| Safe Haskell | None |
|---|---|
| Language | Haskell2010 |
Biobase.Secondary.Pseudoknots
Description
Methods to transform a secondary structure containing pseudoknots into a structure which is pseudoknot-free.
TODO Until a better name is found, this module is home to functions for "de-pseudoknotting" structures.
TODO Check if there are corner-cases remaining when considering 2-diagrams.
Synopsis
- class RemovePseudoKnots a where
- removeByCounting :: a -> a
Documentation
class RemovePseudoKnots a where Source #
Try to removed pseudoknots from the "pairlist". This works by counting for each pair, how many pairs are incompatible with it. Then those with most incompatibilities are successively removed. This function might well remove more than necessary!
Methods
removeByCounting :: a -> a Source #
Instances
| RemovePseudoKnots [ExtPairIdx] Source # | |
Defined in Biobase.Secondary.Pseudoknots Methods removeByCounting :: [ExtPairIdx] -> [ExtPairIdx] Source # | |
| RemovePseudoKnots [PairIdx] Source # | |
Defined in Biobase.Secondary.Pseudoknots Methods removeByCounting :: [PairIdx] -> [PairIdx] Source # | |
| RemovePseudoKnots (Vector ExtPairIdx) Source # | Remove pseudoknotted pairs from extended RNA secondary structures. |
Defined in Biobase.Secondary.Pseudoknots Methods removeByCounting :: Vector ExtPairIdx -> Vector ExtPairIdx Source # | |
| RemovePseudoKnots (Vector PairIdx) Source # | Remove pseudoknotted pairs from RNA secondary structures. |
Defined in Biobase.Secondary.Pseudoknots | |