pattern     K   = Letter 10 ∷ Letter AA n+pattern     L   = Letter 11 ∷ Letter AA n+pattern     M   = Letter 12 ∷ Letter AA n+pattern     N   = Letter 13 ∷ Letter AA n+pattern     P   = Letter 14 ∷ Letter AA n+pattern     Q   = Letter 15 ∷ Letter AA n+pattern     R   = Letter 16 ∷ Letter AA n+pattern     S   = Letter 17 ∷ Letter AA n+pattern     T   = Letter 18 ∷ Letter AA n+pattern     V   = Letter 19 ∷ Letter AA n+pattern     W   = Letter 20 ∷ Letter AA n+pattern     X   = Letter 21 ∷ Letter AA n+pattern     Y   = Letter 22 ∷ Letter AA n+pattern     Z   = Letter 23 ∷ Letter AA n+pattern Any     = Letter 24 ∷ Letter AA n+pattern Unknown = Letter 25 ∷ Letter AA n+pattern Undef   = Letter 26 ∷ Letter AA n  -- * Creating functions and aa data. -aa :: Int -> Letter AA+aa ∷ Int → Letter AA n aa = Letter+{-# Inline aa #-} -aaRange = [Stop .. pred Undef]+aaRange = VU.fromList [Stop .. pred Undef]+{-# NoInline aaRange #-} -instance LetterChar AA where+instance Bounded (Letter AA n) where+    minBound = Stop+    maxBound = Undef++instance LetterChar AA n where   letterChar = aaChar   charLetter = charAA -instance ToJSON (Letter AA) where+instance ToJSON (Letter AA n) where   toJSON = toJSON . letterChar -instance FromJSON (Letter AA) where+instance FromJSON (Letter AA n) where   parseJSON = fmap charLetter . parseJSON ---instance (GHC.IsString f) => ToJSON (Pretty f (Letter AA)) where+--instance (GHC.IsString f) ⇒ ToJSON (Pretty f (Letter AA)) where --  toJSON = toJSON . T.pack . map letterChar . GHC.toList . getPretty  -- | Translate 'Char' amino acid representation into efficient 'AA' newtype. -charAA :: Char -> Letter AA+charAA ∷ Char → Letter AA n charAA = B.findWithDefaultL Undef charBaa {-# INLINE charAA #-}  -- | 'Char' representation of an 'AA'. -aaChar :: Letter AA -> Char+aaChar ∷ Letter AA n → Char aaChar = B.findWithDefaultR '?' charBaa {-# INLINE aaChar #-}  -- * lookup tables -charBaa :: B.Bimap (B.HashMap Char (Letter AA)) (B.HashMap (Letter AA) Char)+charBaa ∷ B.Bimap (B.HashMap Char (Letter AA n)) (B.HashMap (Letter AA n) Char) charBaa = B.fromList   [ ('*',Stop)   , ('A',A)@@ -121,25 +130,30 @@   , ('X',X)   , ('Y',Y)   , ('Z',Z)-  , ('?',Undef)+  , ('?',Unknown)   ] {-# NOINLINE charBaa #-} +-- | List of the twenty "default" amino acids. Used, for example, by HMMer. +twentyAA ∷ VU.Vector (Letter AA n)+twentyAA = VU.fromList [ A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y ]+{-# NoInline twentyAA #-} + -- * instances -instance Show (Letter AA) where+instance Show (Letter AA n) where   show n = [aaChar n] -instance Read (Letter AA) where+instance Read (Letter AA n) where   readsPrec p [] = []   readsPrec p (x:xs)     | x==' ' = readsPrec p xs     | aa <- charAA x = [(aa,xs)]     | otherwise = [] -instance Enum (Letter AA) where+instance Enum (Letter AA n) where     succ Undef      = error "succ/Undef:AA"     succ (Letter x) = Letter $ x+1     pred Stop       = error "pred/Stop:AA"@@ -148,6 +162,6 @@     toEnum k                               = error $ "toEnum/Letter RNA " ++ show k     fromEnum (Letter k) = k -instance MkPrimary (VU.Vector Char) AA where+instance MkPrimary (VU.Vector Char) AA n where   primary = VU.map charAA 

@@ -19,26 +19,26 @@  -- | The hash of a primary sequence. -newtype HashedPrimary t = HashedPrimary { unHashedPrimary :: Int }+newtype HashedPrimary t n = HashedPrimary { unHashedPrimary :: Int }   deriving (Eq,Ord,Ix,Read,Show,Enum,Bounded)  derivingUnbox "HashedPrimary"-  [t| forall a . HashedPrimary a -> Int |] [| unHashedPrimary |] [| HashedPrimary |]+  [t| forall t n . HashedPrimary t n -> Int |] [| unHashedPrimary |] [| HashedPrimary |]  -- | Given a piece of primary sequence information, reduce it to an index. -- The empty input produces an index of 0. -mkHashedPrimary :: forall t . (VU.Unbox (Letter t), Bounded (Letter t), Enum (Letter t)) => Primary t -> HashedPrimary t+mkHashedPrimary :: forall t n . (VU.Unbox (Letter t n), Bounded (Letter t n), Enum (Letter t n)) => Primary t n -> HashedPrimary t n mkHashedPrimary = HashedPrimary . fst . VU.foldl' f (0, 1) where-  f (z, c) n = (z + c * (fromEnum n +1), c * (fromEnum (maxBound :: Letter t) + 1))+  f (z, c) n = (z + c * (fromEnum n +1), c * (fromEnum (maxBound :: Letter t n) + 1)) {-# INLINE mkHashedPrimary #-}  -- | Turn a hash back into a sequence. Will fail if the resulting sequence -- has more than 100 elements. -hash2primary :: forall t . (VU.Unbox (Letter t), Bounded (Letter t), Enum (Letter t)) => HashedPrimary t -> Primary t+hash2primary :: forall t n . (VU.Unbox (Letter t n), Bounded (Letter t n), Enum (Letter t n)) => HashedPrimary t n -> Primary t n hash2primary (HashedPrimary h) = VU.unfoldrN l f h where-  m = fromEnum (maxBound :: Letter t) +1+  m = fromEnum (maxBound :: Letter t n) +1   l = VU.length . VU.takeWhile (>0) . VU.iterateN 100 (`div` m) $ h   f k = if k>0 then Just (toEnum $ ((k-1) `mod` m) , (k-1) `div` m)                else Nothing

