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".

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

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

Methods

minBound :: Edge

maxBound :: Edge

Enum Edge

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

Methods

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

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

Ord Edge

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.

Methods

readsPrec :: Int -> ReadS Edge

readList :: ReadS [Edge]

readPrec :: ReadPrec Edge

readListPrec :: ReadPrec [Edge]

Show Edge

Human-readable Show instance.

Methods

showsPrec :: Int -> Edge -> ShowS

show :: Edge -> String

showList :: [Edge] -> ShowS

Ix Edge

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

Associated Types

type Rep Edge :: * -> *

Methods

from :: Edge -> Rep Edge x

to :: Rep Edge x -> Edge

ToJSON Edge

Methods

toJSON :: Edge -> Value

toEncoding :: Edge -> Encoding

toJSONList :: [Edge] -> Value

toEncodingList :: [Edge] -> Encoding

FromJSON Edge

Methods

parseJSON :: Value -> Parser Edge

parseJSONList :: Value -> Parser [Edge]

Binary Edge

Methods

put :: Edge -> Put

get :: Get Edge

putList :: [Edge] -> Put

Serialize Edge

Methods

put :: Putter Edge

get :: Get Edge

Unbox Edge

IsostericityLookup ExtPair

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

TODO inClass missing

Methods

getClasses :: ExtPair -> [String]

inClass :: String -> [ExtPair]

Vector Vector Edge

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

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]

Methods

removeByCounting :: [ExtPairIdx] -> [ExtPairIdx]

RemovePseudoKnots (Vector ExtPairIdx)

Remove pseudoknotted pairs from extended RNA secondary structures.

Methods

removeByCounting :: Vector ExtPairIdx -> Vector ExtPairIdx

MkD2Secondary (Int, [ExtPairIdx])

Methods

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

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

BaseSelect ((a, a), ExtPairAnnotation) a

extended pairtype annotation given

Methods

baseL :: ((a, a), ExtPairAnnotation) -> a

baseR :: ((a, a), ExtPairAnnotation) -> a

baseP :: ((a, a), ExtPairAnnotation) -> (a, a)

baseT :: ((a, a), ExtPairAnnotation) -> ExtPairAnnotation

updL :: a -> ((a, a), ExtPairAnnotation) -> ((a, a), ExtPairAnnotation)

updR :: a -> ((a, a), ExtPairAnnotation) -> ((a, a), ExtPairAnnotation)

updP :: (a, a) -> ((a, a), ExtPairAnnotation) -> ((a, a), ExtPairAnnotation)

updT :: ExtPairAnnotation -> ((a, a), ExtPairAnnotation) -> ((a, a), ExtPairAnnotation)

type Rep Edge

type Rep Edge = D1 (MetaData "Edge" "Biobase.Secondary.Basepair" "BiobaseXNA-0.9.3.1-GowCVjd9NVABe39cHSIsJW" True) (C1 (MetaCons "Edge" PrefixI True) (S1 (MetaSel (Just Symbol "unEdge") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int)))

data Vector Edge

data Vector Edge = V_Edge (Vector Int)

data MVector s Edge

data 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

Methods

minBound :: CTisomerism

maxBound :: CTisomerism

Enum CTisomerism

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

Methods

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

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

Ord CTisomerism

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.

Methods

readsPrec :: Int -> ReadS CTisomerism

readList :: ReadS [CTisomerism]

readPrec :: ReadPrec CTisomerism

readListPrec :: ReadPrec [CTisomerism]

Show CTisomerism

Human-readable Show instance.

Methods

showsPrec :: Int -> CTisomerism -> ShowS

show :: CTisomerism -> String

showList :: [CTisomerism] -> ShowS

Ix CTisomerism

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

Associated Types

type Rep CTisomerism :: * -> *

Methods

from :: CTisomerism -> Rep CTisomerism x

to :: Rep CTisomerism x -> CTisomerism

ToJSON CTisomerism

Methods

toJSON :: CTisomerism -> Value

toEncoding :: CTisomerism -> Encoding

toJSONList :: [CTisomerism] -> Value

toEncodingList :: [CTisomerism] -> Encoding

FromJSON CTisomerism

Methods

parseJSON :: Value -> Parser CTisomerism

parseJSONList :: Value -> Parser [CTisomerism]

Binary CTisomerism

Methods

put :: CTisomerism -> Put

get :: Get CTisomerism

putList :: [CTisomerism] -> Put

Serialize CTisomerism

Methods

put :: Putter CTisomerism

get :: Get CTisomerism

Unbox CTisomerism

IsostericityLookup ExtPair

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

TODO inClass missing

Methods

getClasses :: ExtPair -> [String]

inClass :: String -> [ExtPair]

Vector Vector CTisomerism

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

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]

Methods

removeByCounting :: [ExtPairIdx] -> [ExtPairIdx]

RemovePseudoKnots (Vector ExtPairIdx)

Remove pseudoknotted pairs from extended RNA secondary structures.

