Safe Haskell	None
Language	Haskell2010

Biobase.Secondary.Basepair

Contents

Newtype for efficient basepair encoding.
Newtypes for extended secondary structures
- Encode which of three edges is engaged in base pairing
- Is the base pair in cis or trans configuration
Types
little helpers

Description

Secondary structure: define basepairs as Int-tuples, the three edges, a nucleotide can use for pairing and the cis/trans isomerism. Both edges and cis/trans come with a tag for "unknown".

Since we often want to make "pairedness" explicit, we have a newtype for this as well.

TODO set ext-annotations to be (isomerism,edge,edge) and have a asString instance to read "cWW" "tSH" and other notation.

Synopsis

newtype Basepair = BP {
- getBP :: Int
}
pattern AA :: Basepair
pattern AC :: Basepair
pattern AG :: Basepair
pattern AU :: Basepair
pattern CA :: Basepair
pattern CC :: Basepair
pattern CG :: Basepair
pattern CU :: Basepair
pattern GA :: Basepair
pattern GC :: Basepair
pattern GG :: Basepair
pattern GU :: Basepair
pattern UA :: Basepair
pattern UC :: Basepair
pattern UG :: Basepair
pattern UU :: Basepair
pattern NS :: Basepair
pattern NoBP :: Basepair
newtype Edge = Edge {
- unEdge :: Int
}
pattern W :: Edge
pattern S :: Edge
pattern H :: Edge
newtype CTisomerism = CT {
- unCT :: Int
}
pattern Cis :: CTisomerism
pattern Trn :: CTisomerism
type PairIdx = (Int, Int)
type Pair n = (Letter RNA n, Letter RNA n)
type ExtPairAnnotation = (CTisomerism, Edge, Edge)
type ExtPairIdx = (PairIdx, ExtPairAnnotation)
type ExtPair n = (Pair n, ExtPairAnnotation)
pattern CHH :: (CTisomerism, Edge, Edge)
pattern CHS :: (CTisomerism, Edge, Edge)
pattern CHW :: (CTisomerism, Edge, Edge)
pattern CSH :: (CTisomerism, Edge, Edge)
pattern CSS :: (CTisomerism, Edge, Edge)
pattern CSW :: (CTisomerism, Edge, Edge)
pattern CWH :: (CTisomerism, Edge, Edge)
pattern CWS :: (CTisomerism, Edge, Edge)
pattern CWW :: (CTisomerism, Edge, Edge)
pattern THH :: (CTisomerism, Edge, Edge)
pattern THS :: (CTisomerism, Edge, Edge)
pattern THW :: (CTisomerism, Edge, Edge)
pattern TSH :: (CTisomerism, Edge, Edge)
pattern TSS :: (CTisomerism, Edge, Edge)
pattern TSW :: (CTisomerism, Edge, Edge)
pattern TWH :: (CTisomerism, Edge, Edge)
pattern TWS :: (CTisomerism, Edge, Edge)
pattern TWW :: (CTisomerism, Edge, Edge)

Newtype for efficient basepair encoding.

newtype Basepair Source #

Encode a base pair as a single Int.

