diff --git a/FormalLanguage/GrammarProduct/Op/Add.hs b/FormalLanguage/GrammarProduct/Op/Add.hs --- a/FormalLanguage/GrammarProduct/Op/Add.hs +++ b/FormalLanguage/GrammarProduct/Op/Add.hs @@ -1,7 +1,7 @@ module FormalLanguage.GrammarProduct.Op.Add where -import Control.Lens hiding (outside) +import Control.Lens hiding (outside,indices) import Control.Lens.Fold import Control.Newtype import Data.List (genericReplicate) @@ -43,10 +43,11 @@ (l^.rules <> r^.rules) -- s (l^.params <> r^.params) + (l^.indices <> r^.indices) (l^.grammarName <> r^.grammarName) False where s | l^.start == r^.start = l^.start - | l^.start /= mempty && r^.start /= mempty = error "add new start symbol" + | l^.start /= mempty && r^.start /= mempty = l^.start -- error "add new start symbol" -- TODO to be discussed ?! | l^.start == mempty = r^.start | r^.start == mempty = l^.start diff --git a/FormalLanguage/GrammarProduct/Op/Linear.hs b/FormalLanguage/GrammarProduct/Op/Linear.hs --- a/FormalLanguage/GrammarProduct/Op/Linear.hs +++ b/FormalLanguage/GrammarProduct/Op/Linear.hs @@ -9,7 +9,7 @@ import Control.Arrow ((&&&)) import Data.Semigroup -import Control.Lens hiding (outside) +import Control.Lens hiding (outside,indices) import Control.Applicative import qualified Data.Set as S import Data.List (groupBy,nub) @@ -30,14 +30,15 @@ instance Semigroup (Linear Grammar) where - (Linear g) <> (Linear h) = Linear $ Grammar sv st tv io rs s p (g^.grammarName ++ h^.grammarName) False where -- ts ns es rs s (g^.name <> h^.name) where - sv = M.fromList . nub . map (_name &&& id) . concatMap _getSymbolList . uniqueSyntacticSymbols $ set rules rs def -- build a temporary @def@ grammar, extract symbols from that one - st = g^.synterms <> h^.synterms - tv = g^.termvars <> h^.termvars - io = g^.outside - rs = S.fromList [ direct l r | l <- g^..rules.folded, r <- h^..rules.folded ] - s = (g^.start) <> (h^.start) - p = (g^.params) <> (h^.params) + (Linear g) <> (Linear h) = Linear $ Grammar sv st tv io rs s p ixs (g^.grammarName ++ h^.grammarName) False where -- ts ns es rs s (g^.name <> h^.name) where + sv = M.fromList . nub . map (_name &&& id) . concatMap _getSymbolList . uniqueSyntacticSymbols $ set rules rs def -- build a temporary @def@ grammar, extract symbols from that one + st = g^.synterms <> h^.synterms + tv = g^.termvars <> h^.termvars + io = g^.outside + rs = S.fromList [ direct l r | l <- g^..rules.folded, r <- h^..rules.folded ] + s = (g^.start) <> (h^.start) + p = (g^.params) <> (h^.params) + ixs = (g^.indices) <> (h^.indices) direct l r = Rule (l^.lhs <> r^.lhs) (l^.attr <> r^.attr) (mergeRHS (l^.rhs) (r^.rhs)) {- ts = g^.tsyms <> h^.tsyms diff --git a/FormalLanguage/GrammarProduct/Op/Subtract.hs b/FormalLanguage/GrammarProduct/Op/Subtract.hs --- a/FormalLanguage/GrammarProduct/Op/Subtract.hs +++ b/FormalLanguage/GrammarProduct/Op/Subtract.hs @@ -3,7 +3,7 @@ import Control.Arrow ((&&&)) import Control.Lens.Fold -import Control.Lens hiding (outside) +import Control.Lens hiding (outside,indices) import Control.Newtype import Data.List (genericReplicate) import Data.Semigroup @@ -24,14 +24,15 @@ | dim l /= dim r = error $ printf "grammars %s and %s have different dimensions, cannot unify. (subtract)" (show l) (show r) | l^.outside /= r^.outside = error $ printf "grammars %s and %s have different inside/outside annotation." (show l) (show r) | otherwise = g - where sv = M.fromList . map ((_name &&& id) . fst) . uniqueSynVarsWithTape $ g - st = M.fromList . map ((_name &&& id) . fst) . uniqueSynTermsWithTape $ g - tv = M.fromList . map ((_name &&& id) . fst) . uniqueBindableTermsWithTape $ g - io = l^.outside - rs = (l^.rules) S.\\ (r^.rules) - s = if (anyOf (folded . lhs) ((l^.start) ==) rs) then l^.start else Symbol [] - p = M.union (l^.params) (r^.params) - g = Grammar sv st tv io rs s p (l^.grammarName ++ r^.grammarName) False + where sv = M.fromList . map ((_name &&& id) . fst) . uniqueSynVarsWithTape $ g + st = M.fromList . map ((_name &&& id) . fst) . uniqueSynTermsWithTape $ g + tv = M.fromList . map ((_name &&& id) . fst) . uniqueBindableTermsWithTape $ g + io = l^.outside + rs = (l^.rules) S.