@@ -18,6 +18,8 @@ import qualified Data.Vector.Unboxed as VU import           Control.Category ((>>>)) +import           Biobase.Types.BioSequence+ import           Biobase.Primary.Letter import           Biobase.Primary.Nuc import qualified Biobase.Primary.Nuc.RNA as R@@ -27,28 +29,28 @@  data DEG -pattern A = Letter  0 :: Letter DEG-pattern C = Letter  1 :: Letter DEG-pattern G = Letter  2 :: Letter DEG-pattern T = Letter  3 :: Letter DEG-pattern U = Letter  4 :: Letter DEG-pattern W = Letter  5 :: Letter DEG-pattern S = Letter  6 :: Letter DEG-pattern M = Letter  7 :: Letter DEG-pattern K = Letter  8 :: Letter DEG-pattern R = Letter  9 :: Letter DEG-pattern Y = Letter 10 :: Letter DEG-pattern B = Letter 11 :: Letter DEG-pattern D = Letter 12 :: Letter DEG-pattern H = Letter 13 :: Letter DEG-pattern V = Letter 14 :: Letter DEG-pattern N = Letter 15 :: Letter DEG+pattern A = Letter  0 :: Letter DEG n+pattern C = Letter  1 :: Letter DEG n+pattern G = Letter  2 :: Letter DEG n+pattern T = Letter  3 :: Letter DEG n+pattern U = Letter  4 :: Letter DEG n+pattern W = Letter  5 :: Letter DEG n+pattern S = Letter  6 :: Letter DEG n+pattern M = Letter  7 :: Letter DEG n+pattern K = Letter  8 :: Letter DEG n+pattern R = Letter  9 :: Letter DEG n+pattern Y = Letter 10 :: Letter DEG n+pattern B = Letter 11 :: Letter DEG n+pattern D = Letter 12 :: Letter DEG n+pattern H = Letter 13 :: Letter DEG n+pattern V = Letter 14 :: Letter DEG n+pattern N = Letter 15 :: Letter DEG n -instance Bounded (Letter DEG) where+instance Bounded (Letter DEG n) where     minBound = A     maxBound = N -instance Enum (Letter DEG) where+instance Enum (Letter DEG n) where     succ N           = error "succ/N:DEG"     succ (Letter x)  = Letter $ x+1     pred A           = error "pred/A:DEG"@@ -95,16 +97,16 @@   N -> 'N' {-# INLINE degChar #-}             -instance Show (Letter DEG) where+instance Show (Letter DEG n) where     show c = [degChar c] -degSeq :: MkPrimary n DEG => n -> Primary DEG+degSeq :: MkPrimary p DEG n => p -> Primary DEG n degSeq = primary -instance MkPrimary (VU.Vector Char) DEG where+instance MkPrimary (VU.Vector Char) DEG n where     primary = VU.map charDEG -instance IsString [Letter DEG] where+instance IsString [Letter DEG n] where     fromString = map charDEG  @@ -119,18 +121,18 @@   fromDegenerate = maybe [] id . flip lookup iupacXDNAchars   toDegenerate   = flip lookup (map swap iupacXDNAchars) . nub . sort -instance Degenerate (Letter RNA) where+instance Degenerate (Letter RNA n) where     fromDegenerate 'T' = []     fromDegenerate x   = map dnaTrna $ fromDegenerate x     toDegenerate   xs  | xs == [R.U] = Just 'U'                        | otherwise  = toDegenerate $ map rnaTdna xs -instance Degenerate (Letter DNA) where+instance Degenerate (Letter DNA n) where     fromDegenerate 'U' = []     fromDegenerate x   = map charDNA $ fromDegenerate x     toDegenerate       = toDegenerate . map dnaChar -instance Degenerate (Letter XNA) where+instance Degenerate (Letter XNA n) where     fromDegenerate = map charXNA . fromDegenerate     toDegenerate   = toDegenerate . map xnaChar 