Constructors

BP
Fields getBP :: Int

Instances

Eq Basepair Source #
Instance details Defined in Biobase.Secondary.Basepair Methods (==) :: Basepair -> Basepair -> Bool # (/=) :: Basepair -> Basepair -> Bool #
Ord Basepair Source #
Instance details Defined in Biobase.Secondary.Basepair Methods compare :: Basepair -> Basepair -> Ordering # (<) :: Basepair -> Basepair -> Bool # (<=) :: Basepair -> Basepair -> Bool # (>) :: Basepair -> Basepair -> Bool # (>=) :: Basepair -> Basepair -> Bool # max :: Basepair -> Basepair -> Basepair # min :: Basepair -> Basepair -> Basepair #
Ix Basepair Source #
Instance details Defined in Biobase.Secondary.Basepair Methods range :: (Basepair, Basepair) -> [Basepair] # index :: (Basepair, Basepair) -> Basepair -> Int # unsafeIndex :: (Basepair, Basepair) -> Basepair -> Int inRange :: (Basepair, Basepair) -> Basepair -> Bool # rangeSize :: (Basepair, Basepair) -> Int # unsafeRangeSize :: (Basepair, Basepair) -> Int
Generic Basepair Source #
Instance details Defined in Biobase.Secondary.Basepair Associated Types type Rep Basepair :: Type -> Type # Methods from :: Basepair -> Rep Basepair x # to :: Rep Basepair x -> Basepair #
Index Basepair Source #
Instance details Defined in Biobase.Secondary.Basepair Associated Types data LimitType Basepair :: Type # Methods linearIndex :: LimitType Basepair -> Basepair -> Int # size :: LimitType Basepair -> Int # inBounds :: LimitType Basepair -> Basepair -> Bool # zeroBound :: Basepair # zeroBound' :: LimitType Basepair # totalSize :: LimitType Basepair -> [Integer] #
IndexStream Basepair Source #
Instance details Defined in Biobase.Secondary.Basepair Methods streamUp :: Monad m => LimitType Basepair -> LimitType Basepair -> Stream m Basepair # streamDown :: Monad m => LimitType Basepair -> LimitType Basepair -> Stream m Basepair #
ToJSON Basepair Source #
Instance details Defined in Biobase.Secondary.Basepair Methods toJSON :: Basepair -> Value # toEncoding :: Basepair -> Encoding # toJSONList :: [Basepair] -> Value # toEncodingList :: [Basepair] -> Encoding #
FromJSON Basepair Source #
Instance details Defined in Biobase.Secondary.Basepair Methods parseJSON :: Value -> Parser Basepair # parseJSONList :: Value -> Parser [Basepair] #
Binary Basepair Source #
Instance details Defined in Biobase.Secondary.Basepair Methods put :: Basepair -> Put # get :: Get Basepair # putList :: [Basepair] -> Put #
Serialize Basepair Source #
Instance details Defined in Biobase.Secondary.Basepair Methods put :: Putter Basepair # get :: Get Basepair #
Unbox Basepair Source #
Instance details Defined in Biobase.Secondary.Basepair
Vector Vector Basepair Source #
Instance details Defined in Biobase.Secondary.Basepair Methods basicUnsafeFreeze :: PrimMonad m => Mutable Vector (PrimState m) Basepair -> m (Vector Basepair) # basicUnsafeThaw :: PrimMonad m => Vector Basepair -> m (Mutable Vector (PrimState m) Basepair) # basicLength :: Vector Basepair -> Int # basicUnsafeSlice :: Int -> Int -> Vector Basepair -> Vector Basepair # basicUnsafeIndexM :: Monad m => Vector Basepair -> Int -> m Basepair # basicUnsafeCopy :: PrimMonad m => Mutable Vector (PrimState m) Basepair -> Vector Basepair -> m () # elemseq :: Vector Basepair -> Basepair -> b -> b #
