packages feed

BiobaseTurner 0.2.0.0 → 0.2.2.0

raw patch · 3 files changed

+27/−33 lines, 3 filesdep −repadep ~BiobaseXNAdep ~PrimitiveArraydep ~vectorPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

Dependencies removed: repa

Dependency ranges changed: BiobaseXNA, PrimitiveArray, vector

API changes (from Hackage documentation)

- Biobase.Turner: instance Show Turner2004
+ Biobase.Turner.Import: allEq :: Eq a => [a] -> Bool
+ Biobase.Turner.Import: d1_30 :: (Enum a, Num a) => [:. Z a]
+ Biobase.Turner.Import: infE :: Double
+ Biobase.Turner.Import: keysPB :: [:. (:. (:. Z Nuc) Nuc) Nuc]
+ Biobase.Turner.Import: keysPBB :: [:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc]
+ Biobase.Turner.Import: keysPP :: [:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc]
+ Biobase.Turner.Import: keysPPBB :: [:. (:. (:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc) Nuc) Nuc]
+ Biobase.Turner.Import: keysPPBBB :: [:. (:. (:. (:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc]
+ Biobase.Turner.Import: keysPPBBBBdna :: [:. (:. (:. (:. (:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc]
+ Biobase.Turner.Import: keysPPBBBBrna :: [:. (:. (:. (:. (:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc]
+ Biobase.Turner.Import: maxP :: :. (:. Z Nuc) Nuc
+ Biobase.Turner.Import: maxPB :: :. (:. (:. Z Nuc) Nuc) Nuc
+ Biobase.Turner.Import: maxPBB :: :. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc
+ Biobase.Turner.Import: maxPP :: :. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc
+ Biobase.Turner.Import: maxPPBB :: :. (:. (:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc) Nuc) Nuc
+ Biobase.Turner.Import: maxPPBBB :: :. (:. (:. (:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc
+ Biobase.Turner.Import: maxPPBBBB :: :. (:. (:. (:. (:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc
+ Biobase.Turner.Import: minP :: :. (:. Z Nuc) Nuc
+ Biobase.Turner.Import: minPB :: :. (:. (:. Z Nuc) Nuc) Nuc
+ Biobase.Turner.Import: minPBB :: :. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc
+ Biobase.Turner.Import: minPP :: :. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc
+ Biobase.Turner.Import: minPPBB :: :. (:. (:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc) Nuc) Nuc
+ Biobase.Turner.Import: minPPBBB :: :. (:. (:. (:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc
+ Biobase.Turner.Import: minPPBBBB :: :. (:. (:. (:. (:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc
+ Biobase.Turner.Import: plist11 :: [(Nuc, Nuc)]
+ Biobase.Turner.Import: plist22dna :: [(Nuc, Nuc)]
+ Biobase.Turner.Import: plist22rna :: [(Nuc, Nuc)]
- Biobase.Turner: Turner2004 :: PrimArray PP Double -> PrimArray PN Double -> PrimArray PN Double -> PrimArray DIM1 Double -> PrimArray PNN Double -> Map ByteString Double -> Double -> Double -> Double -> Double -> PrimArray DIM1 Double -> Double -> PrimArray PPNN Double -> PrimArray PPNNN Double -> PrimArray PPNNNN Double -> PrimArray PNN Double -> PrimArray PNN Double -> PrimArray PNN Double -> PrimArray DIM1 Double -> PrimArray PNN Double -> Double -> Double -> Double -> Double -> Double -> Double -> Double -> PrimArray PNN Double -> PrimArray PP Double -> PrimArray PNN Double -> PrimArray PNN Double -> Double -> Double -> Double -> Turner2004
