fasta 0.7.2.1 → 0.8.0.0

raw patch · 6 files changed

+16/−16 lines, 6 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• fasta.cabal +1/−1
• src/Data/Fasta/ByteString/Lazy/Translation.hs +3/−3
• src/Data/Fasta/ByteString/Translation.hs +3/−3
• src/Data/Fasta/String/Translation.hs +3/−3
• src/Data/Fasta/Text/Lazy/Translation.hs +3/−3
• src/Data/Fasta/Text/Translation.hs +3/−3

@@ -10,7 +10,7 @@ -- PVP summary:      +-+------- breaking API changes --                   | | +----- non-breaking API additions --                   | | | +--- code changes with no API change-version:             0.7.2.1+version:             0.8.0.0  -- A short (one-line) description of the package. synopsis:            A simple, mindless parser for fasta files.

@@ -29,8 +29,8 @@                    | otherwise    -> a : go b  -- | Converts a codon to an amino acid--- Remember, if there is an "N" in that DNA sequence, then it is invalid--- and treated as a gap+-- Remember, if there is an "N" in that DNA sequence, then it is translated+-- as an X, an unknown amino acid. codon2aa :: Codon -> Either BL.ByteString BL.ByteString codon2aa x     | codon `elem` ["GCT", "GCC", "GCA", "GCG"]               = Right "A"@@ -56,7 +56,7 @@     | codon `elem` ["TAA", "TGA", "TAG"]                      = Right "*"     | codon `elem` ["---", "..."]                             = Right "-"     | codon == "~~~"                                          = Right "-"-    | 'N' `BL.elem` codon                                     = Right "-"+    | 'N' `BL.elem` codon                                     = Right "X"     | '-' `BL.elem` codon                                     = Right "-"     | '.' `BL.elem` codon                                     = Right "-"     | otherwise                                               = Left errorMsg

@@ -28,8 +28,8 @@                    | otherwise    -> a : go b  -- | Converts a codon to an amino acid--- Remember, if there is an "N" in that DNA sequence, then it is invalid--- and treated as a gap+-- Remember, if there is an "N" in that DNA sequence, then it is translated+-- as an X, an unknown amino acid. codon2aa :: Codon -> Either B.ByteString B.ByteString codon2aa x     | codon `elem` ["GCT", "GCC", "GCA", "GCG"]               = Right "A"@@ -55,7 +55,7 @@     | codon `elem` ["TAA", "TGA", "TAG"]                      = Right "*"     | codon `elem` ["---", "..."]                             = Right "-"     | codon == "~~~"                                          = Right "-"-    | "N" `B.isInfixOf` codon                                 = Right "-"+    | "N" `B.isInfixOf` codon                                 = Right "X"     | "-" `B.isInfixOf` codon                                 = Right "-"     | "." `B.isInfixOf` codon                                 = Right "-"     | otherwise                                               = Left errorMsg

@@ -18,8 +18,8 @@ import Data.Fasta.String.Types  -- | Converts a codon to an amino acid--- Remember, if there is an "N" in that DNA sequence, then it is invalid--- and treated as a gap+-- Remember, if there is an "N" in that DNA sequence, then it is translated+-- as an X, an unknown amino acid. codon2aa :: Codon -> Either String Char codon2aa x     | codon `elem` ["GCT", "GCC", "GCA", "GCG"]               = Right 'A'@@ -45,7 +45,7 @@     | codon `elem` ["TAA", "TGA", "TAG"]                      = Right '*'     | codon `elem` ["---", "..."]                             = Right '-'     | codon == "~~~"                                          = Right '-'-    | 'N' `elem` codon                                        = Right '-'+    | 'N' `elem` codon                                        = Right 'X'     | '-' `elem` codon                                        = Right '-'     | '.' `elem` codon                                        = Right '-'     | otherwise                                               = Left errorMsg

@@ -19,8 +19,8 @@ import Data.Fasta.Text.Lazy.Types  -- | Converts a codon to an amino acid--- Remember, if there is an "N" in that DNA sequence, then it is invalid--- and treated as a gap+-- Remember, if there is an "N" in that DNA sequence, then it is translated+-- as an X, an unknown amino acid. codon2aa :: Codon -> Either T.Text T.Text codon2aa x     | codon `elem` ["GCT", "GCC", "GCA", "GCG"]               = Right "A"@@ -46,7 +46,7 @@     | codon `elem` ["TAA", "TGA", "TAG"]                      = Right "*"     | codon `elem` ["---", "..."]                             = Right "-"     | codon == "~~~"                                          = Right "-"-    | "N" `T.isInfixOf` codon                                 = Right "-"+    | "N" `T.isInfixOf` codon                                 = Right "X"     | "-" `T.isInfixOf` codon                                 = Right "-"     | "." `T.isInfixOf` codon                                 = Right "-"     | otherwise                                               = Left errorMsg

@@ -18,8 +18,8 @@ import Data.Fasta.Text.Types  -- | Converts a codon to an amino acid--- Remember, if there is an "N" in that DNA sequence, then it is invalid--- and treated as a gap+-- Remember, if there is an "N" in that DNA sequence, then it is translated+-- as an X, an unknown amino acid. codon2aa :: Codon -> Either T.Text T.Text codon2aa x     | codon `elem` ["GCT", "GCC", "GCA", "GCG"]               = Right "A"@@ -45,7 +45,7 @@     | codon `elem` ["TAA", "TGA", "TAG"]                      = Right "*"     | codon `elem` ["---", "..."]                             = Right "-"     | codon == "~~~"                                          = Right "-"-    | "N" `T.isInfixOf` codon                                 = Right "-"+    | "N" `T.isInfixOf` codon                                 = Right "X"     | "-" `T.isInfixOf` codon                                 = Right "-"     | "." `T.isInfixOf` codon                                 = Right "-"     | otherwise                                               = Left errorMsg