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total matches: 126

bioinformatics-toolkit-0.9.0
2 matches
src/Bio/RealWorld/GENCODE.hs
import qualified Data.ByteString.Char8 as B
import           Data.CaseInsensitive  (CI, mk)
import qualified Data.HashMap.Strict   as M
import Data.List.Ordered (nubSort)
import           Data.Maybe            (fromJust)
import Lens.Micro
import Data.List (foldl')
import Data.Char (toLower)


            
src/Bio/RealWorld/GENCODE.hs
        M.elems $ foldl' addUTR (foldl' addExon t exons) utrs

nubGene :: [Gene] -> [Gene]
nubGene gs = nubSort $ map nubG gs
  where
    nubG g = g { geneTranscripts = nubSort $ map nubT $ geneTranscripts g}
    nubT t = t { transExon = nubSort $ transExon t 
               , transUTR = nubSort $ transUTR t  }
{-# INLINE nubGene #-}

readElements :: FilePath
             -> IO ( [Gene]
                   , [(B.ByteString, Transcript)]

            
clash-ghc-1.0.1
12 matches
src-bin-821/Clash/GHCi/UI.hs

wrapCompleter :: String -> (String -> GHCi [String]) -> CompletionFunc GHCi
wrapCompleter breakChars fun = completeWord Nothing breakChars
    $ fmap (map simpleCompletion . nubSort) . fun

wrapIdentCompleter :: (String -> GHCi [String]) -> CompletionFunc GHCi
wrapIdentCompleter = wrapCompleter word_break_chars

wrapIdentCompleterWithModifier :: String -> (Maybe Char -> String -> GHCi [String]) -> CompletionFunc GHCi

            
src-bin-821/Clash/GHCi/UI.hs

wrapIdentCompleterWithModifier :: String -> (Maybe Char -> String -> GHCi [String]) -> CompletionFunc GHCi
wrapIdentCompleterWithModifier modifChars fun = completeWordWithPrev Nothing word_break_chars
    $ \rest -> fmap (map simpleCompletion . nubSort) . fun (getModifier rest)
 where
  getModifier = find (`elem` modifChars)

-- | Return a list of visible module names for autocompletion.
-- (NB: exposed != visible)

            
src-bin-821/Clash/Main.hs
  where
    oneError f =
        "unrecognised flag: " ++ f ++ "\n" ++
        (case match f (nubSort allNonDeprecatedFlags) of
            [] -> ""
            suggs -> "did you mean one of:\n" ++ unlines (map ("  " ++) suggs))
    -- fixes #11789
    -- If the flag contains '=',
    -- this uses both the whole and the left side of '=' for comparing.

            
src-bin-841/Clash/GHCi/UI.hs

wrapCompleter :: String -> (String -> GHCi [String]) -> CompletionFunc GHCi
wrapCompleter breakChars fun = completeWord Nothing breakChars
    $ fmap (map simpleCompletion . nubSort) . fun

wrapIdentCompleter :: (String -> GHCi [String]) -> CompletionFunc GHCi
wrapIdentCompleter = wrapCompleter word_break_chars

wrapIdentCompleterWithModifier :: String -> (Maybe Char -> String -> GHCi [String]) -> CompletionFunc GHCi

            
src-bin-841/Clash/GHCi/UI.hs

wrapIdentCompleterWithModifier :: String -> (Maybe Char -> String -> GHCi [String]) -> CompletionFunc GHCi
wrapIdentCompleterWithModifier modifChars fun = completeWordWithPrev Nothing word_break_chars
    $ \rest -> fmap (map simpleCompletion . nubSort) . fun (getModifier rest)
 where
  getModifier = find (`elem` modifChars)

-- | Return a list of visible module names for autocompletion.
-- (NB: exposed != visible)

            
src-bin-841/Clash/Main.hs
  where
    oneError f =
        "unrecognised flag: " ++ f ++ "\n" ++
        (case match f (nubSort allNonDeprecatedFlags) of
            [] -> ""
            suggs -> "did you mean one of:\n" ++ unlines (map ("  " ++) suggs))
    -- fixes #11789
    -- If the flag contains '=',
    -- this uses both the whole and the left side of '=' for comparing.

            
src-bin-861/Clash/GHCi/UI.hs

wrapCompleter :: String -> (String -> GHCi [String]) -> CompletionFunc GHCi
wrapCompleter breakChars fun = completeWord Nothing breakChars
    $ fmap (map simpleCompletion . nubSort) . fun

wrapIdentCompleter :: (String -> GHCi [String]) -> CompletionFunc GHCi
wrapIdentCompleter = wrapCompleter word_break_chars

wrapIdentCompleterWithModifier :: String -> (Maybe Char -> String -> GHCi [String]) -> CompletionFunc GHCi

            
src-bin-861/Clash/GHCi/UI.hs

wrapIdentCompleterWithModifier :: String -> (Maybe Char -> String -> GHCi [String]) -> CompletionFunc GHCi
wrapIdentCompleterWithModifier modifChars fun = completeWordWithPrev Nothing word_break_chars
    $ \rest -> fmap (map simpleCompletion . nubSort) . fun (getModifier rest)
 where
  getModifier = find (`elem` modifChars)

