name:           RNAwolf
version:        0.3.2.0
author:         Christian Hoener zu Siederdissen, Stephan H Bernhart, Peter F Stadler, Ivo L Hofacker
copyright:      Christian Hoener zu Siederdissen, 2010-2011
homepage:       http://www.tbi.univie.ac.at/software/rnawolf/
maintainer:     choener@tbi.univie.ac.at
category:       Bioinformatics
license:        GPL-3
license-file:   LICENSE
build-type:     Simple
stability:      experimental
cabal-version:  >= 1.6.0
synopsis:
                RNA folding with non-canonical basepairs and base-triplets.
description:
                The algorithm implemented here-in provides extended RNA
                secondary structure prediction. Each predicted nucleotide
                pairing is extended with an annotation describing which of
                three nucleotide edges is engaged in the pairing. In addition,
                each nucleotide may be engaged in more than one pairing.
                .
                .
                The algorithm is described in
                .
                Hoener zu Siederdissen C, Bernhart SH, Stadler PF, Hofacker IL,
                .
                "A Folding Algorithm for Extended RNA Secondary Structures",
                .
                Bioinformatics (2011) 27 (13), i129-136
                .
                <http://www.tbi.univie.ac.at/software/rnawolf/>
                .
                .
                Please note that "experimental" does mean experimental. We are
                mostly concerned with determining a good set of (heuristic)
                rules for run-time reduction currently. This version does
                include stacking and is able to fold sequences of a few hundred
                nucleotides in seconds.
                .
                Triplet calculations will come back with the next version (in a
                few days). The recursions require a number of changes to keep
                the runtimes down (as has been done for the extended loops
                without triplets).
                .
                We have recently split the Biohaskell libraries into smaller
                individual libraries. In addition, stacking, intermediate
                arrays, fusion and newtype-wrapping did require a number of
                changes. Please send a mail, if you encounter strange behaviour
                or bugs.
                .
                Changes in 0.3.2.0
                .
                * simpler training wrapper
                .
                * added parallelism option for multi-core systems (reduce
                  iteration time for the cost of a possible reduction in
                  training efficiency; but should be worth it)
                .
                Changes in 0.3.1.0
                .
                * fixed bugs introduced by bulge/interior/multi-loops

Flag llvm
  description: build using llvm backend
  default: False

library
  build-depends:
    base >= 4 && < 5,
    bytestring,
    containers,
    deepseq,
    directory,
    parallel,
    random,
    vector,
    PrimitiveArray,
    BiobaseXNA,
    BiobaseTrainingData >= 0.1.2.2,
    StatisticalMethods
  exposed-modules:
    BioInf.Keys
    BioInf.Params
    BioInf.Params.Export
    BioInf.Params.Import
    BioInf.PassiveAggressive
    BioInf.RNAwolf
    BioInf.RNAwolf.Bulge
    BioInf.RNAwolf.Extern
    BioInf.RNAwolf.Hairpin
    BioInf.RNAwolf.Interior
    BioInf.RNAwolf.Multibranched
    BioInf.RNAwolf.Stem
    BioInf.RNAwolf.TripletBulge
    BioInf.RNAwolf.TripletStem
    BioInf.RNAwolf.Types

  ghc-options:
    -O2
  if flag(llvm)
    ghc-options:
      -fllvm

executable RNAwolfTrain
  build-depends:
    split,
    cmdargs == 0.7.*
  main-is:
    RNAwolfTrain.hs
  ghc-options:
    -O2 -rtsopts -threaded
  if flag(llvm)
    ghc-options:
      -fllvm

executable RNAwolf
  build-depends:
    cmdargs == 0.7.*
  main-is:
    RNAwolf.hs
  ghc-options:
    -O2 -rtsopts
  if flag(llvm)
    ghc-options:
      -fllvm