Safe Haskell | None |
---|
- basepairing :: Primary -> Subword -> Bool
- structureConstrains :: Maybe D1Secondary -> Subword -> Bool
- structC :: Primary -> Subword -> Bool
- gRNAfold :: (Apply (:. (:. (:. (Arg (Pair (Pair (Pair (:!: Z (GChr Nuc Nuc)) (SRegion Nuc)) (PeekR Nuc)) a4)) Nuc) (Vector Nuc)) Nuc -> a3), Apply (:. (:. (Arg (Pair (Pair (Pair (:!: Z (GChr Nuc Nuc)) (PeekL Nuc)) a2) b)) Nuc) Nuc -> a3), Apply (:. (:. (Arg (Pair (Pair (:!: Z (PeekL Nuc)) (GChr Nuc Nuc)) a4)) Nuc) Nuc -> a3), Apply (Arg (Pair (:!: Z (GChr Nuc Nuc)) a2) -> a3), Apply (:. (Arg (Stack a2)) (Vector Nuc) -> a3), Apply (Arg (Pair (Stack a2) b) -> a3), Apply (Arg (Pair (:!: Z (GChr Nuc Nuc)) b1) -> a3), Apply (Arg (Pair (Stack a4) b1) -> a3), Elms (Pair (Pair (Pair (:!: Z (GChr Nuc Nuc)) (SRegion Nuc)) (PeekR Nuc)) a4) Subword, Elms (Pair (Pair (Pair (:!: Z (GChr Nuc Nuc)) (PeekL Nuc)) a2) b) Subword, Elms (Pair (Pair (Pair (Pair (:!: Z (PeekL Nuc)) (GChr Nuc Nuc)) a4) (GChr Nuc Nuc)) (PeekR Nuc)) a, Elms (Pair (:!: Z (GChr Nuc Nuc)) a2) a, Elms (Pair (Stack a2) (Region Nuc)) a1, Elms (Pair (Stack a2) b) a1, Elms (Pair (:!: Z (GChr Nuc Nuc)) b1) Subword, Elms (Pair (Stack a4) b1) Subword, MkStream m (Pair (Pair (Pair (:!: Z (GChr Nuc Nuc)) (SRegion Nuc)) (PeekR Nuc)) a4) Subword, MkStream m (Pair (Pair (Pair (:!: Z (GChr Nuc Nuc)) (PeekL Nuc)) a2) b) Subword, MkStream m (Pair (Pair (Pair (Pair (:!: Z (PeekL Nuc)) (GChr Nuc Nuc)) a4) (GChr Nuc Nuc)) (PeekR Nuc)) a, MkStream m (Pair (:!: Z (GChr Nuc Nuc)) a2) a, MkStream m (Pair (Stack a2) (Region Nuc)) a1, MkStream m (Pair (Stack a2) b) a1, MkStream m (Pair (:!: Z (GChr Nuc Nuc)) b1) Subword, MkStream m (Pair (Stack a4) b1) Subword, Build a2, Build a4, ValidIndex (Pair (Pair (Pair (:!: Z (GChr Nuc Nuc)) (SRegion Nuc)) (PeekR Nuc)) a4) Subword, ValidIndex (Pair (Pair (Pair (:!: Z (GChr Nuc Nuc)) (PeekL Nuc)) a2) b) Subword, ValidIndex (Pair (Pair (Pair (Pair (:!: Z (PeekL Nuc)) (GChr Nuc Nuc)) a4) (GChr Nuc Nuc)) (PeekR Nuc)) a, ValidIndex (Pair (:!: Z (GChr Nuc Nuc)) a2) a, ValidIndex (Pair (Stack a2) (Region Nuc)) a1, ValidIndex (Pair (Stack a2) b) a1, ValidIndex (Pair (:!: Z (GChr Nuc Nuc)) b1) Subword, ValidIndex (Pair (Stack a4) b1) Subword) => t1 -> (t1 -> Nuc -> Nuc -> Vector Nuc -> Nuc -> Nuc -> a3, t1 -> Fun (:. (:. (:. (Arg (Pair (Pair (Pair (:!: Z (GChr Nuc Nuc)) (SRegion Nuc)) (PeekR Nuc)) a4)) Nuc) (Vector Nuc)) Nuc -> a3), t1 -> Fun (:. (:. (Arg (Pair (Pair (Pair (:!: Z (GChr Nuc Nuc)) (PeekL Nuc)) a2) b)) Nuc) Nuc -> a3), t1 -> Fun (:. (:. (Arg (Pair (Pair (:!: Z (PeekL Nuc)) (GChr Nuc Nuc)) a4)) Nuc) Nuc -> a3), t1 -> Fun (Arg (Pair (:!: Z (GChr Nuc Nuc)) a2) -> a3), t1 -> Fun (:. (Arg (Stack a2)) (Vector Nuc) -> a3), t1 -> Fun (Arg (Pair (Stack a2) b) -> a3), t, t1 -> Fun (Arg (Pair (:!: Z (GChr Nuc Nuc)) b1) -> a3), t1 -> Fun (Arg (Pair (Stack a4) b1) -> a3), t1 -> Vector Nuc -> a3, Stream m a3 -> c) -> a4 -> a2 -> b -> b1 -> Maybe D1Secondary -> Vector Nuc -> (a4, Subword -> c, a2, a -> c, b, a1 -> c, b1, Subword -> c)
