elynx-seq 0.7.2.2 → 0.8.0.0

raw patch · 9 files changed

+38/−33 lines, 9 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• ChangeLog.md +5/−0
• README.md +5/−5
• elynx-seq.cabal +1/−1
• src/ELynx/Alphabet/Character.hs +2/−2
• src/ELynx/Alphabet/DistributionDiversity.hs +5/−5
• src/ELynx/Character/Character.hs +11/−11
• src/ELynx/Character/Codon.hs +4/−4
• src/ELynx/Sequence/Alignment.hs +4/−4
• src/ELynx/Sequence/Translate.hs +1/−1

@@ -5,6 +5,11 @@ ## Unreleased changes  +## Version 0.8.0.0++-   Adapt to breaking changes in upstream libraries (`data-default`).++ ## Version 0.7.2.0  -   `slynx`: Allow global normalization of mixture models.

@@ -2,7 +2,7 @@  # The ELynx Suite -Version: 0.7.2.1.+Version: 0.8.0.0. Reproducible evolution made easy.  <p align="center"><img src="https://travis-ci.org/dschrempf/elynx.svg?branch=master"/></p>@@ -73,9 +73,9 @@     # OR: stack exec slynx -- --help     # OR: slynx --help -    ELynx Suite version 0.7.2.1.+    ELynx Suite version 0.8.0.0.     Developed by Dominik Schrempf.-    Compiled on June 15, 2023, at 19:54 pm, UTC.+    Compiled on October 27, 2024, at 07:14 am, UTC.          Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]                  [-f|--force] [--no-elynx-file] COMMAND@@ -143,9 +143,9 @@     # OR: stack exec slynx -- simulate --help     # OR: slynx simulate --help -    ELynx Suite version 0.7.2.1.+    ELynx Suite version 0.8.0.0.     Developed by Dominik Schrempf.-    Compiled on June 15, 2023, at 19:54 pm, UTC.+    Compiled on October 27, 2024, at 07:14 am, UTC.          Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]                           [-m|--mixture-model MODEL] [-n|--global-normalization]

@@ -1,6 +1,6 @@ cabal-version:      3.0 name:               elynx-seq-version:            0.7.2.2+version:            0.8.0.0 synopsis:           Handle molecular sequences description:   Examine, modify, and simulate molecular sequences in a reproducible way. Please see the README on GitHub at <https://github.com/dschrempf/elynx>.

@@ -68,9 +68,9 @@ fromString = map fromChar  -- | Conversion of 'Character's.-toCVec :: C.Character a => V.Vector Character -> V.Vector a+toCVec :: (C.Character a) => V.Vector Character -> V.Vector a toCVec = V.map (C.fromWord . toWord)  -- | Conversion of 'Character's.-fromCVec :: C.Character a => V.Vector a -> V.Vector Character+fromCVec :: (C.Character a) => V.Vector a -> V.Vector Character fromCVec = V.map (fromWord . C.toWord)

@@ -57,29 +57,29 @@  -- | Effective number of used characters measured using 'entropy'. The result -- only makes sense when the sum of the array is 1.0.-kEffEntropy :: Vector v Double => v Double -> Double+kEffEntropy :: (Vector v Double) => v Double -> Double kEffEntropy v = if e < eps then 1.0 else exp e where e = entropy v  -- | Probability of homoplasy of vector. The result is the probability of -- binomially sampling the same character twice and only makes sense when the -- sum of the array is 1.0.-homoplasy :: Vector v Double => v Double -> Double+homoplasy :: (Vector v Double) => v Double -> Double homoplasy v = V.sum $ V.map (\x -> x * x) v  -- | Effective number of used characters measured using 'homoplasy'. The result -- only makes sense when the sum of the array is 1.0.-kEffHomoplasy :: Vector v Double => v Double -> Double+kEffHomoplasy :: (Vector v Double) => v Double -> Double kEffHomoplasy v = 1.0 / homoplasy v  -- XXX: Use mutable vector; then V.// is much faster. -- Increment element at index in vector by one.-incrementElemIndexByOne :: Vector v Int => [Int] -> v Int -> v Int+incrementElemIndexByOne :: (Vector v Int) => [Int] -> v Int -> v Int incrementElemIndexByOne is v = v V.// zip is es'   where     es' = [v V.! i + 1 | i <- is]  -- For a given code and counts vector, increment the count of the given character.-acc :: Vector v Int => AlphabetSpec -> v Int -> Character -> v Int+acc :: (Vector v Int) => AlphabetSpec -> v Int -> Character -> v Int acc alph vec char = incrementElemIndexByOne is vec   where     is = [S.findIndex c (std alph) | c <- toStd alph char]