-- | Return a list of visible module names for autocompletion.
-- (NB: exposed != visible)

            
src-bin-861/Clash/Main.hs
  where
    oneError f =
        "unrecognised flag: " ++ f ++ "\n" ++
        (case match f (nubSort allNonDeprecatedFlags) of
            [] -> ""
            suggs -> "did you mean one of:\n" ++ unlines (map ("  " ++) suggs))
    -- fixes #11789
    -- If the flag contains '=',
    -- this uses both the whole and the left side of '=' for comparing.

            
src-bin-881/Clash/GHCi/UI.hs

wrapCompleter :: String -> (String -> GHCi [String]) -> CompletionFunc GHCi
wrapCompleter breakChars fun = completeWord Nothing breakChars
    $ fmap (map simpleCompletion . nubSort) . fun

wrapIdentCompleter :: (String -> GHCi [String]) -> CompletionFunc GHCi
wrapIdentCompleter = wrapCompleter word_break_chars

wrapIdentCompleterWithModifier :: String -> (Maybe Char -> String -> GHCi [String]) -> CompletionFunc GHCi

            
src-bin-881/Clash/GHCi/UI.hs

wrapIdentCompleterWithModifier :: String -> (Maybe Char -> String -> GHCi [String]) -> CompletionFunc GHCi
wrapIdentCompleterWithModifier modifChars fun = completeWordWithPrev Nothing word_break_chars
    $ \rest -> fmap (map simpleCompletion . nubSort) . fun (getModifier rest)
 where
  getModifier = find (`elem` modifChars)

-- | Return a list of visible module names for autocompletion.
-- (NB: exposed != visible)

            
src-bin-881/Clash/Main.hs
  where
    oneError f =
        "unrecognised flag: " ++ f ++ "\n" ++
        (case match f (nubSort allNonDeprecatedFlags) of
            [] -> ""
            suggs -> "did you mean one of:\n" ++ unlines (map ("  " ++) suggs))
    -- fixes #11789
    -- If the flag contains '=',
    -- this uses both the whole and the left side of '=' for comparing.

            
darcs-2.14.2
16 matches
src/Darcs/Patch/Conflict.hs
import qualified Data.ByteString       as B (null, ByteString)
import Data.Maybe ( isJust )
import Data.List ( sort, intercalate )
import Data.List.Ordered ( nubSort )

import Darcs.Patch.Effect ( Effect(..) )
import Darcs.Patch.FileHunk ( FileHunk(..), IsHunk, isHunk )
import Darcs.Patch.Inspect ( PatchInspect(..) )
import Darcs.Patch.Invert ( Invert(..) )

            
src/Darcs/Patch/Conflict.hs

listConflictedFiles :: Conflict p => p wX wY -> [FilePath]
listConflictedFiles p =
    nubSort $ concatMap (unseal listTouchedFiles) $ concat $ resolveConflicts p

class (Effect p, PatchInspect (PrimOf p)) => Conflict p where
    resolveConflicts :: p wX wY -> [[Sealed (FL (PrimOf p) wY)]]

    conflictedEffect :: p wX wY -> [IsConflictedPrim (PrimOf p)]

            
src/Darcs/Patch/V1/Commute.hs
import Darcs.Util.Printer ( text, vcat, ($$) )
import Darcs.Patch.V1.Show ( showPatch_ )
import Data.List ( nub, nubBy )
import Data.List.Ordered ( nubSort )
import Darcs.Patch.Witnesses.Sealed
    ( Sealed(..) , mapSeal, unseal, FlippedSeal(..), mapFlipped
    , unsafeUnseal, unsafeUnsealFlipped )
import Darcs.Patch.Witnesses.Eq ( EqCheck(..), Eq2(..) )
import Darcs.Patch.Witnesses.Unsafe

            
src/Darcs/Patch/V1/Commute.hs

instance PrimPatch prim => PatchInspect (RepoPatchV1 prim) where
    -- Recurse on everything, these are potentially spoofed patches
    listTouchedFiles (Merger _ _ p1 p2) = nubSort $ listTouchedFiles p1
                                            ++ listTouchedFiles p2
    listTouchedFiles c@(Regrem{}) = listTouchedFiles $ invert c
    listTouchedFiles (PP p) = listTouchedFiles p

    hunkMatches f (Merger _ _ p1 p2) = hunkMatches f p1 || hunkMatches f p2

            
src/Darcs/Patch/V2/RepoPatch.hs
import qualified Data.ByteString.Char8 as BC ( ByteString, pack )
import Data.Maybe ( fromMaybe )
import Data.List ( partition, nub )
import Data.List.Ordered ( nubSort )

import Darcs.Patch.Annotate ( Annotate(..) )
import Darcs.Patch.Commute ( commuteFL, commuteFLorComplain, commuteRL
                           , commuteRLFL, Commute(..) )
import Darcs.Patch.Conflict ( Conflict(..), CommuteNoConflicts(..)

