ForestStructures 0.0.0.2 → 0.0.1.0

raw patch · 3 files changed

+98/−4 lines, 3 filesdep +bifunctorsdep +lensPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

Dependencies added: bifunctors, lens

API changes (from Hackage documentation)

Files

• Data/Forest/StructuredPaired.hs +82/−0
• ForestStructures.cabal +11/−4
• changelog.md +5/−0

@@ -0,0 +1,82 @@++-- | A semi-specialized forest structure with the following atomic elements:+-- (i) unstructured regions of type @a@, (ii) binary paired regions of type+-- @(b,b)@ with a recursing tree (or insertion between the two @b@'s), (iii)+-- juxtaposition of two elements, and (iv) an empty structure.++module Data.Forest.StructuredPaired where++import Control.Lens+import Data.Bifoldable+import Data.Bifunctor+import Data.Bitraversable+import Data.Monoid+import GHC.Generics (Generic)++import Data.Forest.Static++++-- | A structured forest.++data SPForest r t+  -- | An (unstructured) region with the structured forest. In case @r@ forms a+  -- monoid @SPJ (SPR a) (SPR b) `equiv` SPR (a<>b)@ should hold.+  = SPR r+  -- | A tree within the forest brackets the forest on the left and right side+  -- with elements of type @t@.+  | SPT t (SPForest r t) t+  -- | Juxtaposition of two forests. This allows for simple concatenation of+  -- forests. In particular, there is no particular position, while lists+  -- prefer @x:xs@ vs @xs++[x]@.+  | SPJ [SPForest r t]+  -- | An empty forest. @SPJ SPE SPE `equiv` SPE@ should hold.+  | SPE+  deriving (Read,Show,Eq,Ord,Generic)+makePrisms ''SPForest++instance Bifunctor SPForest where+  first f = \case+    SPR r     → SPR (f r)+    SPT l t r → SPT l (first f t) r+    SPJ xs    → SPJ (map (first f) xs)+    SPE       → SPE+  {-# Inlinable first #-}+  second g = \case+    SPR r     → SPR r+    SPT l t r → SPT (g l) (second g t) (g r)+    SPJ xs    → SPJ (map (second g) xs)+    SPE       → SPE+  {-# Inlinable second #-}+  bimap f g = \case+    SPR r     → SPR (f r)+    SPT l t r → SPT (g l) (bimap f g t) (g r)+    SPJ xs    → SPJ (map (bimap f g) xs)+    SPE       → SPE+  {-# Inlinable bimap #-}++instance Bifoldable SPForest where+  bifoldMap f g = \case+    SPR r     → f r+    SPT l t r → g l <> bifoldMap f g t <> g r+    SPJ xs    → error "Bifoldable" -- mconcatMap (bifoldMap f g) xs+    SPE       → mempty+  {-# Inlinable bifoldMap #-}++instance Bitraversable SPForest where+  bitraverse f g = \case+    SPR r     → SPR <$> f r+    SPT l t r → SPT <$> g l <*> bitraverse f g t <*> g r+    SPJ xs    → error "Bitraversable" -- SPJ <$> bitraverse f g l <*> bitraverse f g r+    SPE       → pure SPE+  {-# Inlinable bitraverse #-}++++-- | Structured Forests can be transformed into static forests.+--+-- TODO types involved!++toStaticForest ∷ SPForest r t → Forest p v a+toStaticForest = undefined+

@@ -1,7 +1,7 @@ name:           ForestStructures-version:        0.0.0.2-author:         Christian Hoener zu Siederdissen, Sarah Berkemer, 2015-2017-copyright:      Christian Hoener zu Siederdissen, 2015-2017+version:        0.0.1.0+author:         Christian Hoener zu Siederdissen 2015-2018, Sarah Berkemer, 2015-2017+copyright:      Christian Hoener zu Siederdissen, 2015-2018 homepage:       https://github.com/choener/ForestStructures bug-reports:    https://github.com/choener/ForestStructures/issues maintainer:     choener@bioinf.uni-leipzig.de@@ -11,7 +11,7 @@ build-type:     Simple stability:      experimental cabal-version:  >= 1.10.0-tested-with:    GHC == 7.10.3, GHC == 8.0.2+tested-with:    GHC == 8.4.4 synopsis:       Tree- and forest structures description:                 This library provides both static and dynamic tree and forest@@ -31,27 +31,34 @@  library   build-depends: base                   >= 4.7      &&  < 5.0+               , bifunctors             >= 5.0                , containers             >= 0.5                , fgl                    >= 5.5+               , lens                   >= 4.0                , QuickCheck             >= 2.0                , unordered-containers   >= 0.2                , vector                 >= 0.10                , vector-th-unbox        >= 0.2   exposed-modules:     Data.Forest.Static+    Data.Forest.StructuredPaired   default-language:     Haskell2010   default-extensions: BangPatterns                     , AllowAmbiguousTypes                     , DataKinds+                    , DeriveGeneric                     , FlexibleContexts                     , GADTs                     , KindSignatures+                    , LambdaCase                     , OverloadedStrings                     , RankNTypes                     , RecordWildCards                     , StandaloneDeriving+                    , TemplateHaskell                     , UndecidableInstances+                    , UnicodeSyntax   ghc-options:     -O2 

@@ -1,3 +1,8 @@+0.0.1.0+-------++- structured forests, mostly for secondary structures of RNA+ 0.0.0.2 -------