@@ -45,48 +45,48 @@   fromWord :: Word8 -> a  -- | Conversion to 'Char'.-toChar :: Character a => a -> Char+toChar :: (Character a) => a -> Char toChar = w2c . toWord  -- | Conversion from 'Char'.-fromChar :: Character a => Char -> a+fromChar :: (Character a) => Char -> a fromChar = fromWord . c2w  -- | Conversion to 'String'.-toString :: Character a => [a] -> String+toString :: (Character a) => [a] -> String toString = map toChar  -- | Conversion from 'String'.-fromString :: Character a => String -> [a]+fromString :: (Character a) => String -> [a] fromString = map fromChar  -- | An extended character type with gaps and unknowns.-class Character a => CharacterX a where+class (Character a) => CharacterX a where   gap :: a  -- | Is the character a gap or unknown?-isGap :: CharacterX a => a -> Bool+isGap :: (CharacterX a) => a -> Bool isGap c = c == gap  -- | IUPAC characters with a mapping to extended characters.-class CharacterX a => CharacterI a where+class (CharacterX a) => CharacterI a where   unknown :: a   iupac :: [a]   toStandard :: a -> [a]  -- | Check if a IUPAC 'CharacterI' is unknown (e.g., N for nucleotides).-isUnknown :: CharacterI a => a -> Bool+isUnknown :: (CharacterI a) => a -> Bool isUnknown c = c == unknown -iupacLookup :: CharacterI a => S.Set a+iupacLookup :: (CharacterI a) => S.Set a iupacLookup = S.fromList iupac  -- | Is the given character a IUPAC character?-isIUPAC :: CharacterI a => a -> Bool+isIUPAC :: (CharacterI a) => a -> Bool isIUPAC c = c `S.member` iupacLookup  -- | Is the given character a standard character?-isStandard :: CharacterI a => a -> Bool+isStandard :: (CharacterI a) => a -> Bool isStandard c = not $ isIUPAC c  -- | Convert between character classes. May throw error.

@@ -50,7 +50,7 @@  -- | Unsafe conversion from vector with at least three elements; only the first -- three elements are used, the rest is discarded.-fromVecUnsafe :: V.Vector v a => v a -> Codon a+fromVecUnsafe :: (V.Vector v a) => v a -> Codon a fromVecUnsafe xs =   Codon (V.head xs, V.head . V.tail $ xs, V.head . V.tail . V.tail $ xs) @@ -63,16 +63,16 @@ instance ToJSON UniversalCode  -- It is important that the map is lazy, because some keys have errors as values.-mapFromLists :: Ord a => [a] -> [a] -> [a] -> [b] -> M.Map (Codon a) b+mapFromLists :: (Ord a) => [a] -> [a] -> [a] -> [b] -> M.Map (Codon a) b mapFromLists xs ys zs as =   M.fromList $ zipWith4 (\f s t a -> (Codon (f, s, t), a)) xs ys zs as -nucs :: Enum a => [a]+nucs :: (Enum a) => [a] nucs = map toEnum [3, 1, 0, 2] -- Order T, C, A , G.  -- Permutation of the triplets PLUS GAPS! I avoid 'Z' because I do not want to -- translate DNAI.-base1, base2, base3 :: Enum a => [a]+base1, base2, base3 :: (Enum a) => [a] base1 = [n | n <- nucs, _ <- [0 .. 3 :: Int], _ <- [0 .. 3 :: Int]] -- base1 = "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG" ++ "-." base2 = [n | _ <- [0 .. 3 :: Int], n <- nucs, _ <- [0 .. 3 :: Int]]

@@ -140,14 +140,14 @@ summarize a = header a <> S.body (toSequences a)  -- Vertical concatenation.-(===) :: V.Unbox a => M.Matrix a -> M.Matrix a -> M.Matrix a+(===) :: (V.Unbox a) => M.Matrix a -> M.Matrix a -> M.Matrix a (===) l r = M.fromRows $ lRs ++ rRs   where     lRs = M.toRows l     rRs = M.toRows r  -- Horizontal concatenation.-(|||) :: V.Unbox a => M.Matrix a -> M.Matrix a -> M.Matrix a+(|||) :: (V.Unbox a) => M.Matrix a -> M.Matrix a -> M.Matrix a (|||) l r = M.fromColumns $ lCs ++ rCs   where     lCs = M.toColumns l@@ -305,7 +305,7 @@     allChars = M.flatten $ matrix a  -- Sample the given sites from a matrix.-subSampleMatrix :: V.Unbox a => [Int] -> M.Matrix a -> M.Matrix a+subSampleMatrix :: (V.Unbox a) => [Int] -> M.Matrix a -> M.Matrix a subSampleMatrix is m =   M.fromColumns $ foldl' (\a i -> M.takeColumn m i : a) [] (reverse is) @@ -314,7 +314,7 @@ subSample is a = a {matrix = m'} where m' = subSampleMatrix is $ matrix a  -- | Randomly sample a given number of sites of the multi sequence alignment.-randomSubSample :: StatefulGen g m => Int -> Alignment -> g -> m Alignment+randomSubSample :: (StatefulGen g m) => Int -> Alignment -> g -> m Alignment randomSubSample n a g = do   let l = length a   is <- replicateM n $ uniformRM (0, l - 1) g

@@ -22,7 +22,7 @@  -- Chop list into chunks of given length. If the last chop is shorter than -- length, it is dropped.-chopVec :: V.Unbox a => Int -> V.Vector a -> [V.Vector a]+chopVec :: (V.Unbox a) => Int -> V.Vector a -> [V.Vector a] chopVec n xs   | V.length xs < n = []   | otherwise = V.take n xs : chopVec n (V.drop n xs)