- pretty :: Monad m => Signature m String (Stream m String)
- type CombSignature m e b = Signature m (e, m (Stream m b)) (Stream m b)
- (<**) :: (Monad m, Eq b, Eq e) => Signature m e e -> Signature m b (Stream m b) -> CombSignature m e b
- rnaFoldConstrained :: Vienna2004 -> Primary -> D1Secondary -> (Deka, [String])
- rnaFold :: Vienna2004 -> Primary -> (Deka, [String])
- rnaFoldFill :: Vienna2004 -> Maybe D1Secondary -> Primary -> IO (Unboxed (Z :. Subword) Deka, Unboxed (Z :. Subword) Deka, Unboxed (Z :. Subword) Deka, Unboxed (Z :. Subword) Deka)
- fillTables :: (MPrimArrayOps arr (:. Z Subword) a, MPrimArrayOps arr1 (:. Z Subword) a1, MPrimArrayOps arr2 (:. Z Subword) a2, MPrimArrayOps arr3 (:. Z Subword) a3, PrimMonad m) => (MTbl t (MutArr m (arr (:. Z Subword) a)), Subword -> m a, MTbl t1 (MutArr m (arr1 (:. Z Subword) a1)), Subword -> m a1, MTbl t2 (MutArr m (arr2 (:. Z Subword) a2)), Subword -> m a2, MTbl t3 (MutArr m (arr3 (:. Z Subword) a3)), Subword -> m a3) -> m ()
- backtrack :: Vienna2004 -> Maybe D1Secondary -> Primary -> (Unboxed (:. Z Subword) Deka, Unboxed (:. Z Subword) Deka, Unboxed (:. Z Subword) Deka, Unboxed (:. Z Subword) Deka) -> [String]
Documentation
basepairing :: Primary -> Subword -> BoolSource
structureConstrains :: Maybe D1Secondary -> Subword -> BoolSource
gRNAfold :: (Apply (:. (:. (:. (Arg (Pair (Pair (Pair (:!: Z (GChr Nuc Nuc)) (SRegion Nuc)) (PeekR Nuc)) a4)) Nuc) (Vector Nuc)) Nuc -> a3), Apply (:. (:. (Arg (Pair (Pair (Pair (:!: Z (GChr Nuc Nuc)) (PeekL Nuc)) a2) b)) Nuc) Nuc -> a3), Apply (:. (:. (Arg (Pair (Pair (:!: Z (PeekL Nuc)) (GChr Nuc Nuc)) a4)) Nuc) Nuc -> a3), Apply (Arg (Pair (:!: Z (GChr Nuc Nuc)) a2) -> a3), Apply (:. (Arg (Stack a2)) (Vector Nuc) -> a3), Apply (Arg (Pair (Stack a2) b) -> a3), Apply (Arg (Pair (:!: Z (GChr Nuc Nuc)) b1) -> a3), Apply (Arg (Pair (Stack a4) b1) -> a3), Elms (Pair (Pair (Pair (:!: Z (GChr Nuc Nuc)) (SRegion Nuc)) (PeekR Nuc)) a4) Subword, Elms (Pair (Pair (Pair (:!: Z (GChr Nuc Nuc)) (PeekL Nuc)) a2) b) Subword, Elms (Pair (Pair (Pair (Pair (:!: Z (PeekL Nuc)) (GChr Nuc Nuc)) a4) (GChr Nuc Nuc)) (PeekR Nuc)) a, Elms (Pair (:!: Z (GChr Nuc Nuc)) a2) a, Elms (Pair (Stack a2) (Region Nuc)) a1, Elms (Pair (Stack a2) b) a1, Elms (Pair (:!: Z (GChr Nuc Nuc)) b1) Subword, Elms (Pair (Stack a4) b1) Subword, MkStream m (Pair (Pair (Pair (:!: Z (GChr