Biobase.Secondary.Basepair

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.

Newtype for efficient basepair encoding.

newtype Basepair

Encode a base pair as a single Int.

Constructors

BP

Fields

• getBP :: Int

Instances

Eq Basepair

Defined in Biobase.Secondary.Basepair

Methods

(==) :: Basepair -> Basepair -> Bool

(/=) :: Basepair -> Basepair -> Bool

Ord Basepair

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

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

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

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

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

Defined in Biobase.Secondary.Basepair

Methods

toJSON :: Basepair -> Value

toEncoding :: Basepair -> Encoding

toJSONList :: [Basepair] -> Value

toEncodingList :: [Basepair] -> Encoding

FromJSON Basepair

Defined in Biobase.Secondary.Basepair

Methods

parseJSON :: Value -> Parser Basepair

parseJSONList :: Value -> Parser [Basepair]

Binary Basepair

Defined in Biobase.Secondary.Basepair

Methods

put :: Basepair -> Put

get :: Get Basepair

putList :: [Basepair] -> Put

Serialize Basepair

Defined in Biobase.Secondary.Basepair

Methods

put :: Putter Basepair

get :: Get Basepair

Unbox Basepair

Defined in Biobase.Secondary.Basepair

Vector Vector Basepair

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

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

Defined in Biobase.Secondary.Convert

Methods

basepairConvert :: Basepair -> ViennaPair

BasepairConvert ViennaPair Basepair

Defined in Biobase.Secondary.Convert

Methods

basepairConvert :: ViennaPair -> Basepair

BasepairConvert Basepair (Letter RNA n, Letter RNA n)

Defined in Biobase.Secondary.Convert

Methods

basepairConvert :: Basepair -> (Letter RNA n, Letter RNA n)

IndexStream z => IndexStream (z :. Basepair)

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

Defined in Biobase.Secondary.Convert

Methods

basepairConvert :: (Letter RNA n, Letter RNA n) -> Basepair

type Rep Basepair

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

Defined in Biobase.Secondary.Basepair

newtype LimitType Basepair = LtBP Basepair

newtype Vector Basepair

Defined in Biobase.Secondary.Basepair

newtype Vector Basepair = V_Basepair (Vector Int)

newtype MVector s Basepair

Defined in Biobase.Secondary.Basepair

newtype MVector s Basepair = MV_Basepair (MVector s 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

Newtypes for extended secondary structures

Encode which of three edges is engaged in base pairing

newtype Edge

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

Defined in Biobase.Secondary.Basepair

Methods

minBound :: Edge

maxBound :: Edge

Enum Edge

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

Defined in Biobase.Secondary.Basepair

Methods

(==) :: Edge -> Edge -> Bool

(/=) :: Edge -> Edge -> Bool

Ord Edge

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

Human-readable Read instance.

Defined in Biobase.Secondary.Basepair

Methods

readsPrec :: Int -> ReadS Edge

readList :: ReadS [Edge]

readPrec :: ReadPrec Edge

readListPrec :: ReadPrec [Edge]

Show Edge

Human-readable Show instance.

Defined in Biobase.Secondary.Basepair

Methods

showsPrec :: Int -> Edge -> ShowS

show :: Edge -> String

showList :: [Edge] -> ShowS

Ix Edge

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

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

Defined in Biobase.Secondary.Basepair

Methods

toJSON :: Edge -> Value

toEncoding :: Edge -> Encoding

toJSONList :: [Edge] -> Value

toEncodingList :: [Edge] -> Encoding

FromJSON Edge

Defined in Biobase.Secondary.Basepair

Methods

parseJSON :: Value -> Parser Edge

parseJSONList :: Value -> Parser [Edge]

Binary Edge

Defined in Biobase.Secondary.Basepair

Methods

put :: Edge -> Put

get :: Get Edge

putList :: [Edge] -> Put

Serialize Edge

Defined in Biobase.Secondary.Basepair

Methods

put :: Putter Edge

get :: Get Edge

Unbox Edge

Defined in Biobase.Secondary.Basepair

Vector Vector Edge

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

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]

Defined in Biobase.Secondary.Pseudoknots

Methods

removeByCounting :: [ExtPairIdx] -> [ExtPairIdx]

RemovePseudoKnots (Vector ExtPairIdx)

Remove pseudoknotted pairs from extended RNA secondary structures.

Defined in Biobase.Secondary.Pseudoknots

Methods

removeByCounting :: Vector ExtPairIdx -> Vector ExtPairIdx

MkD2Secondary (Int, [ExtPairIdx])

Defined in Biobase.Secondary.Diagrams

Methods

mkD2S :: (Int, [ExtPairIdx]) -> D2Secondary

fromD2S :: D2Secondary -> (Int, [ExtPairIdx])

IsostericityLookup (ExtPair n)

For extended basepairs, we take the default mapping and go from there.