+ Biobase.Turner: Turner2004 :: Arr0 PP Double -> Arr0 PN Double -> Arr0 PN Double -> Arr0 DIM1 Double -> Arr0 PNN Double -> Map ByteString Double -> Double -> Double -> Double -> Double -> Arr0 DIM1 Double -> Double -> Arr0 PPNN Double -> Arr0 PPNNN Double -> Arr0 PPNNNN Double -> Arr0 PNN Double -> Arr0 PNN Double -> Arr0 PNN Double -> Arr0 DIM1 Double -> Arr0 PNN Double -> Double -> Double -> Double -> Double -> Double -> Double -> Double -> Arr0 PNN Double -> Arr0 PP Double -> Arr0 PNN Double -> Arr0 PNN Double -> Double -> Double -> Double -> Turner2004
- Biobase.Turner: bulgeL :: Turner2004 -> PrimArray DIM1 Double
+ Biobase.Turner: bulgeL :: Turner2004 -> Arr0 DIM1 Double
- Biobase.Turner: coaxStack :: Turner2004 -> PrimArray PNN Double
+ Biobase.Turner: coaxStack :: Turner2004 -> Arr0 PNN Double
- Biobase.Turner: coaxial :: Turner2004 -> PrimArray PP Double
+ Biobase.Turner: coaxial :: Turner2004 -> Arr0 PP Double
- Biobase.Turner: dangle3 :: Turner2004 -> PrimArray PN Double
+ Biobase.Turner: dangle3 :: Turner2004 -> Arr0 PN Double
- Biobase.Turner: dangle5 :: Turner2004 -> PrimArray PN Double
+ Biobase.Turner: dangle5 :: Turner2004 -> Arr0 PN Double
- Biobase.Turner: extMM :: Turner2004 -> PrimArray PNN Double
+ Biobase.Turner: extMM :: Turner2004 -> Arr0 PNN Double
- Biobase.Turner: hairpinL :: Turner2004 -> PrimArray DIM1 Double
+ Biobase.Turner: hairpinL :: Turner2004 -> Arr0 DIM1 Double
- Biobase.Turner: hairpinMM :: Turner2004 -> PrimArray PNN Double
+ Biobase.Turner: hairpinMM :: Turner2004 -> Arr0 PNN Double
- Biobase.Turner: iloop1x1 :: Turner2004 -> PrimArray PPNN Double
+ Biobase.Turner: iloop1x1 :: Turner2004 -> Arr0 PPNN Double
- Biobase.Turner: iloop1xnMM :: Turner2004 -> PrimArray PNN Double
+ Biobase.Turner: iloop1xnMM :: Turner2004 -> Arr0 PNN Double
- Biobase.Turner: iloop2x1 :: Turner2004 -> PrimArray PPNNN Double
+ Biobase.Turner: iloop2x1 :: Turner2004 -> Arr0 PPNNN Double
- Biobase.Turner: iloop2x2 :: Turner2004 -> PrimArray PPNNNN Double
+ Biobase.Turner: iloop2x2 :: Turner2004 -> Arr0 PPNNNN Double
- Biobase.Turner: iloop2x3MM :: Turner2004 -> PrimArray PNN Double
+ Biobase.Turner: iloop2x3MM :: Turner2004 -> Arr0 PNN Double
- Biobase.Turner: iloopL :: Turner2004 -> PrimArray DIM1 Double
+ Biobase.Turner: iloopL :: Turner2004 -> Arr0 DIM1 Double
- Biobase.Turner: iloopMM :: Turner2004 -> PrimArray PNN Double
+ Biobase.Turner: iloopMM :: Turner2004 -> Arr0 PNN Double
- Biobase.Turner: multiMM :: Turner2004 -> PrimArray PNN Double
+ Biobase.Turner: multiMM :: Turner2004 -> Arr0 PNN Double
- Biobase.Turner: stack :: Turner2004 -> PrimArray PP Double
+ Biobase.Turner: stack :: Turner2004 -> Arr0 PP Double
- Biobase.Turner: tStackCoax :: Turner2004 -> PrimArray PNN Double
+ Biobase.Turner: tStackCoax :: Turner2004 -> Arr0 PNN Double