MVector MVector Basepair Source #
Instance details Defined in Biobase.Secondary.Basepair Methods basicLength :: MVector s Basepair -> Int # basicUnsafeSlice :: Int -> Int -> MVector s Basepair -> MVector s Basepair # basicOverlaps :: MVector s Basepair -> MVector s Basepair -> Bool # basicUnsafeNew :: PrimMonad m => Int -> m (MVector (PrimState m) Basepair) # basicInitialize :: PrimMonad m => MVector (PrimState m) Basepair -> m () # basicUnsafeReplicate :: PrimMonad m => Int -> Basepair -> m (MVector (PrimState m) Basepair) # basicUnsafeRead :: PrimMonad m => MVector (PrimState m) Basepair -> Int -> m Basepair # basicUnsafeWrite :: PrimMonad m => MVector (PrimState m) Basepair -> Int -> Basepair -> m () # basicClear :: PrimMonad m => MVector (PrimState m) Basepair -> m () # basicSet :: PrimMonad m => MVector (PrimState m) Basepair -> Basepair -> m () # basicUnsafeCopy :: PrimMonad m => MVector (PrimState m) Basepair -> MVector (PrimState m) Basepair -> m () # basicUnsafeMove :: PrimMonad m => MVector (PrimState m) Basepair -> MVector (PrimState m) Basepair -> m () # basicUnsafeGrow :: PrimMonad m => MVector (PrimState m) Basepair -> Int -> m (MVector (PrimState m) Basepair) #
BasepairConvert Basepair ViennaPair Source #
Instance details Defined in Biobase.Secondary.Convert Methods basepairConvert :: Basepair -> ViennaPair Source #
BasepairConvert ViennaPair Basepair Source #
Instance details Defined in Biobase.Secondary.Convert Methods basepairConvert :: ViennaPair -> Basepair Source #
BasepairConvert Basepair (Letter RNA n, Letter RNA n) Source #
Instance details Defined in Biobase.Secondary.Convert Methods basepairConvert :: Basepair -> (Letter RNA n, Letter RNA n) Source #
IndexStream z => IndexStream (z :. Basepair) Source #
Instance details Defined in Biobase.Secondary.Basepair Methods streamUp :: Monad m => LimitType (z :. Basepair) -> LimitType (z :. Basepair) -> Stream m (z :. Basepair) # streamDown :: Monad m => LimitType (z :. Basepair) -> LimitType (z :. Basepair) -> Stream m (z :. Basepair) #
BasepairConvert (Letter RNA n, Letter RNA n) Basepair Source #
Instance details Defined in Biobase.Secondary.Convert Methods basepairConvert :: (Letter RNA n, Letter RNA n) -> Basepair Source #
type Rep Basepair Source #
Instance details Defined in Biobase.Secondary.Basepair type Rep Basepair = D1 (MetaData "Basepair" "Biobase.Secondary.Basepair" "BiobaseXNA-0.11.0.0-6sSV7wA2ZNJ62zYFxZDZpd" True) (C1 (MetaCons "BP" PrefixI True) (S1 (MetaSel (Just "getBP") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int)))
newtype LimitType Basepair Source #
Instance details Defined in Biobase.Secondary.Basepair newtype LimitType Basepair = LtBP Basepair
newtype Vector Basepair Source #
Instance details Defined in Biobase.Secondary.Basepair newtype Vector Basepair = V_Basepair (Vector Int)
newtype MVector s Basepair Source #
Instance details Defined in Biobase.Secondary.Basepair newtype MVector s Basepair = MV_Basepair (MVector s Int)