@@ -1,18 +1,21 @@ --- | A newtype with an attached phenotype which allows us to encode--- nucleotides and amino acids. Actual seqence-specific functions can be--- founds in the appropriate modules @AA@ and @Nuc@.+-- | A newtype with an attached phantom type which allows us to encode+-- nucleotides and amino acids. Actual seqence-specific functions can be founds+-- in the appropriate modules @AA@ and @Nuc@.  module Biobase.Primary.Letter where  import           Control.DeepSeq (NFData) import           Data.Aeson import           Data.Binary+import           Data.Coerce+import           Data.Data import           Data.Hashable (Hashable) import           Data.Ix (Ix(..)) import           Data.Serialize (Serialize(..)) import           Data.String (IsString(..))-import           Data.Vector.Fusion.Stream.Monadic (map,Step(..))+import           Data.Typeable+import           Data.Vector.Fusion.Stream.Monadic (map,Step(..),flatten) import           Data.Vector.Unboxed.Deriving import           GHC.Base (remInt,quotInt) import           GHC.Generics (Generic)@@ -27,48 +30,71 @@   --- | A 'Letter' together with its phantom type @t@ encodes bio-sequences.+-- | A 'Letter' together with its phantom type @seqTy@ encodes bio-sequences,+-- while @nameTy@ allows to specify a type-level name for a letter. -newtype Letter t = Letter { getLetter :: Int }-                   deriving (Eq,Ord,Generic,Ix)+newtype Letter (seqTy ∷ *) (nameTy ∷ k) = Letter { getLetter ∷ Int }+  deriving (Eq,Ord,Generic,Ix,Typeable) -instance Binary    (Letter t)-instance Serialize (Letter t)+-- | While @coerce@ will always work, this way restricts the change to just the+-- @nameTy@. -instance NFData (Letter t)+changeNameTy ∷ Letter seqTy nameTy → Letter seqTy newNameTy+{-# Inline changeNameTy #-}+changeNameTy = coerce -type Primary t = VU.Vector (Letter t)+-- | Manual @Data@ instance because @Letter@ should not show its+-- implementation. This also allows for better use of generic programming+-- downstream. +instance (Typeable t, Typeable (Letter t n)) ⇒ Data (Letter t n) where+  toConstr = mkIntegralConstr letterDataType . getLetter+  gunfold _ z c = case constrRep c of+    (IntConstr x) → z (Letter $ fromIntegral x)+    _ → errorWithoutStackTrace $ "Biobase.Primary.Letter.gunfold: Constructor "+          ++ show c+          ++ " is not of type Letter (using Int-rep)"+  dataTypeOf _ = letterDataType+letterDataType = mkDataType "Biobase.Primary.Letter" [letterConstr]+letterConstr   = mkConstr letterDataType "Letter" [] Prefix++instance Binary    (Letter t n)+instance Serialize (Letter t n)++instance NFData (Letter t n)++type Primary t n = VU.Vector (Letter t n)+ -- | Convert 'Letter' types into character forms. @DNA@, @RNA@, and @amino -- acid@ sequences can make use of this. Other @Letter@ types only if they -- have single-char representations. -class LetterChar t where-  letterChar :: Letter t -> Char-  charLetter :: Char -> Letter t+class LetterChar t n where+  letterChar ∷ Letter t n → Char+  charLetter ∷ Char → Letter t n  -- | Conversion from a large number of sequence-like inputs to primary -- sequences. -class MkPrimary n t where-    primary :: n -> Primary t+class MkPrimary c t n where+    primary ∷ c → Primary t n -instance (MkPrimary (VU.Vector Char) t) => MkPrimary String t where+instance MkPrimary (VU.Vector Char) t n ⇒ MkPrimary String t n where     primary = primary . VU.fromList -instance MkPrimary (VU.Vector Char) t =>  MkPrimary T.Text t where+instance MkPrimary (VU.Vector Char) t n ⇒  MkPrimary T.Text t n where     primary = primary . VU.fromList . T.unpack -instance MkPrimary (VU.Vector Char) t => MkPrimary TL.Text t where+instance MkPrimary (VU.Vector Char) t n ⇒ MkPrimary TL.Text t n where     primary = primary . VU.fromList . TL.unpack -instance MkPrimary (VU.Vector Char) t => MkPrimary BS.ByteString t where+instance MkPrimary (VU.Vector Char) t n ⇒ MkPrimary BS.ByteString t n where     primary = primary . VU.fromList . BS.unpack -instance MkPrimary (VU.Vector Char) t => MkPrimary BSL.ByteString t where+instance MkPrimary (VU.Vector Char) t n ⇒ MkPrimary BSL.ByteString t n where     primary = primary . VU.fromList . BSL.unpack -instance (VU.Unbox (Letter t), IsString [Letter t]) => IsString (VU.Vector (Letter t)) where+instance (VU.Unbox (Letter t n), IsString [Letter t n]) ⇒ IsString (VU.Vector (Letter t n)) where     fromString = VU.fromList . fromString  @@ -76,45 +102,57 @@ -- *** Instances for 'Letter'.  derivingUnbox "Letter"-  [t| forall a . Letter a -> Int |] [| getLetter |] [| Letter |]+  [t| forall t n . Letter t n → Int |] [| getLetter |] [| Letter |] -instance Hashable (Letter t)+instance Hashable (Letter t n) -instance Index (Letter l) where-  linearIndex _ _ (Letter i) = i+-- |+--+-- TODO replace @LtLetter Int@ with more specific limits? Maybe some constants?++instance Index (Letter l n) where+  newtype LimitType (Letter l n) = LtLetter (Letter l n)+  linearIndex _ (Letter i) = i   {-# Inline linearIndex #-}-  smallestLinearIndex _ = error "still needed?"-  {-# Inline smallestLinearIndex #-}-  largestLinearIndex (Letter h) = h-  {-# Inline largestLinearIndex #-}-  size _ (Letter h) = h+1+  size (LtLetter (Letter h)) = h+1   {-# Inline size #-}-  inBounds (Letter l) (Letter h) (Letter i) = l <= i && i <= h+  inBounds (LtLetter h) i = zeroBound <= i && i <= h   {-# Inline inBounds #-}+  zeroBound = Letter 0+  {-# Inline zeroBound #-}+  zeroBound' = LtLetter zeroBound+  {-# Inline zeroBound' #-}+  totalSize (LtLetter (Letter k)) = [ fromIntegral k + 1 ]+  {-# Inline totalSize #-} -instance IndexStream z => IndexStream (z:.Letter l) where-  streamUp (ls:.Letter l) (hs:.Letter h) = flatten mk step $ streamUp ls hs+deriving instance Eq      (LimitType (Letter l n))+deriving instance Generic (LimitType (Letter l n))+deriving instance (Read (Letter l n)) ⇒ Read    (LimitType (Letter l n))+deriving instance (Show (Letter l n)) ⇒ Show    (LimitType (Letter l n))+deriving instance Typeable (LimitType (Letter l n))+deriving instance Data (Letter l n) ⇒ Data (LimitType (Letter l n))++instance IndexStream z ⇒ IndexStream (z:.Letter l n) where+  streamUp (ls:..LtLetter l) (hs:..LtLetter h) = flatten mk step $ streamUp ls hs     where mk z = return (z,l)           step (z,k)             | k > h     = return $ Done-            | otherwise = return $ Yield (z:.Letter k) (z,k+1)+            | otherwise = return $ Yield (z:.k) (z,Letter $ getLetter k +1)           {-# Inline [0] mk   #-}           {-# Inline [0] step #-}   {-# Inline streamUp #-}-  streamDown (ls:.Letter l) (hs:.Letter h) = flatten mk step $ streamDown ls hs+  streamDown (ls:..LtLetter l) (hs:..LtLetter h) = flatten mk step $ streamDown ls hs     where mk z = return (z,h)           step (z,k)             | k < l     = return $ Done-            | otherwise = return $ Yield (z:.Letter k) (z,k-1)+            | otherwise = return $ Yield (z:.k) (z,Letter $ getLetter k -1)           {-# Inline [0] mk   #-}           {-# Inline [0] step #-}   {-# Inline streamDown #-} --- TODO temporary, because defaults dont inline--instance IndexStream (Letter l) where-  streamUp l h = map (\(Z:.k) -> k) $ streamUp (Z:.l) (Z:.h)+instance IndexStream (Letter l n) where+  streamUp l h = map (\(Z:.k) → k) $ streamUp (ZZ:..l) (ZZ:..h)+  streamDown l h = map (\(Z:.k) → k) $ streamDown (ZZ:..l) (ZZ:..h)   {-# Inline streamUp #-}-  streamDown l h = map (\(Z:.k) -> k) $ streamDown (Z:.l) (Z:.h)   {-# Inline streamDown #-} 

@@ -1,9 +1,9 @@ -{-# Language CPP #-}--#if __GLASGOW_HASKELL__ < 710-{-# LANGUAGE OverlappingInstances #-}-#endif+--  {-# Language CPP #-}+--  +--  #if __GLASGOW_HASKELL__ < 710+--  {-# LANGUAGE OverlappingInstances #-}+--  #endif  -- | Convert between different nucleotide representations @@ -12,7 +12,7 @@ import           Control.Lens (iso, from) import qualified Data.Vector.Unboxed as VU -import           Biobase.Types.Sequence (Transcribe(..))+import           Biobase.Types.BioSequence (Transcribe(..),RNA,DNA)  import           Biobase.Primary.Letter (Letter(..), Primary) import qualified Biobase.Primary.Nuc.DNA as D@@ -90,23 +90,23 @@ -- ** Transcription between RNA and DNA. Both on the individual sequence level, -- and on the level of primary sequence data. -instance Transcribe (Letter R.RNA) where-  type TranscribeTo (Letter R.RNA) = Letter D.DNA+instance Transcribe (Letter RNA n) where+  type TranscribeTo (Letter RNA n) = Letter DNA n   transcribe = iso rnaTdna dnaTrna   {-# Inline transcribe #-} -instance Transcribe (Letter D.DNA) where-  type TranscribeTo (Letter D.DNA) = Letter R.RNA+instance Transcribe (Letter DNA n) where+  type TranscribeTo (Letter DNA n) = Letter RNA n   transcribe = from transcribe   {-# Inline transcribe #-} -instance Transcribe (Primary R.RNA) where-  type TranscribeTo (Primary R.RNA) = Primary D.DNA+instance Transcribe (Primary RNA n) where+  type TranscribeTo (Primary RNA n) = Primary DNA n   transcribe = iso (VU.map rnaTdna) (VU.map dnaTrna)   {-# Inline transcribe #-} -instance Transcribe (Primary D.DNA) where-  type TranscribeTo (Primary D.DNA) = Primary R.RNA+instance Transcribe (Primary DNA n) where+  type TranscribeTo (Primary DNA n) = Primary RNA n   transcribe = iso (VU.map dnaTrna) (VU.map rnaTdna)   {-# Inline transcribe #-} 