Files

Biobase/Turner.hs view
@@ -16,7 +16,7 @@ import Biobase.Primary import Biobase.Secondary import Data.PrimitiveArray-import Data.PrimitiveArray.Unboxed+import Data.PrimitiveArray.Unboxed.Zero  -- | The parameters. Turner parameters are set by the Import module for -- nucleotides n,a,c,g,u. All values that are not read (or are ".") will end up@@ -34,26 +34,26 @@ type PPNNNN = PPNNN:.Nuc  data Turner2004 = Turner2004-  { stack :: PrimArray PP Double-  , dangle3 :: PrimArray PN Double-  , dangle5 :: PrimArray PN Double-  , hairpinL :: PrimArray DIM1 Double-  , hairpinMM :: PrimArray PNN Double+  { stack :: Arr0 PP Double+  , dangle3 :: Arr0 PN Double+  , dangle5 :: Arr0 PN Double+  , hairpinL :: Arr0 DIM1 Double+  , hairpinMM :: Arr0 PNN Double   , hairpinLookup :: M.Map ByteString Double   , hairpinGGG :: Double   , hairpinCslope :: Double   , hairpinCintercept :: Double   , hairpinC3 :: Double-  , bulgeL :: PrimArray DIM1 Double+  , bulgeL :: Arr0 DIM1 Double   , bulgeSingleC :: Double-  , iloop1x1 :: PrimArray PPNN Double-  , iloop2x1 :: PrimArray PPNNN Double-  , iloop2x2 :: PrimArray PPNNNN Double-  , iloopMM :: PrimArray PNN Double-  , iloop2x3MM :: PrimArray PNN Double-  , iloop1xnMM :: PrimArray PNN Double-  , iloopL :: PrimArray DIM1 Double-  , multiMM :: PrimArray PNN Double+  , iloop1x1 :: Arr0 PPNN Double+  , iloop2x1 :: Arr0 PPNNN Double+  , iloop2x2 :: Arr0 PPNNNN Double+  , iloopMM :: Arr0 PNN Double+  , iloop2x3MM :: Arr0 PNN Double+  , iloop1xnMM :: Arr0 PNN Double+  , iloopL :: Arr0 DIM1 Double+  , multiMM :: Arr0 PNN Double   , ninio :: Double   , maxNinio :: Double   , multiOffset :: Double@@ -61,12 +61,12 @@   , multiHelix :: Double   , multiAsym :: Double   , multiStrain :: Double-  , extMM :: PrimArray PNN Double-  , coaxial :: PrimArray PP Double -- no intervening unpaired nucleotides-  , coaxStack :: PrimArray PNN Double-  , tStackCoax :: PrimArray PNN Double+  , extMM :: Arr0 PNN Double+  , coaxial :: Arr0 PP Double -- no intervening unpaired nucleotides+  , coaxStack :: Arr0 PNN Double+  , tStackCoax :: Arr0 PNN Double   , largeLoop :: Double   , termAU :: Double   , intermolecularInit :: Double-  } deriving (Show)+  } deriving ()
Biobase/Turner/Import.hs view
@@ -37,6 +37,7 @@ module Biobase.Turner.Import where  import Control.Arrow+import Data.Array.Repa.Index import Data.ByteString.Char8 as BS import Data.ByteString.Lex.Double import Data.Char@@ -45,10 +46,9 @@ import Data.Iteratee.IO as I import Data.List.Split import Data.Map as M+import Data.Maybe (fromJust) import qualified Data.List as L import System.FilePath.Posix-import Data.Maybe (fromJust)-import Data.Array.Repa.Index  import Biobase.Primary import Biobase.Secondary@@ -233,18 +233,13 @@ miscFromFile :: FilePath -> IO [[Double]] miscFromFile fp = run =<< enumFile 8192 fp iMiscLoop --- | +-- |  tabFromFile :: FilePath -> IO [(ByteString,Double)] tabFromFile fp = run =<< enumFile 8192 fp iTabulated  allEq [] = True allEq (x:xs) = L.all (==x) xs--{--test1 = blockFromFile "/home/choener/Documents/Workdata/TurnerRNA2004/RNA/loop.dat"-test2 = fromDir "/home/choener/Documents/Workdata/TurnerRNA2004/RNA" "" ".dat"--}  type Prefix = FilePath type Suffix = FilePath
BiobaseTurner.cabal view
@@ -1,5 +1,5 @@ name:           BiobaseTurner-version:        0.2.0.0+version:        0.2.2.0 author:         Christian Hoener zu Siederdissen maintainer:     choener@tbi.univie.ac.at homepage:       http://www.tbi.univie.ac.at/~choener/@@ -40,10 +40,9 @@     filepath,     iteratee,     split,-    BiobaseXNA >= 0.6.0.0,-    vector >= 0.9,-    repa >= 2.0,-    PrimitiveArray >= 0.1.1.2+    vector         == 0.9.*   ,+    BiobaseXNA     == 0.6.2.0 ,+    PrimitiveArray == 0.2.0.0    exposed-modules:     Biobase.Turner