pattern AA :: Basepair Source #

pattern AC :: Basepair Source #

pattern AG :: Basepair Source #

pattern AU :: Basepair Source #

pattern CA :: Basepair Source #

pattern CC :: Basepair Source #

pattern CG :: Basepair Source #

pattern CU :: Basepair Source #

pattern GA :: Basepair Source #

pattern GC :: Basepair Source #

pattern GG :: Basepair Source #

pattern GU :: Basepair Source #

pattern UA :: Basepair Source #

pattern UC :: Basepair Source #

pattern UG :: Basepair Source #

pattern UU :: Basepair Source #

pattern NS :: Basepair Source #

pattern NoBP :: Basepair Source #

Newtypes for extended secondary structures

Encode which of three edges is engaged in base pairing

newtype Edge Source #

Each nucleotide in a pair may be paired using one of three edges: watson-crick, sugar, or hoogsteen.

Constructors

Edge
Fields unEdge :: Int

Instances

Bounded Edge Source #
Instance details Defined in Biobase.Secondary.Basepair Methods minBound :: Edge # maxBound :: Edge #
Enum Edge Source #
Instance details Defined in Biobase.Secondary.Basepair Methods succ :: Edge -> Edge # pred :: Edge -> Edge # toEnum :: Int -> Edge # fromEnum :: Edge -> Int # enumFrom :: Edge -> [Edge] # enumFromThen :: Edge -> Edge -> [Edge] # enumFromTo :: Edge -> Edge -> [Edge] # enumFromThenTo :: Edge -> Edge -> Edge -> [Edge] #
Eq Edge Source #
Instance details Defined in Biobase.Secondary.Basepair Methods (==) :: Edge -> Edge -> Bool # (/=) :: Edge -> Edge -> Bool #
Ord Edge Source #
Instance details Defined in Biobase.Secondary.Basepair Methods compare :: Edge -> Edge -> Ordering # (<) :: Edge -> Edge -> Bool # (<=) :: Edge -> Edge -> Bool # (>) :: Edge -> Edge -> Bool # (>=) :: Edge -> Edge -> Bool # max :: Edge -> Edge -> Edge # min :: Edge -> Edge -> Edge #
Read Edge Source #	Human-readable Read instance.
Instance details Defined in Biobase.Secondary.Basepair Methods readsPrec :: Int -> ReadS Edge # readList :: ReadS [Edge] # readPrec :: ReadPrec Edge # readListPrec :: ReadPrec [Edge] #
Show Edge Source #	Human-readable Show instance.
Instance details Defined in Biobase.Secondary.Basepair Methods showsPrec :: Int -> Edge -> ShowS # show :: Edge -> String # showList :: [Edge] -> ShowS #
Ix Edge Source #
Instance details Defined in Biobase.Secondary.Basepair Methods range :: (Edge, Edge) -> [Edge] # index :: (Edge, Edge) -> Edge -> Int # unsafeIndex :: (Edge, Edge) -> Edge -> Int inRange :: (Edge, Edge) -> Edge -> Bool # rangeSize :: (Edge, Edge) -> Int # unsafeRangeSize :: (Edge, Edge) -> Int
Generic Edge Source #
Instance details Defined in Biobase.Secondary.Basepair Associated Types type Rep Edge :: Type -> Type # Methods from :: Edge -> Rep Edge x # to :: Rep Edge x -> Edge #
ToJSON Edge Source #
Instance details Defined in Biobase.Secondary.Basepair Methods toJSON :: Edge -> Value # toEncoding :: Edge -> Encoding # toJSONList :: [Edge] -> Value # toEncodingList :: [Edge] -> Encoding #
FromJSON Edge Source #
Instance details Defined in Biobase.Secondary.Basepair Methods parseJSON :: Value -> Parser Edge # parseJSONList :: Value -> Parser [Edge] #
Binary Edge Source #
Instance details Defined in Biobase.Secondary.Basepair Methods put :: Edge -> Put # get :: Get Edge # putList :: [Edge] -> Put #
Serialize Edge Source #