@@ -17,24 +17,22 @@ import qualified Data.Vector.Generic.Mutable as VGM import qualified Data.Vector.Unboxed as VU +import           Biobase.Types.BioSequence (DNA)+ import           Biobase.Primary.Bounds import           Biobase.Primary.Letter   --- | DNA nucleotides.--data DNA- -- Single-character names for nucleotides. -pattern A = Letter 0 :: Letter DNA-pattern C = Letter 1 :: Letter DNA-pattern G = Letter 2 :: Letter DNA-pattern T = Letter 3 :: Letter DNA-pattern N = Letter 4 :: Letter DNA+pattern A = Letter 0 :: Letter DNA n+pattern C = Letter 1 :: Letter DNA n+pattern G = Letter 2 :: Letter DNA n+pattern T = Letter 3 :: Letter DNA n+pattern N = Letter 4 :: Letter DNA n -instance Enum (Letter DNA) where+instance Enum (Letter DNA n) where     succ N          = error "succ/N:DNA"     succ (Letter x) = Letter $ x+1     pred A          = error "pred/A:DNA"@@ -43,7 +41,7 @@     toEnum k                = error $ "toEnum/Letter DNA " ++ show k     fromEnum (Letter k) = k -instance LetterChar DNA where+instance LetterChar DNA n where   letterChar = dnaChar   charLetter = charDNA @@ -53,7 +51,7 @@ --instance (MkPrimary (VU.Vector Char) DNA) => FromJSON (Primary DNA) where --  parseJSON = fmap (primary :: String -> Primary DNA) . parseJSON -acgt :: [Letter DNA]+acgt :: [Letter DNA n] acgt = [A .. T]  charDNA = toUpper >>> \case@@ -76,28 +74,28 @@ -- underlying @Char@s actually represent a DNA sequence. This allows typesafe -- modification of DNA sequences since only @[A,C,G,T,N]@ are allowed. -cdna ∷ Iso' Char (Letter DNA)+cdna ∷ Iso' Char (Letter DNA n) cdna = iso charDNA dnaChar -instance Show (Letter DNA) where+instance Show (Letter DNA n) where     show c = [dnaChar c] -instance Read (Letter DNA) where+instance Read (Letter DNA n) where   readsPrec p [] = []   readsPrec p (x:xs)     | x==' ' = readsPrec p xs     | otherwise = [(charDNA x, xs)] -dnaSeq :: MkPrimary n DNA => n -> Primary DNA+dnaSeq :: MkPrimary p DNA n => p -> Primary DNA n dnaSeq = primary -instance Bounded (Letter DNA) where+instance Bounded (Letter DNA n) where     minBound = A     maxBound = N -instance MkPrimary (VU.Vector Char) DNA where+instance MkPrimary (VU.Vector Char) DNA n where     primary = VU.map charDNA -instance IsString [Letter DNA] where+instance IsString [Letter DNA n] where     fromString = map charDNA 

@@ -5,10 +5,12 @@ import           Control.Lens (Iso', iso) import           Data.Aeson import           Data.Char (toUpper)+import           Data.Data import           Data.Ix (Ix(..)) import           Data.Primitive.Types import           Data.String import           Data.Tuple (swap)+import           Data.Typeable import qualified Data.ByteString.Builder as BB import qualified Data.ByteString.Char8 as BS import qualified Data.ByteString.Lazy.Char8 as BSL@@ -18,26 +20,24 @@ import qualified Data.Vector.Generic.Mutable as VGM import qualified Data.Vector.Unboxed as VU +import           Biobase.Types.BioSequence (RNA)+ import           Biobase.Primary.Bounds import           Biobase.Primary.Letter   --- | RNA nucleotides.--data RNA--pattern A = Letter 0 :: Letter RNA-pattern C = Letter 1 :: Letter RNA-pattern G = Letter 2 :: Letter RNA-pattern U = Letter 3 :: Letter RNA-pattern N = Letter 4 :: Letter RNA+pattern A = Letter 0 ∷ Letter RNA n+pattern C = Letter 1 ∷ Letter RNA n+pattern G = Letter 2 ∷ Letter RNA n+pattern U = Letter 3 ∷ Letter RNA n+pattern N = Letter 4 ∷ Letter RNA n -instance Bounded (Letter RNA) where+instance Bounded (Letter RNA n) where     minBound = A     maxBound = N -instance Enum (Letter RNA) where+instance Enum (Letter RNA n) where     succ N          = error "succ/N:RNA"     succ (Letter x) = Letter $ x+1     pred A          = error "pred/A:RNA"@@ -46,14 +46,14 @@     toEnum k                = error $ "toEnum/Letter RNA " ++ show k     fromEnum (Letter k) = k -instance LetterChar RNA where+instance LetterChar RNA n where   letterChar = rnaChar   charLetter = charRNA -instance ToJSON (Letter RNA) where+instance ToJSON (Letter RNA n) where   toJSON = toJSON . letterChar -instance FromJSON (Letter RNA) where+instance FromJSON (Letter RNA n) where   parseJSON = fmap charLetter . parseJSON  -- We encode 'Primary RNA' directly as a string.@@ -64,50 +64,50 @@ --  toJSON = toJSON . VU.toList . VU.map letterChar -- --instance FromJSON (Primary RNA) where---  parseJSON = fmap (primary :: String -> Primary RNA) . parseJSON+--  parseJSON = fmap (primary ∷ String → Primary RNA) . parseJSON  -acgu :: [Letter RNA]+acgu ∷ [Letter RNA n] acgu = [A .. U]  charRNA = toUpper >>> \case-    'A' -> A-    'C' -> C-    'G' -> G-    'U' -> U-    _   -> N+    'A' → A+    'C' → C+    'G' → G+    'U' → U+    _   → N {-# INLINE charRNA #-}  rnaChar = \case-  A -> 'A'-  C -> 'C'-  G -> 'G'-  U -> 'U'-  N -> 'N'+  A → 'A'+  C → 'C'+  G → 'G'+  U → 'U'+  N → 'N' {-# INLINE rnaChar #-}              -- | An isomorphism from 'Char' to 'Letter RNA'. This assumes that the -- underlying @Char@s actually represent an RNA sequence. This allows typesafe -- modification of RNA sequences since only @[A,C,G,U,N]@ are allowed. -crna ∷ Iso' Char (Letter RNA)+crna ∷ Iso' Char (Letter RNA n) crna = iso charRNA rnaChar -instance Show (Letter RNA) where+instance Show (Letter RNA n) where     show c = [rnaChar c] -instance Read (Letter RNA) where+instance Read (Letter RNA n) where   readsPrec p [] = []   readsPrec p (x:xs)     | x==' ' = readsPrec p xs     | otherwise = [(charRNA x, xs)] -rnaSeq :: MkPrimary n RNA => n -> Primary RNA+rnaSeq ∷ MkPrimary p RNA n ⇒ p → Primary RNA n rnaSeq = primary -instance MkPrimary (VU.Vector Char) RNA where+instance MkPrimary (VU.Vector Char) RNA n where     primary = VU.map charRNA -instance IsString [Letter RNA] where+instance IsString [Letter RNA n] where     fromString = map charRNA 

