BiobaseBlast-0.3.0.0: Biobase/SubstMatrix/Hints.hs

module Biobase.SubstMatrix.Hints where

import Statistics.Odds
import Numeric.Discretized

import Biobase.SubstMatrix.Types



-- | Provide recommendations for both, substitution matrix to use, and gap
-- cost.

recommendByQueryLength ∷ Int → (String, GapCost (DiscLogOdds Unknown))
recommendByQueryLength k
  | k <  35 = ("PAM30"   , gc ( -9) (-1))
  | k <= 50 = ("PAM70"   , gc (-10) (-1))
  | k <= 85 = ("BLOSUM80", gc (-10) (-1))
  | k >  85 = ("BLOSUM62", gc (-10) (-1))
  where gc init cont = GapCost { gcInit = DiscLogOdds $ Discretized init, gcCont = DiscLogOdds $ Discretized cont }