Instance details Defined in Biobase.Secondary.Basepair Methods put :: Putter Edge # get :: Get Edge #
Unbox Edge Source #
Instance details Defined in Biobase.Secondary.Basepair
Vector Vector Edge Source #
Instance details Defined in Biobase.Secondary.Basepair Methods basicUnsafeFreeze :: PrimMonad m => Mutable Vector (PrimState m) Edge -> m (Vector Edge) # basicUnsafeThaw :: PrimMonad m => Vector Edge -> m (Mutable Vector (PrimState m) Edge) # basicLength :: Vector Edge -> Int # basicUnsafeSlice :: Int -> Int -> Vector Edge -> Vector Edge # basicUnsafeIndexM :: Monad m => Vector Edge -> Int -> m Edge # basicUnsafeCopy :: PrimMonad m => Mutable Vector (PrimState m) Edge -> Vector Edge -> m () # elemseq :: Vector Edge -> Edge -> b -> b #
MVector MVector Edge Source #
Instance details Defined in Biobase.Secondary.Basepair Methods basicLength :: MVector s Edge -> Int # basicUnsafeSlice :: Int -> Int -> MVector s Edge -> MVector s Edge # basicOverlaps :: MVector s Edge -> MVector s Edge -> Bool # basicUnsafeNew :: PrimMonad m => Int -> m (MVector (PrimState m) Edge) # basicInitialize :: PrimMonad m => MVector (PrimState m) Edge -> m () # basicUnsafeReplicate :: PrimMonad m => Int -> Edge -> m (MVector (PrimState m) Edge) # basicUnsafeRead :: PrimMonad m => MVector (PrimState m) Edge -> Int -> m Edge # basicUnsafeWrite :: PrimMonad m => MVector (PrimState m) Edge -> Int -> Edge -> m () # basicClear :: PrimMonad m => MVector (PrimState m) Edge -> m () # basicSet :: PrimMonad m => MVector (PrimState m) Edge -> Edge -> m () # basicUnsafeCopy :: PrimMonad m => MVector (PrimState m) Edge -> MVector (PrimState m) Edge -> m () # basicUnsafeMove :: PrimMonad m => MVector (PrimState m) Edge -> MVector (PrimState m) Edge -> m () # basicUnsafeGrow :: PrimMonad m => MVector (PrimState m) Edge -> Int -> m (MVector (PrimState m) Edge) #
RemovePseudoKnots [ExtPairIdx] Source #
Instance details Defined in Biobase.Secondary.Pseudoknots Methods removeByCounting :: [ExtPairIdx] -> [ExtPairIdx] Source #
RemovePseudoKnots (Vector ExtPairIdx) Source #	Remove pseudoknotted pairs from extended RNA secondary structures.
Instance details Defined in Biobase.Secondary.Pseudoknots Methods removeByCounting :: Vector ExtPairIdx -> Vector ExtPairIdx Source #
MkD2Secondary (Int, [ExtPairIdx]) Source #
Instance details Defined in Biobase.Secondary.Diagrams Methods mkD2S :: (Int, [ExtPairIdx]) -> D2Secondary Source # fromD2S :: D2Secondary -> (Int, [ExtPairIdx]) Source #
IsostericityLookup (ExtPair n) Source #	For extended basepairs, we take the default mapping and go from there. TODO inClass missing
Instance details Defined in Biobase.Secondary.Isostericity Methods getClasses :: ExtPair n -> [String] Source # inClass :: String -> [ExtPair n] Source #
type Rep Edge Source #
Instance details Defined in Biobase.Secondary.Basepair type Rep Edge = D1 (MetaData "Edge" "Biobase.Secondary.Basepair" "BiobaseXNA-0.11.0.0-6sSV7wA2ZNJ62zYFxZDZpd" True) (C1 (MetaCons "Edge" PrefixI True) (S1 (MetaSel (Just "unEdge") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int)))
newtype Vector Edge Source #
Instance details Defined in Biobase.Secondary.Basepair newtype Vector Edge = V_Edge (Vector Int)
newtype MVector s Edge Source #
Instance details Defined in Biobase.Secondary.Basepair newtype MVector s Edge = MV_Edge (MVector s Int)

