module Biobase.Secondary.Vienna where
import Data.Ix
import Data.Primitive.Types
import qualified Data.Vector.Generic as VG
import qualified Data.Vector.Generic.Mutable as VGM
import qualified Data.Vector.Unboxed as VU
import Data.Tuple (swap)
import Biobase.Primary
import Biobase.Primary.Bounds
newtype ViennaPair = ViennaPair Int
deriving (Eq,Ord,Ix)
(vpNP:vpCG:vpGC:vpGU:vpUG:vpAU:vpUA:vpNS:_) = map ViennaPair [0..]
class MkViennaPair a where
mkViennaPair :: a -> ViennaPair
fromViennaPair :: ViennaPair -> a
instance MkViennaPair (Nuc,Nuc) where
mkViennaPair (b1,b2)
| b1==nC&&b2==nG = vpCG
| b1==nG&&b2==nC = vpGC
| b1==nG&&b2==nU = vpGU
| b1==nU&&b2==nG = vpUG
| b1==nA&&b2==nU = vpAU
| b1==nU&&b2==nA = vpUA
| otherwise = vpNS
fromViennaPair p
| p==vpCG = (nC,nG)
| p==vpGC = (nG,nC)
| p==vpGU = (nG,nU)
| p==vpUG = (nU,nG)
| p==vpAU = (nA,nU)
| p==vpUA = (nU,nA)
| otherwise = error "non-standard pairs can't be backcasted"
deriving instance VGM.MVector VU.MVector ViennaPair
deriving instance VG.Vector VU.Vector ViennaPair
deriving instance VU.Unbox ViennaPair
deriving instance Prim ViennaPair
instance Enum ViennaPair where
toEnum x
| x>=0 && x<=7 = ViennaPair x
| otherwise = error $ "can't make to enum" ++ show x
fromEnum (ViennaPair x) = x
instance Bounded ViennaPair where
minBound = vpNP
maxBound = vpNS
instance Bounds ViennaPair where
minNormal = vpCG
maxNormal = vpUA
minExtended = vpNP
maxExtended = vpNS
instance Show ViennaPair where
show x
| Just s <- x `lookup` pairToString = s
instance Read ViennaPair where
readsPrec p [] = []
readsPrec p [x] = []
readsPrec p (x:y:xs)
| x ==' ' = readsPrec p (y:xs)
| Just n <- (x:y:[]) `lookup` s2p = [(n,xs)]
| otherwise = []
where s2p = (map swap pairToString)
revPair :: ViennaPair -> ViennaPair
revPair p
| p==vpCG = vpGC
| p==vpGC = vpCG
| p==vpGU = vpUG
| p==vpUG = vpGU
| p==vpAU = vpUA
| p==vpUA = vpAU
| p==vpNP = vpNP
| p==vpNS = vpNS
cguaP = [vpCG..vpUA]
cgnsP = [vpCG..vpNS]
pairToString = [(vpCG,"CG"),(vpGC,"GC"),(vpUA,"UA"),(vpAU,"AU"),(vpGU,"GU"),(vpUG,"UG"),(vpNS,"NS"),(vpNP,"NP")]