BioInf.RNAfold.Library

A library of helpers for ADPfusion algorithms.

Documentation

base' :: Primary -> DIM2 -> Scalar Nuc

baseLr' :: Primary -> DIM2 -> Scalar (Nuc :!: Nuc)

Nucleotide, second one to the right. The assertion allows a size of one or two to capture special cases of looking outside of the bounds (used by justStemF in RNAfold).

baselR' :: Primary -> DIM2 -> Scalar (Nuc :!: Nuc)

region' :: Vector Nuc -> DIM2 -> Scalar (Vector Nuc)

primary' :: Primary -> DIM2 -> Scalar ((Primary :!: Int) :!: Int)

A Primary together with the lowest included nucleotide and the highest included nucleotide.

primaryPR' :: Primary -> DIM2 -> Scalar ((Primary :!: Int) :!: Int)

A Primary together with the lowest included nucleotide and the highest included nucleotide.

primaryPL' :: Primary -> DIM2 -> Scalar ((Primary :!: Int) :!: Int)

A Primary together with the lowest included nucleotide and the highest included nucleotide.

regionpl' :: Vector Nuc -> DIM2 -> Scalar (Vector Nuc)

Vector of nucleotides peeking one nucleotide to the left.

regionpr' :: Vector Nuc -> DIM2 -> Scalar (Vector Nuc)

Vector of nucleotides peeaking one nucleotide to the right.

basepairing' :: (Num t, Ord t, MkViennaPair (elm, elm), PrimArrayOps arr (:. Z t) elm) => arr (:. Z t) elm -> :. (:. Z t) t -> Bool

Tests if (i,j) is a valid base pair.

stackpairing' :: (Enum t, Num t, Ord t, MkViennaPair (elm, elm), PrimArrayOps arr (:. Z t) elm) => arr (:. Z t) elm -> t -> :. (:. Z t) t -> Bool

constrained :: (t1 -> t) -> t1 -> t

reglen' :: Primary -> DIM2 -> Scalar Int

reglenpl' :: Primary -> DIM2 -> Scalar (Nuc, Nuc, Int)

reglenpr' :: Primary -> DIM2 -> Scalar (Int, Nuc, Nuc)

empty :: DIM2 -> Scalar Bool

True, if the subword at ij is empty.