BioInf.RNAfold

Documentation

testRNAfold :: String -> (Int, [String])

testInput :: [Char]

test :: (Int, [String])

rnafold :: Vienna2004 -> Primary -> ST s (Arr0 DIM2 Int, Arr0 DIM2 Int, Arr0 DIM2 Int, Arr0 DIM2 Int)

(*~+) :: (Monad m1, Monad m, Num head, Num head1, Ord head) => xs -> ys -> Box ((:. (:. tail head1) head2, t, t1) -> m (:. (:. (:. tail head1) head1) head2, t, t1)) ((:. (:. (:. tail1 head) head) head, t2, t3) -> m1 (Step (:. (:. (:. tail1 head) head) head, t2, t3) (:. (:. (:. tail1 head) head) head, t2, t3))) xs ys

(+~*) :: (Monad m1, Monad m, Num head, Num head1, Ord head, Ord head1) => xs -> ys -> Box ((:. (:. tail head1) head1, t, t1) -> m (:. (:. (:. tail head1) head1) head1, t, t1)) ((:. (:. (:. tail1 head2) head) head, t2, t3) -> m1 (Step (:. (:. (:. tail1 head2) head) head, t2, t3) (:. (:. (:. tail1 head2) head) head, t2, t3))) xs ys

(&~+) :: (Monad m1, Monad m, Num head, Num head1, Ord head) => xs -> ys -> Box ((:. (:. tail head1) head2, t, t1) -> m (:. (:. (:. tail head1) head1) head2, t, t1)) ((:. (:. (:. tail1 head) head) head, t2, t3) -> m1 (Step (:. (:. (:. tail1 head) head) head, t2, t3) (:. (:. (:. tail1 head) head) head, t2, t3))) xs ys

(+~&) :: (Monad m1, Monad m, Num head, Num head1, Ord head, Ord head1) => xs -> ys -> Box ((:. (:. tail head1) head1, t, t1) -> m (:. (:. (:. tail head1) head1) head1, t, t1)) ((:. (:. (:. tail1 head2) head) head, t2, t3) -> m1 (Step (:. (:. (:. tail1 head2) head) head, t2, t3) (:. (:. (:. tail1 head2) head) head, t2, t3))) xs ys

(---~+) :: (Monad m1, Monad m, Num head, Num head1, Ord head) => xs -> ys -> Box ((:. (:. tail head1) head2, t, t1) -> m (:. (:. (:. tail head1) head1) head2, t, t1)) ((:. (:. (:. tail1 head) head) head, t2, t3) -> m1 (Step (:. (:. (:. tail1 head) head) head, t2, t3) (:. (:. (:. tail1 head) head) head, t2, t3))) xs ys

(+~@) :: (Monad m1, Monad m, Num head, Num head1, Ord head, Ord head1) => xs -> ys -> Box ((:. (:. tail head1) head1, t, t1) -> m (:. (:. (:. tail head1) head1) head1, t, t1)) ((:. (:. (:. tail1 head2) head) head, t2, t3) -> m1 (Step (:. (:. (:. tail1 head2) head) head, t2, t3) (:. (:. (:. tail1 head2) head) head, t2, t3))) xs ys

(+~---) :: (Monad m1, Monad m, Num head, Num head1, Ord head, Ord head1) => xs -> ys -> Box ((:. (:. tail head1) head1, t, t1) -> m (:. (:. (:. tail head1) head1) head1, t, t1)) ((:. (:. (:. tail1 head2) head) head, t2, t3) -> m1 (Step (:. (:. (:. tail1 head2) head) head, t2, t3) (:. (:. (:. tail1 head2) head) head, t2, t3))) xs ys

(@~+) :: (Monad m1, Monad m, Num head, Num head1, Ord head) => xs -> ys -> Box ((:. (:. tail head1) head2, t, t1) -> m (:. (:. (:. tail head1) head1) head2, t, t1)) ((:. (:. (:. tail1 head) head) head, t2, t3) -> m1 (Step (:. (:. (:. tail1 head) head) head, t2, t3) (:. (:. (:. tail1 head) head) head, t2, t3))) xs ys

backtracking

btRNAfold :: Vienna2004 -> Primary -> (Arr0 DIM2 Int, Arr0 DIM2 Int, Arr0 DIM2 Int, Arr0 DIM2 Int) -> [String]

different energy functions (very simplified signature)

Functions that will be part of a bioinformatics DP library

adjustStream :: Int -> (DIM2 -> Stream (ST s) Int) -> DIM2 -> Stream (ST s) Int

adjustStreamBT :: Int -> (DIM2 -> Stream elm) -> DIM2 -> Stream elm

(.!.) :: (Monad m, Num head, Num head1, Ord head, Ord head1) => (:. (:. Z head1) head -> Stream m a) -> (Stream m a -> t, head) -> :. (:. Z head1) head -> t

with :: (Monad m, Num a) => (t -> m a) -> (t -> Bool) -> t -> m a

withBT :: Monad m => (t -> m [a]) -> (t -> Bool) -> t -> m [a]

fillTables :: PrimMonad m => MArr0 (PrimState m) DIM2 Int -> (DIM2 -> m Int) -> MArr0 (PrimState m) DIM2 Int -> (DIM2 -> m Int) -> MArr0 (PrimState m) DIM2 Int -> (DIM2 -> m Int) -> MArr0 (PrimState m) DIM2 Int -> (DIM2 -> m Int) -> m ()