            
src/Darcs/Patch/V2/RepoPatch.hs
    listTouchedFiles (Etacilpud p) = nonTouches p
    listTouchedFiles (Normal p) = listTouchedFiles p
    listTouchedFiles (Conflictor x c p) =
        nubSort $ concatMap nonTouches x ++ listTouchedFiles c ++ nonTouches p
    listTouchedFiles (InvConflictor x c p) =
        nubSort $ concatMap nonTouches x ++ listTouchedFiles c ++ nonTouches p

    hunkMatches f (Duplicate p) = nonHunkMatches f p
    hunkMatches f (Etacilpud p) = nonHunkMatches f p
    hunkMatches f (Normal p) = hunkMatches f p
    hunkMatches f (Conflictor x c p) =

            
src/Darcs/Repository/Merge.hs
import Darcs.Prelude

import Control.Monad ( when, unless )
import Data.List.Ordered ( nubSort )
import System.Exit ( exitSuccess )

import Darcs.Util.Tree( Tree )
import Darcs.Util.External ( backupByCopying )


            
src/Darcs/Repository/Merge.hs
                       -> FL p wX wY
                       -> IO Bool
announceMergeConflicts cmd allowConflicts externalMerge resolved_pw =
  case nubSort $ listTouchedFiles resolved_pw of
    [] -> return False
    cfs -> if allowConflicts `elem` [YesAllowConflicts,YesAllowConflictsAndMark]
              || externalMerge /= NoExternalMerge
           then do putDocLnWith fancyPrinters $
                     redText "We have conflicts in the following files:" $$ text (unlines cfs)

            
src/Darcs/UI/Commands/Add.hs
import Control.Exception ( catch, IOException )
import Control.Monad ( when, unless )
import Data.List ( (\\), nub )
import Data.List.Ordered ( nubSort )
import Data.Maybe ( isNothing, maybeToList )
import Darcs.Util.Printer ( text )
import Darcs.Util.Tree ( Tree, findTree, expand )
import Darcs.Util.Path
    ( floatPath, anchorPath, parents

            
src/Darcs/UI/Commands/Add.hs
    flist' <- if parseFlags O.recursive opts
              then expandDirs (includeBoring opts) origfiles
              else return origfiles
    let flist = nubSort (parlist ++ toFilePath `map` flist')
    nboring <- if includeBoring opts
               then return darcsdirFilter
               else boringFileFilter
    mapM_ (putWarning opts . text . ((msgSkipping msgs ++ " boring file ")++)) $
        flist \\ nboring flist

            
src/Darcs/UI/Commands/MarkConflicts.hs
import Darcs.Prelude

import System.Exit ( exitSuccess )
import Data.List.Ordered ( nubSort, isect )
import Control.Monad ( when, unless )
import Control.Exception ( catch, IOException )

import Darcs.Util.Prompt ( promptYorn )
import Darcs.Util.SignalHandler ( withSignalsBlocked )

            
src/Darcs/UI/Commands/MarkConflicts.hs

-- | Convert a list of 'SubPath's to a 'PathSet'.
sps2ps :: [SubPath] -> PathSet
sps2ps = Only . nubSort

-- | Convert a list of repo paths to a 'PathSet'.
-- Partial function! Use only with repo paths.
fps2ps :: [FilePath] -> PathSet
fps2ps = sps2ps . map fp2sp

            
src/Darcs/UI/Commands/MarkConflicts.hs
-- | Lift a function transforming a list of 'FilePath' to one that
-- transforms a 'PathSet'.
liftToPathSet :: ([FilePath] -> [FilePath]) -> PathSet -> PathSet
liftToPathSet f = fmap (nubSort . map fp2sp . f . map sp2fp)

-- | Convert a 'FilePath' to a 'SubPath'.
--
-- Note: Should call this only with paths we get from the repository.
-- This guarantees that they are relative (to the repo dir).

            
src/Darcs/UI/Commands/WhatsNew.hs
import Control.Monad.State ( evalStateT, liftIO )
import Darcs.Util.Tree ( Tree )
import System.Exit ( ExitCode (..), exitSuccess, exitWith )
import Data.List.Ordered ( nubSort )

import Darcs.Patch
    ( PrimOf, PrimPatch, RepoPatch
    , applyToTree, plainSummaryPrims, primIsHunk
    )

            
src/Darcs/UI/Commands/WhatsNew.hs
    let scan = scanKnown (lookForAdds opts) (O.includeBoring ? opts)
    existing_files <- do
      files <- if null args then return Nothing
               else Just . nubSort <$> fixSubPaths fps args
      when (files == Just []) $ fail "No valid arguments were given."
      files' <- traverse
        (filterExistingPaths
          repo (verbosity ? opts) (useIndex ? opts) scan (lookForMoves opts))
        files

            
src/Darcs/UI/Completion.hs
import Darcs.Prelude

import Data.List ( (\\), stripPrefix )
import Data.List.Ordered ( nubSort, minus )
import Data.Maybe ( mapMaybe )

import Darcs.Patch ( listTouchedFiles )

import Darcs.Repository.Flags