@@ -16,6 +16,8 @@ import qualified Data.Vector.Unboxed as VU import           Control.Category ((>>>)) +import           Biobase.Types.BioSequence+ import           Biobase.Primary.Bounds import           Biobase.Primary.Letter @@ -23,20 +25,18 @@  -- | Combine both, RNA and DNA. -data XNA--pattern A = Letter 0 :: Letter XNA-pattern C = Letter 1 :: Letter XNA-pattern G = Letter 2 :: Letter XNA-pattern T = Letter 3 :: Letter XNA-pattern U = Letter 4 :: Letter XNA-pattern N = Letter 5 :: Letter XNA+pattern A = Letter 0 :: Letter XNA n+pattern C = Letter 1 :: Letter XNA n+pattern G = Letter 2 :: Letter XNA n+pattern T = Letter 3 :: Letter XNA n+pattern U = Letter 4 :: Letter XNA n+pattern N = Letter 5 :: Letter XNA n -instance Bounded (Letter XNA) where+instance Bounded (Letter XNA n) where     minBound = A     maxBound = N -instance Enum (Letter XNA) where+instance Enum (Letter XNA n) where     succ N          = error "succ/N:XNA"     succ (Letter x) = Letter $ x+1     pred A          = error "pred/A:XNA"@@ -45,7 +45,7 @@     toEnum k                = error $ "toEnum/Letter XNA " ++ show k     fromEnum (Letter k) = k -instance LetterChar XNA where+instance LetterChar XNA n where   letterChar = xnaChar   charLetter = charXNA @@ -73,21 +73,21 @@   N -> 'N' {-# INLINE xnaChar #-}             -instance Show (Letter XNA) where+instance Show (Letter XNA n) where     show c = [xnaChar c] -instance Read (Letter XNA) where+instance Read (Letter XNA n) where   readsPrec p [] = []   readsPrec p (x:xs)     | x==' ' = readsPrec p xs     | otherwise = [(charXNA x, xs)] -xnaSeq :: MkPrimary n XNA => n -> Primary XNA+xnaSeq :: MkPrimary p XNA n => p -> Primary XNA n xnaSeq = primary -instance MkPrimary (VU.Vector Char) XNA where+instance MkPrimary (VU.Vector Char) XNA n where     primary = VU.map charXNA -instance IsString [Letter XNA] where+instance IsString [Letter XNA n] where     fromString = map charXNA 

@@ -16,15 +16,15 @@  newtype Pretty f a = Pretty { getPretty :: f a } -instance (LetterChar x) => ToJSON (Pretty VU.Vector (Letter x)) where+instance (LetterChar x n) => ToJSON (Pretty VU.Vector (Letter x n)) where   toJSON = String . T.pack . map letterChar . VU.toList . getPretty -instance (LetterChar x) => ToJSON (Pretty V.Vector (Letter x)) where+instance (LetterChar x n) => ToJSON (Pretty V.Vector (Letter x n)) where   toJSON = String . T.pack . map letterChar . V.toList . getPretty -instance (LetterChar x, VS.Storable (Letter x)) => ToJSON (Pretty VS.Vector (Letter x)) where+instance (LetterChar x n, VS.Storable (Letter x n)) => ToJSON (Pretty VS.Vector (Letter x n)) where   toJSON = String . T.pack . map letterChar . VS.toList . getPretty -instance (LetterChar x) => ToJSON (Pretty [] (Letter x)) where+instance (LetterChar x n) => ToJSON (Pretty [] (Letter x n)) where   toJSON = String . T.pack . map letterChar . getPretty 

@@ -15,6 +15,7 @@  module Biobase.Primary.Trans where +import           Control.Lens import           Control.Arrow ((***)) import           Data.ByteString.Char8 (ByteString,unpack) import           Data.FileEmbed (embedFile)@@ -23,12 +24,55 @@ import qualified Data.Map.Strict as M import qualified Data.Vector.Unboxed as VU +import           Biobase.Types.BioSequence+import           Biobase.Types.Codon+ import           Biobase.Primary.AA import           Biobase.Primary.Nuc import           Biobase.Primary.Letter+import           Biobase.GeneticCodes.Translation+import           Biobase.GeneticCodes.Types   +-- | Transform translation tables into the @Letter DNA/Letter AA@ format.++letterTranslationTable ∷ TranslationTable Char Char → TranslationTable (Letter DNA n) (Letter AA n)+letterTranslationTable tbl = TranslationTable+  { _codonToAminoAcid  = M.fromList . map (ftriplet *** felement) . M.toList $ tbl^.codonToAminoAcid+  , _aminoAcidtoCodons = M.fromList . map (charAA *** map felement) . M.toList $ tbl^.aminoAcidtoCodons+  , _tableID           = tbl^.tableID+  , _tableName         = tbl^.tableName+  } where ftriplet ∷ Codon Char → Codon (Letter DNA n)+          ftriplet = over each charDNA+          felement ∷ TranslationElement Char Char → TranslationElement (Letter DNA n) (Letter AA n)+          felement = over (baseCodon.each) charDNA . over aminoAcid charAA++instance Translation (Codon (Letter DNA n)) where+  type TargetType (Codon (Letter DNA n)) = Letter AA n+  type CodonType (Codon (Letter DNA n)) = Letter DNA n+  type AAType (Codon (Letter DNA n)) = Letter AA n+  translate tbl t = maybe Unknown _aminoAcid $ M.lookup t (tbl^.codonToAminoAcid)+  {-# Inline translate #-}++instance Translation (Primary DNA n) where+  type TargetType (Primary DNA n) = Primary AA n+  type CodonType (Primary DNA n) = Letter DNA n+  type AAType (Primary DNA n) = Letter AA n+  -- |+  --+  -- TODO we could consider returning @Nothing@ in case the input is not+  -- power-of-three.+  translate tbl xs = VU.unfoldrN (VU.length xs `div` 3) go xs+    where go (VU.splitAt 3 → (hs,ts))+            | VU.length hs < 3 = Nothing+            | otherwise        = Just (aa,ts)+            where [a,b,c] = VU.toList hs+                  aa      = translate tbl $ Codon a b c+  {-# Inline translate #-}+++{- -- | Using the codon table, create an amino acid sequence from a @DNA@ -- sequence (encoded as 'Primary DNA'). Suffixed @seq@ as we deal with -- sequences, not letters.@@ -73,4 +117,5 @@  codonListEmbedded :: ByteString codonListEmbedded = $(embedFile "sources/codontable")+-} 