\\ (r^.rules) + s = if (anyOf (folded . lhs) ((l^.start) ==) rs) then l^.start else Symbol [] + p = M.union (l^.params) (r^.params) + ixs = M.union (l^.indices) (r^.indices) + g = Grammar sv st tv io rs s p ixs (l^.grammarName ++ r^.grammarName) False {- subtract l r diff --git a/GrammarProducts.cabal b/GrammarProducts.cabal --- a/GrammarProducts.cabal +++ b/GrammarProducts.cabal @@ -1,8 +1,9 @@ name: GrammarProducts -version: 0.1.0.0 +version: 0.1.1.0 author: Christian Hoener zu Siederdissen, 2013-2015 copyright: Christian Hoener zu Siederdissen, 2013-2015 -homepage: http://www.bioinf.uni-leipzig.de/gADP/ +homepage: https://github.com/choener/GrammarProducts +bug-reports: https://github.com/choener/GrammarProducts/issues maintainer: choener@bioinf.uni-leipzig.de category: Formal Languages, Bioinformatics license: GPL-3 @@ -13,6 +14,8 @@ tested-with: GHC == 7.8.4, GHC == 7.10.1 synopsis: Grammar products and higher-dimensional grammars description: + + . An algebra of liner and context-free grammars. . This library provides the implementation of our theory of @@ -35,25 +38,9 @@ pretty-printed in various ways (LaTeX, ANSI, Haskell module with signature and grammar). . - . - . - Formal background can be found in two papers: - . - @ - Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler. - Product Grammars for Alignment and Folding. - 2014. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 99. - - @ - . - and - . - @ - Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler - How to Multiply Dynamic Programming Algorithms - Brazilian Symposium on Bioinformatics (BSB 2013) - Lecture Notes in Bioinformatics 8213, Springer, Heidelberg - @ + The formal background can be found in two papers given in the + README. The gADP homepage has further details, tutorials, + examples. . @@ -69,23 +56,20 @@ default: False manual: True -flag llvm - description: build using LLVM - default: False - manual: True - library build-depends: base >= 4.7 && < 4.9 + , ADPfusion >= 0.4.1 && < 0.4.2 , ansi-wl-pprint >= 0.6 && < 0.7 , bytestring >= 0.10 && < 0.11 , containers >= 0.5 && < 0.6 , data-default >= 0.5 && < 0.6 - , FormalGrammars == 0.2.0.* + , FormalGrammars >= 0.2.1 && < 0.2.2 , lens >= 4 && < 5 , newtype >= 0.2 && < 0.3 , parsers >= 0.12 && < 0.13 + , PrimitiveArray >= 0.6.0.1 && < 0.6.2 , semigroups >= 0.15 && < 0.17 , template-haskell >= 2 && < 3 , transformers >= 0.4 && < 0.5 @@ -153,13 +137,13 @@ executable AlignGlobal if flag(examples) build-depends: base >= 4.7 && < 4.9 - , ADPfusion == 0.4.0.* + , ADPfusion , containers , FormalGrammars , GrammarProducts - , PrimitiveArray == 0.6.0.* + , PrimitiveArray , template-haskell - , vector == 0.10.* + , vector >= 0.10 && < 0.11 buildable: True else buildable: False @@ -183,11 +167,6 @@ -funbox-strict-fields -funfolding-use-threshold1000 -funfolding-keeness-factor1000 - if flag(llvm) - ghc-options: - -fllvm - -optlo-O3 - -fllvm-tbaa diff --git a/README.md b/README.md --- a/README.md +++ b/README.md @@ -1,17 +1,27 @@ -Grammar Products -================ +# GrammarProducts: Products of formal languages [![Build Status](https://travis-ci.org/choener/GrammarProducts.svg?branch=master)](https://travis-ci.org/choener/GrammarProducts) -[*generalized ADPfusion Homepage*](http://www.bioinf.uni-leipzig.de/Software/gADP/) +[*generalized Algebraic Dynamic Programming Homepage*](http://www.bioinf.uni-leipzig.de/Software/gADP/) An algebra of liner and context-free grammars. +1. Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler. + *Product Grammars for Alignment and Folding* + 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics. 99 + [paper](http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6819790) +1. Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler. + *How to Multiply Dynamic Programming Algorithms* + 2013, Brazilian Symposium on Bioinformatics (BSB 2013) + Lecture Notes in Bioinformatics 8213. Springer, Heidelberg. + [paper](http://dx.doi.org/10.1007/978-3-319-02624-4_8) [preprint](http://www.bioinf.uni-leipzig.de/Software/gADP/gramprod/hoe-hof-2013.pdf) + #### Contact -Christian Hoener zu Siederdissen -choener@bioinf.uni-leipzig.de -Leipzig University, Leipzig, Germany +Christian Hoener zu Siederdissen +Leipzig University, Leipzig, Germany +choener@bioinf.uni-leipzig.de +http://www.bioinf.uni-leipzig.de/~choener/ diff --git a/changelog.md b/changelog.md --- a/changelog.md +++ b/changelog.md @@ -1,3 +1,9 @@ +0.1.1.0 +------- + +- FormalGrammar == 0.2.1.x with revamped indexed rules system +- new travis.yml + 0.1.0.0 -------