BiobaseXNA- Efficient RNA/DNA representations




A special class of bounds for RNA/pair encodings that are used to index into tables. We typically encode more in the alphabets than we want to use to index, so in order to keep things simple, we have specialized bounds.



class Bounded a => Bounds a whereSource

minNormal and maxNormal encode for, say, ACGU; while minExtended and maxExtended would allow N as well. See Biobase.RNA and Biobase.RNA.ViennaPair for instances.


Bounds Nuc

Special bounds for energy / score arrays

Bounds CTisomerism 
Bounds Edge 
Bounds ViennaPair 
(Bounds a, Bounds b) => Bounds (a, b) 
(Bounds a, Bounds b, Bounds c) => Bounds (a, b, c) 
(Bounds a, Bounds b, Bounds c, Bounds d) => Bounds (a, b, c, d) 
(Bounds a, Bounds b, Bounds c, Bounds d, Bounds e) => Bounds (a, b, c, d, e) 
(Bounds a, Bounds b, Bounds c, Bounds d, Bounds e, Bounds f) => Bounds (a, b, c, d, e, f) 

Instances for tuples of size 2-6