diff --git a/Diagrams/TwoD/ProbabilityGrid.hs b/Diagrams/TwoD/ProbabilityGrid.hs new file mode 100644 --- /dev/null +++ b/Diagrams/TwoD/ProbabilityGrid.hs @@ -0,0 +1,67 @@ + +-- | Probability grid square drawing routines. + +module Diagrams.TwoD.ProbabilityGrid where + +import Data.List (genericLength) +import Data.List.Split (chunksOf) +import Diagrams.Backend.Postscript +import Diagrams.Backend.SVG +import Diagrams.Prelude +import Diagrams.TwoD +import Diagrams.TwoD.Text +import Numeric.Log + + + +-- | Fill weight for our grid. If the fill weight is @logarithmic@, then +-- the line length is @1 / (1 + log value)@ otherwise it is @value@. + +data FillWeight = FWlog | FWlinear + +-- | A single square in our grid. + +-- gridSquare :: FillWeight -> Log Double +gridSquare + :: (Monoid m, Semigroup m, TrailLike (QDiagram b V2 Double m)) + => FillWeight -> Log Double -> QDiagram b V2 Double m +gridSquare (fw :: FillWeight) (v :: Log Double) = g `beneath` (z # scale s) + where s = case fw of + FWlog -> 1 / (1 - ln v) + FWlinear -> exp $ ln v + z = square 1 # lw 0 # fc blue # centerXY + g = square 1 # lc black + +-- | Draw the actual grid. + +grid + :: ( Renderable (Diagrams.TwoD.Text.Text Double) b + , Renderable (Path V2 Double) b) + => FillWeight + -> t + -> Int + -> [String] + -> [String] + -> [Log Double] + -> QDiagram b V2 Double Any +grid (fw :: FillWeight) n m (ns :: [String]) (ms :: [String]) (vs :: [Log Double]) + | null ns && null ms = grd + | otherwise = (grd ||| ns') === ms' + where ns' = if null ns then mempty else vcat $ map (\t -> (square 1) `beneath` (text t # scale (0.9 / genericLength t))) ns + ms' = if null ms then mempty else hcat $ map (\t -> (square 1) `beneath` (text t # scale (0.9 / genericLength t))) ms + grd = vcat $ map hcat $ map (map (gridSquare fw)) $ chunksOf m $ vs + +-- | Render as @svg@. + +svgGridFile :: FilePath -> FillWeight -> Int -> Int -> [String] -> [String] -> [Log Double] -> IO () +svgGridFile fname fw n m ns ms vs = renderPretty fname size $ g + where size = ((*100) . fromIntegral) <$> mkSizeSpec2D (Just m) (Just n) -- Nothing Nothing -- n n + g = grid fw n m ns ms vs + +-- | Render as @eps@. + +epsGridFile :: String -> FillWeight -> Int -> Int -> [String] -> [String] -> [Log Double] -> IO () +epsGridFile fname fw n m ns ms vs = renderDia Postscript (PostscriptOptions fname size EPS) g + where size = ((*100) . fromIntegral) <$> mkSizeSpec2D (Just m) (Just n) + g = grid fw n m ns ms vs + diff --git a/LICENSE b/LICENSE new file mode 100644 --- /dev/null +++ b/LICENSE @@ -0,0 +1,30 @@ +Copyright Christian Hoener zu Siederdissen 2016 + +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + + * Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following + disclaimer in the documentation and/or other materials provided + with the distribution. + + * Neither the name of Christian Hoener zu Siederdissen nor the names of other + contributors may be used to endorse or promote products derived + from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/PrimitiveArray-Pretty.cabal b/PrimitiveArray-Pretty.cabal new file mode 100644 --- /dev/null +++ b/PrimitiveArray-Pretty.cabal @@ -0,0 +1,81 @@ +Name: PrimitiveArray-Pretty +Version: 0.0.0.1 +License: BSD3 +License-file: LICENSE +Maintainer: choener@bioinf.uni-leipzig.de +author: Christian Hoener zu Siederdissen, 2016 +copyright: Christian Hoener zu Siederdissen, 2016 +homepage: https://github.com/choener/PrimitiveArray-Pretty +bug-reports: https://github.com/choener/PrimitiveArray-Pretty/issues +Stability: Experimental +Category: Data +Build-type: Simple +Cabal-version: >=1.10.0 +tested-with: GHC == 7.8.4, GHC == 7.10.3 +Synopsis: Pretty-printing for primitive arrays +Description: + + . + A Pretty-printer for Primitive Arrays. + . + The idea is not so much to provide pretty-printing for single + arrays, but rather to allow for simple prettyfication of + typical array data. In particular we want to have simplified + pretty-printing of Inside/Outside combinations of arrays. + + + +extra-source-files: + README.md + changelog.md + + + +Library + Exposed-modules: + Diagrams.TwoD.ProbabilityGrid + build-depends: base >= 4.7 && < 4.9 + , diagrams >= 1.3 && < 1.4 + , diagrams-lib >= 1.3 && < 1.4 + , diagrams-svg >= 1.3 && < 1.4 + , diagrams-postscript >= 1.3 && < 1.4 + , log-domain >= 0.10 && < 0.11 + , split >= 0.2 && < 0.3 + default-extensions: BangPatterns + , TypeFamilies + , FlexibleContexts + , ScopedTypeVariables + default-language: + Haskell2010 + ghc-options: + -O2 + -funbox-strict-fields + + + +test-suite properties + type: + exitcode-stdio-1.0 + main-is: + properties.hs + ghc-options: + -threaded -rtsopts -with-rtsopts=-N + hs-source-dirs: + tests + default-language: + Haskell2010 + default-extensions: CPP + , TemplateHaskell + build-depends: base + , PrimitiveArray-Pretty + , QuickCheck + , test-framework >= 0.8 && < 0.9 + , test-framework-quickcheck2 >= 0.3 && < 0.4 + , test-framework-th >= 0.2 && < 0.3 + + + +source-repository head + type: git + location: git://github.com/choener/PrimitiveArray-Pretty + diff --git a/README.md b/README.md new file mode 100644 --- /dev/null +++ b/README.md @@ -0,0 +1,18 @@ +[![Build Status](https://travis-ci.org/choener/PrimitiveArray-Pretty.svg?branch=master)](https://travis-ci.org/choener/PrimitiveArray-Pretty) + +# PrimitiveArray-Pretty + +[*generalized Algebraic Dynamic Programming Homepage*](http://www.bioinf.uni-leipzig.de/Software/gADP/) + +Prettyprinting for tables that holds probability information. Currently mostly +useful for pretty-printing the result of Inside-Outside calculations. + + + +#### Contact + +Christian Hoener zu Siederdissen +Leipzig University, Leipzig, Germany +choener@bioinf.uni-leipzig.de +http://www.bioinf.uni-leipzig.de/~choener/ + diff --git a/Setup.hs b/Setup.hs new file mode 100644 --- /dev/null +++ b/Setup.hs @@ -0,0 +1,2 @@ +import Distribution.Simple +main = defaultMain diff --git a/changelog.md b/changelog.md new file mode 100644 --- /dev/null +++ b/changelog.md @@ -0,0 +1,4 @@ +0.0.0.1 +------- + +- initial checkin diff --git a/tests/properties.hs b/tests/properties.hs new file mode 100644 --- /dev/null +++ b/tests/properties.hs @@ -0,0 +1,8 @@ + +module Main where + + + +main :: IO () +main = return () +