biostockholm 0.2.2 → 0.3

raw patch · 4 files changed

+12/−12 lines, 4 filesdep ~attoparsec-conduitdep ~blaze-builder-conduitdep ~conduitPVP ok

version bump matches the API change (PVP)

Dependency ranges changed: attoparsec-conduit, blaze-builder-conduit, conduit

API changes (from Hackage documentation)

Files

• biostockholm.cabal +4/−4
• src/Bio/Sequence/Stockholm.hs +2/−2
• src/Bio/Sequence/Stockholm/Document.hs +2/−2
• src/Bio/Sequence/Stockholm/Stream.hs +4/−4

@@ -1,5 +1,5 @@ Name:                biostockholm-Version:             0.2.2+Version:             0.3 Synopsis:            Parsing and rendering of Stockholm files (used by Pfam, Rfam and Infernal). License:             BSD3 License-file:        LICENSE@@ -40,11 +40,11 @@       , containers         >= 0.2   && < 0.5       , bytestring         == 0.9.*       , deepseq            >= 1.1   && < 1.4-      , conduit            == 0.2.*+      , conduit            == 0.4.*       , attoparsec         == 0.10.*-      , attoparsec-conduit == 0.2.*+      , attoparsec-conduit == 0.4.*       , blaze-builder      == 0.3.*-      , blaze-builder-conduit == 0.2.*+      , blaze-builder-conduit == 0.4.*        , biocore            >= 0.1   && < 0.3 

@@ -67,12 +67,12 @@ -- multiple files are read independently.  If you need to process -- large Stockholm files, consider using the streaming interface -- on "Bio.Sequence.Stockholm.Stream".-parseStockholm :: C.ResourceThrow m => C.Conduit B.ByteString m Stockholm+parseStockholm :: C.MonadThrow m => C.Conduit B.ByteString m Stockholm parseStockholm = parseEvents C.=$= parseDoc   -- | Pretty prints an Stockholm file.-renderStockholm :: C.ResourceUnsafeIO m => C.Conduit Stockholm m B.ByteString+renderStockholm :: C.MonadUnsafeIO m => C.Conduit Stockholm m B.ByteString renderStockholm = renderDoc C.=$= renderEvents  

@@ -323,7 +323,7 @@   -- | Conduit that parses 'Event'@s@ into documents 'Stockholm'.-parseDoc :: C.Resource m => C.Conduit Event m Stockholm+parseDoc :: Monad m => C.Conduit Event m Stockholm parseDoc = C.conduitState LookingForHeader push close     where @@ -383,7 +383,7 @@   -- | Conduit that renders 'Stockholm'@s@ into 'Event'@s@.-renderDoc :: C.Resource m => C.Conduit Stockholm m Event+renderDoc :: Monad m => C.Conduit Stockholm m Event renderDoc = CL.concatMap toEvents     where       toEvents (Stockholm file clmn seqs) =

@@ -90,14 +90,14 @@   -- | Conduit that parses a file into events.-parseEvents :: C.ResourceThrow m => C.Conduit B.ByteString m Event+parseEvents :: C.MonadThrow m => C.Conduit B.ByteString m Event parseEvents = C.sequenceSink LookingForHeader go     where       go LookingForHeader = do         dropSpaces         let emit = C.Emit InsideStockholm . (:[])-        insideLine C.=$ sinkParser $  C.Stop <$  A8.endOfInput-                                  <|> emit   <$> headerParser+        insideLine C.=$ (sinkParser $  C.Stop <$  A8.endOfInput+                                   <|> emit   <$> headerParser)        go InsideStockholm = do         dropSpaces@@ -133,5 +133,5 @@   -- | Conduit that pretty prints an event stream into a file.-renderEvents :: C.ResourceUnsafeIO m => C.Conduit Event m B.ByteString+renderEvents :: C.MonadUnsafeIO m => C.Conduit Event m B.ByteString renderEvents = CL.map eventPrinter C.=$= builderToByteString