pattern W :: Edge Source #

pattern S :: Edge Source #

pattern H :: Edge Source #

Is the base pair in cis or trans configuration

newtype CTisomerism Source #

Nucleotides in a pairing may be in the cis(==?) or trans(==?) state.

Constructors

CT
Fields unCT :: Int

Instances

Bounded CTisomerism Source #
Instance details Defined in Biobase.Secondary.Basepair Methods minBound :: CTisomerism # maxBound :: CTisomerism #
Enum CTisomerism Source #
Instance details Defined in Biobase.Secondary.Basepair Methods succ :: CTisomerism -> CTisomerism # pred :: CTisomerism -> CTisomerism # toEnum :: Int -> CTisomerism # fromEnum :: CTisomerism -> Int # enumFrom :: CTisomerism -> [CTisomerism] # enumFromThen :: CTisomerism -> CTisomerism -> [CTisomerism] # enumFromTo :: CTisomerism -> CTisomerism -> [CTisomerism] # enumFromThenTo :: CTisomerism -> CTisomerism -> CTisomerism -> [CTisomerism] #
Eq CTisomerism Source #
Instance details Defined in Biobase.Secondary.Basepair Methods (==) :: CTisomerism -> CTisomerism -> Bool # (/=) :: CTisomerism -> CTisomerism -> Bool #
Ord CTisomerism Source #
Instance details Defined in Biobase.Secondary.Basepair Methods compare :: CTisomerism -> CTisomerism -> Ordering # (<) :: CTisomerism -> CTisomerism -> Bool # (<=) :: CTisomerism -> CTisomerism -> Bool # (>) :: CTisomerism -> CTisomerism -> Bool # (>=) :: CTisomerism -> CTisomerism -> Bool # max :: CTisomerism -> CTisomerism -> CTisomerism # min :: CTisomerism -> CTisomerism -> CTisomerism #
Read CTisomerism Source #	Human-readable Read instance.
Instance details Defined in Biobase.Secondary.Basepair Methods readsPrec :: Int -> ReadS CTisomerism # readList :: ReadS [CTisomerism] # readPrec :: ReadPrec CTisomerism # readListPrec :: ReadPrec [CTisomerism] #
Show CTisomerism Source #	Human-readable Show instance.
Instance details Defined in Biobase.Secondary.Basepair Methods showsPrec :: Int -> CTisomerism -> ShowS # show :: CTisomerism -> String # showList :: [CTisomerism] -> ShowS #
Ix CTisomerism Source #
Instance details Defined in Biobase.Secondary.Basepair Methods range :: (CTisomerism, CTisomerism) -> [CTisomerism] # index :: (CTisomerism, CTisomerism) -> CTisomerism -> Int # unsafeIndex :: (CTisomerism, CTisomerism) -> CTisomerism -> Int inRange :: (CTisomerism, CTisomerism) -> CTisomerism -> Bool # rangeSize :: (CTisomerism, CTisomerism) -> Int # unsafeRangeSize :: (CTisomerism, CTisomerism) -> Int
Generic CTisomerism Source #
Instance details Defined in Biobase.Secondary.Basepair Associated Types type Rep CTisomerism :: Type -> Type # Methods from :: CTisomerism -> Rep CTisomerism x # to :: Rep CTisomerism x -> CTisomerism #
ToJSON CTisomerism Source #
Instance details Defined in Biobase.Secondary.Basepair Methods toJSON :: CTisomerism -> Value # toEncoding :: CTisomerism -> Encoding # toJSONList :: [CTisomerism] -> Value # toEncodingList :: [CTisomerism] -> Encoding #
FromJSON CTisomerism Source #
Instance details Defined in Biobase.Secondary.Basepair Methods parseJSON :: Value -> Parser CTisomerism # parseJSONList :: Value -> Parser [CTisomerism] #
Binary CTisomerism Source #
Instance details Defined in Biobase.Secondary.Basepair Methods put :: CTisomerism -> Put # get :: Get CTisomerism # putList :: [CTisomerism] -> Put #
Serialize CTisomerism Source #
Instance details Defined in Biobase.Secondary.Basepair Methods put :: Putter CTisomerism # get :: Get CTisomerism #
Unbox CTisomerism Source #
Instance details Defined in Biobase.Secondary.Basepair