TODO inClass missing

Defined in Biobase.Secondary.Isostericity

Methods

getClasses :: ExtPair n -> [String]

inClass :: String -> [ExtPair n]

type Rep Edge

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

Defined in Biobase.Secondary.Basepair

newtype Vector Edge = V_Edge (Vector Int)

newtype MVector s Edge

Defined in Biobase.Secondary.Basepair

newtype MVector s Edge = MV_Edge (MVector s Int)

pattern W :: Edge

pattern S :: Edge

pattern H :: Edge

Is the base pair in cis or trans configuration

newtype CTisomerism

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

Constructors

CT

Fields

• unCT :: Int

Instances

Bounded CTisomerism

Defined in Biobase.Secondary.Basepair

Methods

minBound :: CTisomerism

maxBound :: CTisomerism

Enum CTisomerism

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

Defined in Biobase.Secondary.Basepair

Methods

(==) :: CTisomerism -> CTisomerism -> Bool

(/=) :: CTisomerism -> CTisomerism -> Bool

Ord CTisomerism

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

Human-readable Read instance.

Defined in Biobase.Secondary.Basepair

Methods

readsPrec :: Int -> ReadS CTisomerism

readList :: ReadS [CTisomerism]

readPrec :: ReadPrec CTisomerism

readListPrec :: ReadPrec [CTisomerism]

Show CTisomerism

Human-readable Show instance.

Defined in Biobase.Secondary.Basepair

Methods

showsPrec :: Int -> CTisomerism -> ShowS

show :: CTisomerism -> String

showList :: [CTisomerism] -> ShowS

Ix CTisomerism

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

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

Defined in Biobase.Secondary.Basepair

Methods

toJSON :: CTisomerism -> Value

toEncoding :: CTisomerism -> Encoding

toJSONList :: [CTisomerism] -> Value

toEncodingList :: [CTisomerism] -> Encoding

FromJSON CTisomerism

Defined in Biobase.Secondary.Basepair

Methods

parseJSON :: Value -> Parser CTisomerism

parseJSONList :: Value -> Parser [CTisomerism]

Binary CTisomerism

Defined in Biobase.Secondary.Basepair

Methods

put :: CTisomerism -> Put

get :: Get CTisomerism

putList :: [CTisomerism] -> Put

Serialize CTisomerism

Defined in Biobase.Secondary.Basepair

Methods

put :: Putter CTisomerism

get :: Get CTisomerism

Unbox CTisomerism

Defined in Biobase.Secondary.Basepair

Vector Vector CTisomerism

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

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]

Defined in Biobase.Secondary.Pseudoknots

Methods

removeByCounting :: [ExtPairIdx] -> [ExtPairIdx]

RemovePseudoKnots (Vector ExtPairIdx)

Remove pseudoknotted pairs from extended RNA secondary structures.

Defined in Biobase.Secondary.Pseudoknots

Methods

removeByCounting :: Vector ExtPairIdx -> Vector ExtPairIdx

MkD2Secondary (Int, [ExtPairIdx])

Defined in Biobase.Secondary.Diagrams

Methods

mkD2S :: (Int, [ExtPairIdx]) -> D2Secondary

fromD2S :: D2Secondary -> (Int, [ExtPairIdx])

IsostericityLookup (ExtPair n)

For extended basepairs, we take the default mapping and go from there.

TODO inClass missing

Defined in Biobase.Secondary.Isostericity

Methods

getClasses :: ExtPair n -> [String]

inClass :: String -> [ExtPair n]

type Rep CTisomerism

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

Defined in Biobase.Secondary.Basepair

newtype Vector CTisomerism = V_CTisomerism (Vector Int)

newtype MVector s CTisomerism

Defined in Biobase.Secondary.Basepair

newtype MVector s CTisomerism = MV_CTisomerism (MVector s Int)

pattern Cis :: CTisomerism

pattern Trn :: CTisomerism

Types

type PairIdx = (Int, Int)

A basepair is simply a pair of Ints which are 0-indexing a sequence.

type Pair n = (Letter RNA n, Letter RNA n)

A pair as a tuple containing Nucs.

type ExtPairAnnotation = (CTisomerism, Edge, Edge)

Annotation for a basepair.

type ExtPairIdx = (PairIdx, ExtPairAnnotation)

An extended basepair is a basepair, annotated with edge and CTisomerism.

type ExtPair n = (Pair n, ExtPairAnnotation)

An extended basepair, with nucleotides an annotation.

little helpers

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)