Methods

removeByCounting :: Vector ExtPairIdx -> Vector ExtPairIdx

MkD2Secondary (Int, [ExtPairIdx])

Methods

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

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

BaseSelect ((a, a), ExtPairAnnotation) a

extended pairtype annotation given

Methods

baseL :: ((a, a), ExtPairAnnotation) -> a

baseR :: ((a, a), ExtPairAnnotation) -> a

baseP :: ((a, a), ExtPairAnnotation) -> (a, a)

baseT :: ((a, a), ExtPairAnnotation) -> ExtPairAnnotation

updL :: a -> ((a, a), ExtPairAnnotation) -> ((a, a), ExtPairAnnotation)

updR :: a -> ((a, a), ExtPairAnnotation) -> ((a, a), ExtPairAnnotation)

updP :: (a, a) -> ((a, a), ExtPairAnnotation) -> ((a, a), ExtPairAnnotation)

updT :: ExtPairAnnotation -> ((a, a), ExtPairAnnotation) -> ((a, a), ExtPairAnnotation)

type Rep CTisomerism

type Rep CTisomerism = D1 (MetaData "CTisomerism" "Biobase.Secondary.Basepair" "BiobaseXNA-0.9.3.1-GowCVjd9NVABe39cHSIsJW" True) (C1 (MetaCons "CT" PrefixI True) (S1 (MetaSel (Just Symbol "unCT") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int)))

data Vector CTisomerism

data Vector CTisomerism = V_CTisomerism (Vector Int)

data MVector s CTisomerism

data 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 = (Letter RNA, Letter RNA)

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 = (Pair, 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)

tuple-like selection

class BaseSelect a b | a -> b where

Selection of nucleotides and/or type classes independent of which type we are looking at.

Minimal complete definition

baseL, baseR, baseP, baseT, updL, updR, updP, updT

Methods

baseL :: a -> b

select first index or nucleotide

baseR :: a -> b

select second index or nucleotide

baseP :: a -> (b, b)

select both nucleotides as pair

baseT :: a -> ExtPairAnnotation

select basepair type if existing or return default cWW

updL :: b -> a -> a

update first index or nucleotide

updR :: b -> a -> a

update second index or nucleotide

updP :: (b, b) -> a -> a

update complete pair

updT :: ExtPairAnnotation -> a -> a

update basepair type, error if not possible due to type a

Instances

BaseSelect ((a, a), ExtPairAnnotation) a

extended pairtype annotation given

Methods

baseL :: ((a, a), ExtPairAnnotation) -> a

baseR :: ((a, a), ExtPairAnnotation) -> a

baseP :: ((a, a), ExtPairAnnotation) -> (a, a)

baseT :: ((a, a), ExtPairAnnotation) -> ExtPairAnnotation

updL :: a -> ((a, a), ExtPairAnnotation) -> ((a, a), ExtPairAnnotation)

updR :: a -> ((a, a), ExtPairAnnotation) -> ((a, a), ExtPairAnnotation)

updP :: (a, a) -> ((a, a), ExtPairAnnotation) -> ((a, a), ExtPairAnnotation)

updT :: ExtPairAnnotation -> ((a, a), ExtPairAnnotation) -> ((a, a), ExtPairAnnotation)

BaseSelect (a, a) a

simple cis/wc-wc basepairs

Methods

baseL :: (a, a) -> a

baseR :: (a, a) -> a

baseP :: (a, a) -> (a, a)

baseT :: (a, a) -> ExtPairAnnotation

updL :: a -> (a, a) -> (a, a)

updR :: a -> (a, a) -> (a, a)

updP :: (a, a) -> (a, a) -> (a, a)

updT :: ExtPairAnnotation -> (a, a) -> (a, a)