@@ -1,10 +1,13 @@ --- | A 'Letter' with unknown annotation. We sometimes want to encode that--- we are dealing with @Letter@s in an alphabet, but we do not want to--- commit to a certain alphabet (just yet).+-- | A 'Letter' with unknown annotation. We sometimes want to encode that we+-- are dealing with @Letter@s in an alphabet, but we do not want to commit to a+-- certain alphabet (just yet). -- -- This module allows us to make explicit that we do not know the specific -- alphabet type yet.+--+-- One should NEVER blindly coerce, since the order and limits of @Letter@'s+-- might well be different.  module Biobase.Primary.Unknown where @@ -44,44 +47,36 @@  -- | Creating an unknown letter. -unk :: Int -> Letter Unknown+unk ∷ Int → Letter Unknown n unk = Letter    -- *** instances -instance Show (Letter Unknown) where+instance Show (Letter Unknown n) where   show (Letter i) = "U " ++ show i -instance Read (Letter Unknown) where+instance Read (Letter Unknown n) where   readPrec = parens $ do     Lex.Ident u <- lexP     case u of-      "U" -> unk <$> readPrec-      _   -> RP.pfail+      "U" → unk <$> readPrec+      _   → RP.pfail -instance Enum (Letter Unknown) where+instance Enum (Letter Unknown n) where     succ (Letter x) = Letter $ x+1     pred (Letter x) = Letter $ x-1     toEnum = Letter     fromEnum = getLetter -instance MkPrimary (VU.Vector Int) Unknown where+instance MkPrimary (VU.Vector Int) Unknown n where   primary = VU.map Letter   {-# Inline primary #-} -instance ToJSON (Letter Unknown) where+instance ToJSON (Letter Unknown n) where   toJSON = toJSON . getLetter -instance FromJSON (Letter Unknown) where+instance FromJSON (Letter Unknown n) where   parseJSON = fmap Letter . parseJSON--{--instance ToJSON (Primary Unknown) where-  toJSON = toJSON . map (show . getLetter) . VU.toList--instance FromJSON (Primary Unknown) where-  parseJSON = fmap (VU.fromList . map (Letter . read)) . parseJSON--} 

@@ -1,8 +1,8 @@  module Biobase.Secondary --  ( module Biobase.Secondary.Basepair-  ( module Biobase.Secondary.Constraint-  , module Biobase.Secondary.Diagrams+--  ( module Biobase.Secondary.Constraint+  ( module Biobase.Secondary.Diagrams   , module Biobase.Secondary.Isostericity   , module Biobase.Secondary.Pseudoknots   , module Biobase.Secondary.Structure@@ -10,7 +10,7 @@   ) where  --import Biobase.Secondary.Basepair-import Biobase.Secondary.Constraint+--import Biobase.Secondary.Constraint import Biobase.Secondary.Diagrams import Biobase.Secondary.Isostericity import Biobase.Secondary.Pseudoknots

@@ -19,7 +19,7 @@ import           Data.Primitive.Types import           Data.Serialize (Serialize) import           Data.Tuple (swap)-import           Data.Vector.Fusion.Stream.Monadic (map,Step(..))+import           Data.Vector.Fusion.Stream.Monadic (map,Step(..),flatten) import           Data.Vector.Unboxed.Deriving import           GHC.Base (remInt,quotInt) import           GHC.Generics@@ -28,6 +28,7 @@ import qualified Data.Vector.Unboxed as VU import           Text.Read +import           Biobase.Types.BioSequence import           Data.PrimitiveArray hiding (Complement(..),map)  import           Biobase.Primary@@ -51,10 +52,11 @@ instance FromJSON  Basepair instance ToJSON    Basepair -deriving instance Index Basepair+instance Index Basepair where+  newtype LimitType Basepair = LtBP Basepair  instance IndexStream z => IndexStream (z:.Basepair) where-  streamUp (ls:.BP l) (hs:.BP h) = flatten mk step $ streamUp ls hs+  streamUp (ls:..LtBP (BP l)) (hs:..LtBP (BP h)) = flatten mk step $ streamUp ls hs     where mk z = return (z,l)           step (z,k)             | k > h     = return $ Done@@ -62,7 +64,7 @@           {-# Inline [0] mk   #-}           {-# Inline [0] step #-}   {-# Inline streamUp #-}-  streamDown (ls:.BP l) (hs:.BP h) = flatten mk step $ streamDown ls hs+  streamDown (ls:..LtBP (BP l)) (hs:..LtBP (BP h)) = flatten mk step $ streamDown ls hs     where mk z = return (z,h)           step (z,k)             | k < l     = return $ Done@@ -218,7 +220,7 @@  -- | A pair as a tuple containing 'Nuc's. -type Pair = (Letter RNA,Letter RNA)+type Pair n = (Letter RNA n, Letter RNA n)  -- | Annotation for a basepair. @@ -230,7 +232,7 @@  -- | An extended basepair, with nucleotides an annotation. -type ExtPair = (Pair,ExtPairAnnotation)+type ExtPair n = (Pair n, ExtPairAnnotation)   

@@ -1,107 +0,0 @@---- | Simple oldstyle RNAfold constraints. A constraint yields a bonus or--- malus to energy.--module Biobase.Secondary.Constraint where--import           Data.Char (toLower)-import           Data.Primitive.Types-import           Prelude as P-import qualified Data.Vector.Generic as VG-import qualified Data.Vector.Generic.Mutable as VGM-import qualified Data.Vector.Unboxed as VU--import           Data.PrimitiveArray--import           Biobase.Secondary.Diagrams------ | We can create a constraint from different sources.--class MkConstraint a where-  mkConstraint :: a -> Constraint---- | A constraint is nothing more than a vector of constraint characters--- together with a possible pairing for each character.--newtype Constraint = Constraint {unConstraint :: VU.Vector (Char,Int)}-  deriving (Show,Read,Eq)--bonusCC :: VU.Vector Char-bonusCC = VU.fromList "()<>|"-{-# NOINLINE bonusCC #-}--nobonusCC :: VU.Vector Char-nobonusCC = VU.fromList ".x"-{-# NOINLINE nobonusCC #-}---- | Given a 'Constraint', create an NxN matrix with bonus energies. These--- energies can be included in all pair-creating functions and will disallow or--- strongly favor certain pairings, while others will receive neither bonus nor--- malus.------ In case, a pair (i,j) is annotated as both, bonus- and malus-receiving, it--- will be set to receive a malus. This can happen, if something like "<" would--- give a bonus, but "x" gives a malus (and other cases).------ TODO and again, we should parametrize over "Energy", "Score", etc (that is,--- Prim a)--bonusTable :: Double -> Double -> Constraint -> Unboxed (Z:.Int:.Int) Double-bonusTable bonus malus (Constraint constraint) = arr where-  arr = fromAssocs (Z:.0:.0) (Z:.n:.n) 0 $ bonusBr ++ bonusAn ++ bonusBa ++ malusBr ++ malusAn ++ malusX-  n = VU.length constraint -1-  infixl 1 `xor`-  xor a b = a && not b || not a && b-  -- "()" bonus energies-  bonusBr = [ (Z:.i:.j,bonus)-            | (i,('(',j)) <- zip [0..] $ VU.toList constraint-            ]-  malusBr = [ (Z:.i:.j,malus)-            | i <- [0..n]-            , j <- [i..n]-            , let bi = constraint VU.! i-            , let bj = constraint VU.! j-            , fst bi == '(' && snd bi /= j || fst bj == ')' && snd bj /= i-            ]-  bonusAn = [ (Z:.i:.j,bonus)-            | i<-[0..n]-            , fst (constraint VU.! i) == '<'-            , j<-[i+1..n]-            ] ++-            [ (Z:.i:.j,bonus)-            | j<-[0..n]-            , fst (constraint VU.! j) == '>'-            , i<-[0..j-1]-            ]-  malusAn = [ (Z:.i:.j,malus)-            | i<-[0..n]-            , j<-[i+1..n]-            , fst (constraint VU.! j) == '<'-            ] ++-            [ (Z:.i:.j,malus)-            | i<-[0..n]-            , j<-[i+1..n]-            , fst (constraint VU.! i) == '>'-            ]-  bonusBa = [ (Z:.i:.j,bonus)-            | i<-[0..n]-            , j<-[i+1..n]-            , fst (constraint VU.! i) == '|' || fst (constraint VU.! j) == '|'-            ]-  malusX  = [ (Z:.i:.j,malus)-            | i<-[0..n]-            , j<-[i+1..n]-            , fst (constraint VU.! i) == 'x' || fst (constraint VU.! j) == 'x'-            ]---- * Instances--instance MkConstraint String where-  mkConstraint xs = mkConstraint . VU.fromList . P.map toLower $ xs--instance MkConstraint (VU.Vector Char) where-  mkConstraint cs = Constraint $ VU.zip cs ks where-    (D1S ks) = mkD1S cs-

