text-compression 0.1.0.18 → 0.1.0.19

raw patch · 3 files changed

+66/−120 lines, 3 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• CHANGELOG.md +4/−0
• src/Data/FMIndex.hs +61/−119
• text-compression.cabal +1/−1

@@ -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.

@@ -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)  {--------------------}

@@ -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.