BioInf.RNAwolf.Extern
Contents
Description
External loops are complete substructures, of which zero to many sit on the chain of nucleotides.
- fLeftUnpaired :: BaseF (NExtn -> Features (Vector (PairIdx, Double)))
- btLeftUnpaired :: Params -> Primary -> NExtn -> NBT -> NBT
- fStem :: BaseF (NStem -> Features (Vector (PairIdx, Double)))
- btStem :: Params -> Primary -> NExtn -> NStem -> NBT -> NBT
- fOne :: BaseF (Features (Vector (PairIdx, Double)))
- btOne :: Params -> Primary -> NExtn -> NBT
- fStems :: BaseF (NStem -> NExtn -> Features (Vector (Int, Double)))
- btStems :: Params -> Primary -> NStem -> NExtn -> NBT -> NBT -> NBT
Unpaired left nucleotide
fLeftUnpaired :: BaseF (NExtn -> Features (Vector (PairIdx, Double)))Source
An external loop with an unpaired nucleotide to the left
btLeftUnpaired :: Params -> Primary -> NExtn -> NBT -> NBTSource
Backtracking a structure with an unpaired nucleotide to the left.
FIXME In btLeftUnpaired, allow only non-empty structures on the right. It would be nice to make the recursion scheme take care of that.
exactly one stem with indices (i,k), i<k<=j
fStem :: BaseF (NStem -> Features (Vector (PairIdx, Double)))Source
Energy for exactly one stem at (i,k)
btStem :: Params -> Primary -> NExtn -> NStem -> NBT -> NBTSource
Backtrack one stem with right index k.
The neutral element for energy. This is an unpaired stretch between (i,j)
fOne :: BaseF (Features (Vector (PairIdx, Double)))Source
This one is important as otherwise, some stretches of nucleotides will always have to be paired. (Obviously, I forgot to add this one for a time...)