Nuc Nuc)) (SRegion Nuc)) (PeekR Nuc)) a4) Subword, MkStream m (Pair (Pair (Pair (:!: Z (GChr Nuc Nuc)) (PeekL Nuc)) a2) b) Subword, MkStream m (Pair (Pair (Pair (Pair (:!: Z (PeekL Nuc)) (GChr Nuc Nuc)) a4) (GChr Nuc Nuc)) (PeekR Nuc)) a, MkStream m (Pair (:!: Z (GChr Nuc Nuc)) a2) a, MkStream m (Pair (Stack a2) (Region Nuc)) a1, MkStream m (Pair (Stack a2) b) a1, MkStream m (Pair (:!: Z (GChr Nuc Nuc)) b1) Subword, MkStream m (Pair (Stack a4) b1) Subword, Build a2, Build a4, ValidIndex (Pair (Pair (Pair (:!: Z (GChr Nuc Nuc)) (SRegion Nuc)) (PeekR Nuc)) a4) Subword, ValidIndex (Pair (Pair (Pair (:!: Z (GChr Nuc Nuc)) (PeekL Nuc)) a2) b) Subword, ValidIndex (Pair (Pair (Pair (Pair (:!: Z (PeekL Nuc)) (GChr Nuc Nuc)) a4) (GChr Nuc Nuc)) (PeekR Nuc)) a, ValidIndex (Pair (:!: Z (GChr Nuc Nuc)) a2) a, ValidIndex (Pair (Stack a2) (Region Nuc)) a1, ValidIndex (Pair (Stack a2) b) a1, ValidIndex (Pair (:!: Z (GChr Nuc Nuc)) b1) Subword, ValidIndex (Pair (Stack a4) b1) Subword) => t1 -> (t1 -> Nuc -> Nuc -> Vector Nuc -> Nuc -> Nuc -> a3, t1 -> Fun (:. (:. (:. (Arg (Pair (Pair (Pair (:!: Z (GChr Nuc Nuc)) (SRegion Nuc)) (PeekR Nuc)) a4)) Nuc) (Vector Nuc)) Nuc -> a3), t1 -> Fun (:. (:. (Arg (Pair (Pair (Pair (:!: Z (GChr Nuc Nuc)) (PeekL Nuc)) a2) b)) Nuc) Nuc -> a3), t1 -> Fun (:. (:. (Arg (Pair (Pair (:!: Z (PeekL Nuc)) (GChr Nuc Nuc)) a4)) Nuc) Nuc -> a3), t1 -> Fun (Arg (Pair (:!: Z (GChr Nuc Nuc)) a2) -> a3), t1 -> Fun (:. (Arg (Stack a2)) (Vector Nuc) -> a3), t1 -> Fun (Arg (Pair (Stack a2) b) -> a3), t, t1 -> Fun (Arg (Pair (:!: Z (GChr Nuc Nuc)) b1) -> a3), t1 -> Fun (Arg (Pair (Stack a4) b1) -> a3), t1 -> Vector Nuc -> a3, Stream m a3 -> c) -> a4 -> a2 -> b -> b1 -> Maybe D1Secondary -> Vector Nuc -> (a4, Subword -> c, a2, a -> c, b, a1 -> c, b1, Subword -> c)Source
type CombSignature m e b = Signature m (e, m (Stream m b)) (Stream m b)Source
(<**) :: (Monad m, Eq b, Eq e) => Signature m e e -> Signature m b (Stream m b) -> CombSignature m e bSource
rnaFoldConstrained :: Vienna2004 -> Primary -> D1Secondary -> (Deka, [String])Source
rnaFoldFill :: Vienna2004 -> Maybe D1Secondary -> Primary -> IO (Unboxed (Z :. Subword) Deka, Unboxed (Z :. Subword) Deka, Unboxed (Z :. Subword) Deka, Unboxed (Z :. Subword) Deka)Source
fillTables :: (MPrimArrayOps arr (:. Z Subword) a, MPrimArrayOps arr1 (:. Z Subword) a1, MPrimArrayOps arr2 (:. Z Subword) a2, MPrimArrayOps arr3 (:. Z Subword) a3, PrimMonad m) => (MTbl t (MutArr m (arr (:. Z Subword) a)), Subword -> m a, MTbl t1 (MutArr m (arr1 (:. Z Subword) a1)), Subword -> m a1, MTbl t2 (MutArr m (arr2 (:. Z Subword) a2)), Subword -> m a2, MTbl t3 (MutArr m (arr3 (:. Z Subword) a3)), Subword -> m a3) -> m ()Source