Vector Vector CTisomerism Source #
Instance details Defined in Biobase.Secondary.Basepair Methods basicUnsafeFreeze :: PrimMonad m => Mutable Vector (PrimState m) CTisomerism -> m (Vector CTisomerism) # basicUnsafeThaw :: PrimMonad m => Vector CTisomerism -> m (Mutable Vector (PrimState m) CTisomerism) # basicLength :: Vector CTisomerism -> Int # basicUnsafeSlice :: Int -> Int -> Vector CTisomerism -> Vector CTisomerism # basicUnsafeIndexM :: Monad m => Vector CTisomerism -> Int -> m CTisomerism # basicUnsafeCopy :: PrimMonad m => Mutable Vector (PrimState m) CTisomerism -> Vector CTisomerism -> m () # elemseq :: Vector CTisomerism -> CTisomerism -> b -> b #
MVector MVector CTisomerism Source #
Instance details Defined in Biobase.Secondary.Basepair Methods basicLength :: MVector s CTisomerism -> Int # basicUnsafeSlice :: Int -> Int -> MVector s CTisomerism -> MVector s CTisomerism # basicOverlaps :: MVector s CTisomerism -> MVector s CTisomerism -> Bool # basicUnsafeNew :: PrimMonad m => Int -> m (MVector (PrimState m) CTisomerism) # basicInitialize :: PrimMonad m => MVector (PrimState m) CTisomerism -> m () # basicUnsafeReplicate :: PrimMonad m => Int -> CTisomerism -> m (MVector (PrimState m) CTisomerism) # basicUnsafeRead :: PrimMonad m => MVector (PrimState m) CTisomerism -> Int -> m CTisomerism # basicUnsafeWrite :: PrimMonad m => MVector (PrimState m) CTisomerism -> Int -> CTisomerism -> m () # basicClear :: PrimMonad m => MVector (PrimState m) CTisomerism -> m () # basicSet :: PrimMonad m => MVector (PrimState m) CTisomerism -> CTisomerism -> m () # basicUnsafeCopy :: PrimMonad m => MVector (PrimState m) CTisomerism -> MVector (PrimState m) CTisomerism -> m () # basicUnsafeMove :: PrimMonad m => MVector (PrimState m) CTisomerism -> MVector (PrimState m) CTisomerism -> m () # basicUnsafeGrow :: PrimMonad m => MVector (PrimState m) CTisomerism -> Int -> m (MVector (PrimState m) CTisomerism) #
RemovePseudoKnots [ExtPairIdx] Source #
Instance details Defined in Biobase.Secondary.Pseudoknots Methods removeByCounting :: [ExtPairIdx] -> [ExtPairIdx] Source #
RemovePseudoKnots (Vector ExtPairIdx) Source #	Remove pseudoknotted pairs from extended RNA secondary structures.
Instance details Defined in Biobase.Secondary.Pseudoknots Methods removeByCounting :: Vector ExtPairIdx -> Vector ExtPairIdx Source #
MkD2Secondary (Int, [ExtPairIdx]) Source #
Instance details Defined in Biobase.Secondary.Diagrams Methods mkD2S :: (Int, [ExtPairIdx]) -> D2Secondary Source # fromD2S :: D2Secondary -> (Int, [ExtPairIdx]) Source #
IsostericityLookup (ExtPair n) Source #	For extended basepairs, we take the default mapping and go from there. TODO inClass missing
Instance details Defined in Biobase.Secondary.Isostericity Methods getClasses :: ExtPair n -> [String] Source # inClass :: String -> [ExtPair n] Source #
type Rep CTisomerism Source #
Instance details Defined in Biobase.Secondary.Basepair type Rep CTisomerism = D1 (MetaData "CTisomerism" "Biobase.Secondary.Basepair" "BiobaseXNA-0.11.0.0-6sSV7wA2ZNJ62zYFxZDZpd" True) (C1 (MetaCons "CT" PrefixI True) (S1 (MetaSel (Just "unCT") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int)))
newtype Vector CTisomerism Source #
Instance details Defined in Biobase.Secondary.Basepair newtype Vector CTisomerism = V_CTisomerism (Vector Int)
newtype MVector s CTisomerism Source #
Instance details Defined in Biobase.Secondary.Basepair newtype MVector s CTisomerism = MV_CTisomerism (MVector s Int)