BiobaseVienna 0.2.2.2 → 0.2.2.3

raw patch · 2 files changed

+11/−7 lines, 2 filesPVP: minor bump suggested

API additions: PVP suggests at least a minor version bump

API changes (from Hackage documentation)

Files

• Biobase/Vienna/ImportPar.hs +10/−6
• BiobaseVienna.cabal +1/−1

@@ -15,6 +15,7 @@ import Data.Array.Repa.Shape import qualified Data.Map as M import Control.Monad.Identity+import Data.Maybe (fromJust)  import Data.PrimitiveArray import Data.PrimitiveArray.Unboxed.Zero@@ -24,8 +25,10 @@ import Biobase.Vienna import Biobase.Vienna.Import +import Debug.Trace  + -- | split the input into different blocks. Each block has a name (prefixed # -- in the file) and some data. @@ -93,11 +96,11 @@         , iloop1xnMM = blockAssocs minPBB maxPBB pbbKeys $ lookup "# mismatch_interior_1n" bs         , iloopL = blockAssocs (Z:.0) (Z:.30) thirty $ lookup "# interior" bs         , multiMM = blockAssocs minPBB maxPBB pbbKeys $ lookup "# mismatch_multi" bs-        , ninio = 999999-        , maxNinio = 999999-        , multiOffset = 999999-        , multiNuc = 999999-        , multiHelix = 999999+        , ninio = single 0 $ lookup "# NINIO" bs+        , maxNinio = single 2 $ lookup "# NINIO" bs+        , multiOffset = single 2 $ lookup "# ML_params" bs+        , multiNuc = single 0 $ lookup "# ML_params" bs+        , multiHelix = single 4 $ lookup "# ML_params" bs         , multiAsym = 999999         , multiStrain = 999999         , extMM = blockAssocs minPBB maxPBB pbbKeys $ lookup "# mismatch_exterior" bs@@ -105,7 +108,7 @@         , coaxStack = fromAssocs minPBB maxPBB 999999 []         , tStackCoax = fromAssocs minPBB maxPBB 999999 []         , largeLoop = 999999-        , termAU = 999999+        , termAU = single 2 $ lookup "# Misc" bs         , intermolecularInit = 999999         }       vEnth = Vienna2004@@ -146,6 +149,7 @@         }   in (vEner,vEnth) +single k (Just (Block xs)) = xs !! k thirty = P.map (Z:.) [0..30] pbKeys = [ (Z:.x:.y) | x<-cgnsP, y<-nacgu ] ppKeys = [ (Z:.x:.y) | x<-cgnsP, y<-cgnsP ]

@@ -1,5 +1,5 @@ name:           BiobaseVienna-version:        0.2.2.2+version:        0.2.2.3 author:         Christian Hoener zu Siederdissen maintainer:     choener@tbi.univie.ac.at homepage:       http://www.tbi.univie.ac.at/~choener/