BioInf.MCFoldDP

TODO bonus system for matching () bracking still broken?!

Documentation

fold :: MotifDB -> Primary -> Constraint -> Tables

Folding wrapper

foldST :: MotifDB -> Primary -> Constraint -> ST s Tables

Folding in the ST monad. the number of dncm tables is the same as the number of known double NCMs.

backtrack :: MotifDB -> Double -> Primary -> Constraint -> Tables -> [(Double, D1Secondary)]

Backtracking suboptimal results

Combining NCMs

fncmSingle :: MotifDB -> Primary -> Constraint -> Int -> Int -> Double

singleNCM insertion

fncmDS :: MotifDB -> Primary -> Constraint -> Int -> Int -> Int -> Int -> Table2 -> Double

double NCM extend single NCM. We do not care that this is comparatively slow as it is called only a few times, anyway.

TODO make faster (better lookup system) TODO otherwise case TODO eats another ~10% performance

fncmDD :: MotifDB -> Primary -> Constraint -> Int -> Int -> Int -> Int -> [Table2] -> Vector (Int, Double)

double NCM extending another double NCM.

TODO this one could profit from performance improvements. But check first vs. multibranch timings TODO remove otherwise case TODO improve performance, eats ~66% of total time TODO improve: return empty vector on error, write special minimum function that has eInf on empty

fStemExt :: [Table2] -> Int -> Int -> Vector (Int, Int, Double)

Add one stem for external calculations

TODO make efficient

fStemExtExt :: [Table2] -> Table2 -> Int -> Int -> Vector (Int, Int, Double)

Combine stems for external calculations

fMulti :: MotifDB -> Primary -> Constraint -> Int -> Int -> Table2 -> Table2 -> Vector (Int, Double)

Close a multibranched loop with a singleNCM

TODO close with singleNCM

fMMbrStem :: Int -> Int -> Table2 -> Table2 -> Vector (Int, Double)

Connect a partial multibranched structure with a hairpin. Note that the dncm hairpin part wants one table, not the list of all tables.

fMStem :: Int -> Int -> Table2 -> Vector (Int, Double)

Add the first stem

fInterior :: MotifDB -> Primary -> Constraint -> Int -> Int -> Table2 -> Vector ((Int, Int), Double)

Interior loops of some size

TODO this could profit from a log-based scoring function

Helper functions

mkTable2 :: (Num t, Constants b, PrimArrayOpsM (t, t) b m) => t -> m (PrimArray (t, t) b, PrimArrayM (t, t) b m)

The default two-dim table

mkTable2With :: (Num t, PrimArrayOpsM (t, t) b m) => b -> t -> m (PrimArray (t, t) b, PrimArrayM (t, t) b m)

Create a 2-dim table

vuminimumP :: (Ord a, Constants a, Unbox t, Unbox a) => Vector (t, a) -> a

minimum for unboxed vectors, capturing possible 0-length. Vectors in this algorithm always carry positional information.

TODO the next version of the vector library should handle VU.map snd better

vuminimum :: (Ord a, Constants a, Unbox a) => Vector a -> a

types and constants

type Table2 = PrimArray (Int, Int) Double

type Table4 = PrimArray (Int, Int, Int, Int) Double

type Tables = (Table2, [Table2], Table2, Table2, Table2)

bonusScore :: Double

giveBonus :: Constraint -> Int -> Int -> Double

Give a certain bonusScore for the constraints that have been fulfilled.

TODO should we be more lenient with constraints that would increase the total energy?