@@ -4,6 +4,8 @@  module Biobase.Secondary.Convert where +import           Biobase.Types.BioSequence+ import           Biobase.Primary.Letter import           Biobase.Primary.Nuc.RNA import           Biobase.Secondary.Basepair@@ -24,14 +26,14 @@  -- ** @(RNA,RNA) <-> Basepair@ -instance BasepairConvert (Letter RNA,Letter RNA) Basepair where+instance BasepairConvert (Letter RNA n,Letter RNA n) Basepair where   basepairConvert (l,r)     | l >= A && l <= U && r >= A && r <= U     = BP $ 4 * getLetter l + getLetter r     | otherwise = NoBP   {-# Inline basepairConvert #-} -instance BasepairConvert Basepair (Letter RNA, Letter RNA) where+instance BasepairConvert Basepair (Letter RNA n, Letter RNA n) where   basepairConvert k     | k == NoBP || k == NS = (N,N)     | otherwise = let (l,r) = getBP k `divMod` 4 in (Letter l, Letter r)@@ -41,7 +43,7 @@  -- ** @(RNA,RNA) <-> ViennaPair@ -instance BasepairConvert (Letter RNA, Letter RNA) ViennaPair where+instance BasepairConvert (Letter RNA n, Letter RNA n) ViennaPair where   basepairConvert = \case     (C,G) -> SV.CG     (G,C) -> SV.GC@@ -52,7 +54,7 @@     _     -> SV.NS   {-# Inline basepairConvert #-} -instance BasepairConvert ViennaPair (Letter RNA, Letter RNA) where+instance BasepairConvert ViennaPair (Letter RNA n, Letter RNA n) where   basepairConvert = \case     SV.CG -> (C,G)     SV.GC -> (G,C)

@@ -43,7 +43,7 @@ -- -- TODO inClass missing -instance IsostericityLookup ExtPair where+instance IsostericityLookup (ExtPair n) where   getClasses p     | Just cs <- M.lookup p defaultIsostericityMap     = cs@@ -54,7 +54,7 @@ -- -- TODO inClass missing -instance IsostericityLookup Pair where+instance IsostericityLookup (Pair n) where   getClasses p     | Just cs <- M.lookup (p,CWW) defaultIsostericityMap     = cs@@ -77,7 +77,7 @@  -- | Process CSV list-of-lists to get the isostericity data. -mkIsostericityList :: [[[String]]] -> [(ExtPair, [String])]+mkIsostericityList :: [[[String]]] -> [(ExtPair n, [String])] mkIsostericityList gs = nubBy ((==) `on` fst) . concatMap turn . concatMap f $ gs where   f g = map (\e ->  ( ( let [x,y] = fst e                         in (charRNA x, charRNA y), read bpt

@@ -9,7 +9,7 @@ import           Data.Primitive.Types import           Data.Serialize (Serialize(..)) import           Data.Tuple (swap)-import           Data.Vector.Fusion.Stream.Monadic (map,Step(..))+import           Data.Vector.Fusion.Stream.Monadic (map,Step(..),flatten) import           Data.Vector.Unboxed.Deriving import           GHC.Base (remInt,quotInt) import           GHC.Generics (Generic)@@ -20,6 +20,7 @@ import qualified Prelude as P  import           Data.PrimitiveArray hiding (Complement(..),map)+import           Biobase.Types.BioSequence  import           Biobase.Primary.Letter import           Biobase.Primary.Nuc@@ -38,40 +39,34 @@ instance ToJSON    (ViennaPair)  instance Index ViennaPair where-  linearIndex _ _ (ViennaPair p) = p+  data LimitType ViennaPair+    = Canonical | Extended+  linearIndex _ (ViennaPair p) = p   {-# Inline linearIndex #-}-  smallestLinearIndex _ = error "still needed?"-  {-# Inline smallestLinearIndex #-}-  largestLinearIndex (ViennaPair p) = p-  {-# Inline largestLinearIndex #-}-  size _ (ViennaPair h) = h+1+  size h = case h of { Canonical → 7; Extended → 9 }   {-# Inline size #-}-  inBounds (ViennaPair l) (ViennaPair h) (ViennaPair p) = l <= p && p <= h+  inBounds h (ViennaPair p) = 0 <= p && p < size h   {-# Inline inBounds #-}  instance IndexStream z => IndexStream (z:.ViennaPair) where-  streamUp (ls:.ViennaPair l) (hs:.ViennaPair h) = flatten mk step $ streamUp ls hs-    where mk z = return (z,l)+  streamUp (ls:..l) (hs:..h) = flatten mk step $ streamUp ls hs+    where mk z = return (z,size l - 1)           step (z,k)-            | k > h     = return $ Done-            | otherwise = return $ Yield (z:.ViennaPair k) (z,k+1)+            | k > size h -1 = return $ Done+            | otherwise     = return $ Yield (z:.ViennaPair k) (z,k+1)           {-# Inline [0] mk   #-}           {-# Inline [0] step #-}   {-# Inline streamUp #-}-  streamDown (ls:.ViennaPair l) (hs:.ViennaPair h) = flatten mk step $ streamDown ls hs-    where mk z = return (z,h)+  streamDown (ls:..l) (hs:..h) = flatten mk step $ streamDown ls hs+    where mk z = return (z,size h - 1)           step (z,k)-            | k < l     = return $ Done-            | otherwise = return $ Yield (z:.ViennaPair k) (z,k-1)+            | k < size l -1 = return $ Done+            | otherwise     = return $ Yield (z:.ViennaPair k) (z,k-1)           {-# Inline [0] mk   #-}           {-# Inline [0] step #-}   {-# Inline streamDown #-}  instance IndexStream ViennaPair where-  streamUp l h = map (\(Z:.k) -> k) $ streamUp (Z:.l) (Z:.h)-  {-# Inline streamUp #-}-  streamDown l h = map (\(Z:.k) -> k) $ streamDown (Z:.l) (Z:.h)-  {-# Inline streamDown #-}   @@ -112,7 +107,7 @@   {-# INLINE fromViennaPair #-} -} -isViennaPair :: Letter RNA -> Letter RNA -> Bool+isViennaPair :: Letter RNA m -> Letter RNA n -> Bool isViennaPair l r =  l==C && r==G                  || l==G && r==C                  || l==A && r==U@@ -121,8 +116,8 @@                  || l==U && r==G {-# INLINE isViennaPair #-} -viennaPairTable :: Unboxed (Z:.Letter RNA:.Letter RNA) ViennaPair-viennaPairTable = fromAssocs (Z:.N:.N) (Z:.U:.U) NS+viennaPairTable :: Unboxed (Z:.Letter RNA n:.Letter RNA n) ViennaPair+viennaPairTable = fromAssocs (ZZ:..LtLetter maxBound:..LtLetter maxBound) NS   [ (Z:.C:.G , CG)   , (Z:.G:.C , GC)   , (Z:.G:.U , GU)

