biocore 0.1 → 0.2

raw patch · 3 files changed

+16/−7 lines, 3 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• biocore.cabal +5/−1
• src/Bio/Core/Sequence.hs +6/−5
• src/Bio/Core/Strand.hs +5/−1

@@ -1,5 +1,5 @@ Name:      biocore-Version:   0.1+Version:   0.2 License:   LGPL  Cabal-Version:       >= 1.6@@ -16,6 +16,10 @@ Tested-With:         GHC==6.12.3 Build-Type:          Simple -- Data-Files:++Source-repository head+  Type:     darcs+  Location: http://malde.org/~ketil/biohaskell/biocore/  Library   Build-Depends:     base >= 3 && < 5, bytestring

@@ -9,7 +9,7 @@     'Data.ByteString.Lazy' and 'Data.ByteString.Lazy.Char8'. -} -{-# Language GeneralizedNewtypeDeriving #-}+{-# LANGUAGE GeneralizedNewtypeDeriving, DeriveDataTypeable #-}  module Bio.Core.Sequence (   -- * Data definitions@@ -26,23 +26,24 @@ import qualified Data.ByteString.Lazy.Char8 as LC import qualified Data.ByteString.Lazy as L import Data.Int+import Data.Typeable (Typeable) import Data.Word import Data.String  -- | Sequence data are lazy bytestrings of ASCII characters.-newtype SeqData  = SeqData { unSD :: LC.ByteString } deriving (Eq,Ord,IsString)+newtype SeqData  = SeqData { unSD :: LC.ByteString } deriving (Eq,Ord,IsString,Show,Typeable)  -- | Sequence data are lazy bytestrings of ASCII characters.-newtype SeqLabel = SeqLabel { unSL :: LC.ByteString } deriving (Eq,Ord,IsString)+newtype SeqLabel = SeqLabel { unSL :: LC.ByteString } deriving (Eq,Ord,IsString,Show,Typeable)  -- | A quality value is in the range 0..255. newtype Qual     = Qual { unQual :: Word8 } deriving (Show,Eq,Ord,Num)  -- | Quality data are lazy bytestrings of 'Qual's.-newtype QualData = QualData { unQD :: L.ByteString } deriving (Eq,Ord)+newtype QualData = QualData { unQD :: L.ByteString } deriving (Eq,Ord,Show,Typeable)  -- | An 'Offset' is a zero-based index into a sequence-newtype Offset   = Offset { unOff :: Int64 } deriving (Show,Eq,Ord,Num)+newtype Offset   = Offset { unOff :: Int64 } deriving (Show,Eq,Ord,Num,Enum,Real,Integral,Typeable)  -- | The 'BioSeq' class models sequence data, and any data object that --   represents a biological sequence should implement it.

@@ -1,6 +1,10 @@+{-# LANGUAGE DeriveDataTypeable #-}+ {-| Define common data types for features of sequences -}  module Bio.Core.Strand (Strand(..)) where +import Data.Typeable (Typeable)+ -- | A 'Strand' is either plus (forward) or minus (reverse or reverse-complement)-data Strand = Plus | Minus deriving (Eq,Ord,Read,Show)+data Strand = Plus | Minus deriving (Eq,Ord,Read,Show,Typeable)