diff --git a/CHANGELOG.md b/CHANGELOG.md --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -76,3 +76,7 @@ ## 0.1.0.18 -- 2022-12-02 * Added additional FM-index functionality for the locate operation. + +## 0.1.0.19 + +* Reworked FM-index functions. diff --git a/src/Data/FMIndex.hs b/src/Data/FMIndex.hs --- a/src/Data/FMIndex.hs +++ b/src/Data/FMIndex.hs @@ -77,9 +77,7 @@ textFMIndexCount, -- * Locate operations bytestringFMIndexLocate, - bytestringPCFMIndexLocate, - textFMIndexLocate, - textPCFMIndexLocate + textFMIndexLocate ) where import Data.BWT @@ -94,7 +92,7 @@ import Data.Char() import Data.Foldable() import Data.Maybe as DMaybe (isNothing,fromJust) -import Data.Sequence as DS (Seq(..),ViewL(..),fromList,index,viewl) +import Data.Sequence as DS (Seq(..),ViewL(..),fromList,index,viewl,(<|)) import Data.STRef() import Data.Text as DText import Data.Text.Encoding as DTE (decodeUtf8,encodeUtf8) @@ -508,56 +506,59 @@ {-Count operations.-} --- | Takes a pattern ('ByteString') +-- | Takes a list of pattern(s) of 'ByteString's -- and an input 'ByteString' --- and returns the number of occurences of the pattern +-- and returns the number of occurences of the pattern(s) -- in the input 'ByteString'. -bytestringFMIndexCount :: ByteString +bytestringFMIndexCount :: [ByteString] -> ByteString - -> CIntB -bytestringFMIndexCount (BSC8.uncons -> Nothing) _ = Nothing -bytestringFMIndexCount _ (BSC8.uncons -> Nothing) = Nothing -bytestringFMIndexCount pat input = do + -> Seq (ByteString,CIntB) +bytestringFMIndexCount [] _ = DS.Empty +bytestringFMIndexCount _ (BSC8.uncons -> Nothing) = DS.Empty +bytestringFMIndexCount (currentpat:restofpats) input = do let bytestringfmindex = bytestringToBWTToFMIndexB input let patternf = fmap (BSC8.singleton) $ DS.fromList $ - BSC8.unpack pat - runST $ countFMIndexB patternf - bytestringfmindex + BSC8.unpack currentpat + let countf = runST $ countFMIndexB patternf + bytestringfmindex + (currentpat,countf) DS.<| (bytestringFMIndexCount restofpats input) --- | Takes a pattern ('Text') +-- | Takes a list of pattern(s) of 'Text's -- and an input 'Text' --- and returns the number of occurences of the pattern +-- and returns the number of occurences of the pattern(s) -- in the input 'Text'. -textFMIndexCount :: Text +textFMIndexCount :: [Text] -> Text - -> CIntT -textFMIndexCount "" _ = Nothing -textFMIndexCount _ "" = Nothing -textFMIndexCount pat input = do + -> Seq (Text,CIntT) +textFMIndexCount [] _ = DS.Empty +textFMIndexCount _ "" = DS.Empty +textFMIndexCount (currentpat:restofpats) input = do let textfmindex = textToBWTToFMIndexT input let patternf = fmap (DText.singleton) $ DS.fromList $ - DText.unpack pat - runST $ countFMIndexT patternf - textfmindex + DText.unpack currentpat + let countf = runST $ countFMIndexT patternf + textfmindex + (currentpat,countf) DS.<| (textFMIndexCount restofpats input) {-------------------} {-Locate operations.-} --- | Takes a pattern ('ByteString') +-- | Takes a list of pattern(s) of 'ByteString's -- and an input 'ByteString' --- and returns the indexe(s) of occurences of the pattern +-- and returns the indexe(s) of occurences of the pattern(s) -- in the input 'ByteString'. --- The output is not sorted. -bytestringFMIndexLocate :: ByteString +-- The output indices are __1__-based, +-- and are __not__ sorted. +bytestringFMIndexLocate :: [ByteString] -> ByteString - -> LIntB -bytestringFMIndexLocate (BSC8.uncons -> Nothing) _ = DS.Empty -bytestringFMIndexLocate _ (BSC8.uncons -> Nothing) = DS.Empty -bytestringFMIndexLocate pat input = do + -> Seq (ByteString,LIntB) +bytestringFMIndexLocate [] _ = DS.Empty +bytestringFMIndexLocate _ (BSC8.uncons -> Nothing) = DS.Empty +bytestringFMIndexLocate (currentpat:restofpats) input = do let bytestringsa = createSuffixArray $ fmap (BS.singleton) $ DS.fromList $ @@ -565,59 +566,30 @@ let bfmindex = bytestringToBWTToFMIndexB input let patternf = fmap (BSC8.singleton) $ DS.fromList $ - BSC8.unpack pat - let indices = runST $ locateFMIndexB patternf - bfmindex - fmap (\x -> if | isNothing x - -> Nothing - | otherwise - -> Just $ - suffixstartpos $ - DS.index bytestringsa ((fromJust x) - 1) - ) indices - --- | Takes a pattern ('ByteString'), --- an input ('ByteString') --- and a pre-computed 'FMIndexB' of the input 'ByteString' --- and returns the indexe(s) of occurences of the pattern --- using the pre-computed 'FMIndexB' --- in the input 'ByteString'. --- The output is not sorted. -bytestringPCFMIndexLocate :: ByteString - -> ByteString - -> FMIndexB - -> LIntB -bytestringPCFMIndexLocate (BSC8.uncons -> Nothing) _ _ = DS.Empty -bytestringPCFMIndexLocate _ (BSC8.uncons -> Nothing) _ = DS.Empty -bytestringPCFMIndexLocate pat input bfmindex = do - let bytestringsa = createSuffixArray $ - fmap (BS.singleton) $ - DS.fromList $ - BS.unpack input - let patternf = fmap (BSC8.singleton) $ - DS.fromList $ - BSC8.unpack pat - let indices = runST $ locateFMIndexB patternf + BSC8.unpack currentpat + let indices = runST $ locateFMIndexB patternf bfmindex - fmap (\x -> if | isNothing x - -> Nothing - | otherwise - -> Just $ - suffixstartpos $ - DS.index bytestringsa ((fromJust x) - 1) - ) indices + let indicesf = fmap (\x -> if | isNothing x + -> Nothing + | otherwise + -> Just $ + suffixstartpos $ + DS.index bytestringsa ((fromJust x) - 1) + ) indices + (currentpat,indicesf) DS.<| (bytestringFMIndexLocate restofpats input) --- | Takes a pattern ('Text') +-- | Takes a list of pattern(s) of 'Text's -- and an input 'Text' --- and returns the indexe(s) of occurences of the pattern +-- and returns the indexe(s) of occurences of the pattern(s) -- in the input 'Text'. --- The output is not sorted. -textFMIndexLocate :: Text +-- The output indices are __1__-based, +-- and are __not__ sorted. +textFMIndexLocate :: [Text] -> Text - -> LIntT -textFMIndexLocate "" _ = DS.Empty -textFMIndexLocate _ "" = DS.Empty -textFMIndexLocate pat input = do + -> Seq (Text,LIntT) +textFMIndexLocate [] _ = DS.Empty +textFMIndexLocate _ "" = DS.Empty +textFMIndexLocate (currentpat:restofpats) input = do let textsa = createSuffixArray $ fmap (DText.singleton) $ DS.fromList $ @@ -625,46 +597,16 @@ let tfmindex = textToBWTToFMIndexT input let patternf = fmap (DText.singleton) $ DS.fromList $ - DText.unpack pat - let indices = runST $ locateFMIndexT patternf - tfmindex - fmap (\x -> if | isNothing x - -> Nothing - | otherwise - -> Just $ - suffixstartpos $ - DS.index textsa ((fromJust x) - 1) - ) indices - --- | Takes a pattern ('Text'), --- an input ('Text') --- and a pre-computed 'FMIndexT' of the input 'Text --- and returns the indexe(s) of occurences of the pattern --- using the pre-computed 'FMIndexT' --- in the input 'Text'. --- The output is not sorted. -textPCFMIndexLocate :: Text - -> Text - -> FMIndexT - -> LIntT -textPCFMIndexLocate "" _ _ = DS.Empty -textPCFMIndexLocate _ "" _ = DS.Empty -textPCFMIndexLocate pat input tfmindex = do - let textsa = createSuffixArray $ - fmap (DText.singleton) $ - DS.fromList $ - DText.unpack input - let patternf = fmap (DText.singleton) $ - DS.fromList $ - DText.unpack pat + DText.unpack currentpat let indices = runST $ locateFMIndexT patternf tfmindex - fmap (\x -> if | isNothing x - -> Nothing - | otherwise - -> Just $ - suffixstartpos $ - DS.index textsa ((fromJust x) - 1) - ) indices + let indicesf = fmap (\x -> if | isNothing x + -> Nothing + | otherwise + -> Just $ + suffixstartpos $ + DS.index textsa ((fromJust x) - 1) + ) indices + (currentpat,indicesf) DS.<| (textFMIndexLocate restofpats input) {--------------------} diff --git a/text-compression.cabal b/text-compression.cabal --- a/text-compression.cabal +++ b/text-compression.cabal @@ -20,7 +20,7 @@ -- PVP summary: +-+------- breaking API changes -- | | +----- non-breaking API additions -- | | | +--- code changes with no API change -version: 0.1.0.18 +version: 0.1.0.19 -- A short (one-line) description of the package. synopsis: A text compression library.