name:           RNAFold
version:        0.0.2.1
author:         Christian Hoener zu Siederdissen (Haskell), Ivo L. Hofacker et al (ViennaRNA)
maintainer:     choener@tbi.univie.ac.at
copyright:      Christian Hoener zu Siederdissen, 2010
category:       Bioinformatics
synopsis:       RNA secondary structure prediction
license:        GPL-3
license-file:   LICENSE
build-type:     Simple
stability:      experimental
cabal-version:  >= 1.4.0
description:
                Provides the folding functions as used in the ViennaRNA
                package. Here, they are in Haskell form to be used by Haskell
                programs.
                .
                - This is a release aimed at testing Data.Vector
                - Expect major performance issues with GHC < 6.13!

library
  build-depends:
    base >=4 && <5,
    containers,
    vector >=0.7,
    primitive >=0.3,

    Biobase >=0.0.2,
    BiobaseTurner >=0.0.2,
    BiobaseVienna >=0.0.2,
    BiobaseTypes >=0.0.2,
    HsTools >=0.0.1.1,
    PrimitiveArray >=0.0.2 && <0.0.3

  exposed-modules:
    BioInf.RNAFold,
    BioInf.RNAFold.Energy,
    BioInf.RNAFold.EnergyInt,
    BioInf.RNAEval,
    BioInf.RNAFold.Functions

  if impl(ghc > 6.13)
    ghc-options:
      -Odph
      -fllvm
      -fforce-recomp
      -funbox-strict-fields
      -fllvm
      -optlo-O3
      -optlc-O3
      -fdicts-cheap
      -fspec-constr
      -funbox-strict-fields
      -funfolding-use-threshold=100
      -funfolding-creation-threshold=100
  else
    ghc-options:-Odph

--    -fno-method-sharing -- performance does not improve!
--    -fdicts-cheap
--    -fspec-constr
--    -funbox-strict-fields
--    -funfolding-use-threshold=100
--    -funfolding-creation-threshold=100