@@ -1,18 +1,18 @@+cabal-version:  2.2 name:           BiobaseXNA-version:        0.10.0.0+version:        0.11.0.0 author:         Christian Hoener zu Siederdissen maintainer:     choener@bioinf.uni-leipzig.de homepage:       https://github.com/choener/BiobaseXNA bug-reports:    https://github.com/choener/BiobaseXNA/issues-copyright:      Christian Hoener zu Siederdissen, 2011 - 2017+copyright:      Christian Hoener zu Siederdissen, 2011 - 2019 category:       Bioinformatics synopsis:       Efficient RNA/DNA/Protein Primary/Secondary Structure-license:        GPL-3+license:        BSD-3-Clause license-file:   LICENSE build-type:     Simple stability:      experimental-tested-with:    GHC == 7.10.3, GHC == 8.0.1-cabal-version:  >= 1.10.0+tested-with:    GHC == 8.4.4 description:                 This is a base library for bioinformatics with emphasis on RNA                 and DNA primary structure as well as amino acid sequences.@@ -45,8 +45,7 @@   sources/iupac-nucleotides  --library+common deps   build-depends: base                     >= 4.7      &&  < 5.0                , aeson                    >= 1.0                , attoparsec               >= 0.13@@ -57,6 +56,7 @@                , cereal-vector            >= 0.2                , containers               >= 0.5                , csv                      >= 0.1+               , data-default             >= 0.7                , deepseq                  >= 1.3                , file-embed               >= 0.0.8                , hashable                 >= 1.2@@ -67,55 +67,36 @@                , split                    >= 0.2                , text                     >= 1.0                , tuple                    >= 0.3-               , vector                   >= 0.10+               , vector                   >= 0.11                , vector-binary-instances  >= 0.2                , vector-th-unbox          >= 0.2                --                , bimaps                   == 0.1.0.*-               , BiobaseTypes             == 0.1.3.*-               , ForestStructures         == 0.0.0.*-               , PrimitiveArray           == 0.8.0.*-  exposed-modules:-    Biobase.Primary-    Biobase.Primary.AA-    Biobase.Primary.Bounds-    Biobase.Primary.Hashed-    Biobase.Primary.IUPAC-    Biobase.Primary.Letter-    Biobase.Primary.Nuc-    Biobase.Primary.Nuc.Conversion-    Biobase.Primary.Nuc.DNA-    Biobase.Primary.Nuc.RNA-    Biobase.Primary.Nuc.XNA-    Biobase.Primary.Pretty-    Biobase.Primary.Trans-    Biobase.Primary.Unknown-    Biobase.Secondary-    Biobase.Secondary.New-    Biobase.Secondary.Basepair-    Biobase.Secondary.Constraint-    Biobase.Secondary.Convert-    Biobase.Secondary.Diagrams-    Biobase.Secondary.Isostericity-    Biobase.Secondary.Pseudoknots-    Biobase.Secondary.Structure-    Biobase.Secondary.Vienna+               , BiobaseENA               == 0.0.0.*+               , BiobaseTypes             == 0.2.0.*+               , ForestStructures         == 0.0.1.*+               , PrimitiveArray           == 0.9.1.*   default-extensions: BangPatterns+                    , DataKinds+                    , DeriveDataTypeable+                    , DeriveFunctor                     , DeriveGeneric+                    , DeriveGeneric+                    , DeriveTraversable                     , EmptyDataDecls                     , FlexibleContexts                     , FlexibleInstances                     , GeneralizedNewtypeDeriving                     , LambdaCase-                    , PolyKinds-                    , DeriveFunctor-                    , DeriveTraversable-                    , DeriveGeneric                     , MultiParamTypeClasses                     , PatternSynonyms+                    , PolyKinds+                    , RankNTypes+                    , RecordWildCards                     , ScopedTypeVariables                     , StandaloneDeriving                     , TemplateHaskell+                    , TypeApplications                     , TypeFamilies                     , TypeOperators                     , UndecidableInstances@@ -127,8 +108,42 @@     -O2 -funbox-strict-fields  +library+  import:+    deps+  exposed-modules:+    -- new+    Biobase.Primary.AA+    Biobase.Primary.Letter+    Biobase.Primary.Nuc.RNA+    Biobase.Primary.Unknown+    -- old+    Biobase.Primary+    Biobase.Primary.Bounds+    Biobase.Primary.Hashed+    Biobase.Primary.IUPAC+    Biobase.Primary.Nuc+    Biobase.Primary.Nuc.Conversion+    Biobase.Primary.Nuc.DNA+    Biobase.Primary.Nuc.XNA+    Biobase.Primary.Pretty+    Biobase.Primary.Trans+    Biobase.Secondary+    Biobase.Secondary.New+    Biobase.Secondary.Basepair+--    Biobase.Secondary.Constraint+    Biobase.Secondary.Convert+    Biobase.Secondary.Diagrams+    Biobase.Secondary.Isostericity+    Biobase.Secondary.Pseudoknots+    Biobase.Secondary.Structure+    Biobase.Secondary.Vienna ++ executable SubOptDistance+  import:+    deps   build-depends: base                , BiobaseXNA                , cmdargs      >= 0.10@@ -136,18 +151,12 @@     SubOptDistance.hs   hs-source-dirs:     src-  default-language:-    Haskell2010-  default-extensions: DeriveDataTypeable-                    , NoMonomorphismRestriction-                    , RecordWildCards-                    , ScopedTypeVariables-  ghc-options:-    -O2    test-suite properties+  import:+    deps   type:     exitcode-stdio-1.0   main-is:@@ -165,7 +174,6 @@                , tasty              >= 0.11                , tasty-quickcheck   >= 0.8                , tasty-th           >= 0.1-               , vector                --                , BiobaseXNA 

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If not, see <http://www.gnu.org/licenses/>.--Also add information on how to contact you by electronic and paper mail.+Copyright Christian Hoener zu Siederdissen 2011-2019 -  If the program does terminal interaction, make it output a short-notice like this when it starts in an interactive mode:+All rights reserved. -    <program>  Copyright (C) <year>  <name of author>-    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.  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@@ -1,3 +1,6 @@+0.11.0.0+--------+ 0.10.0.0 --------