bio-0.4.6: A bioinformatics library Source code Contents Index

Bio.Util.TestBase

Synopsis

data Test = forall t . Testable t => T String t newtype Nucleotide = N Char newtype Quality = Q Word8 fromN :: Nucleotide -> Char fromQ :: Quality -> Word8 newtype EST = E (Sequence Nuc) newtype ESTq = Eq (Sequence Nuc) newtype Protein = P (Sequence Amino) newtype EST_short = ES (Sequence Nuc) newtype EST_long = EL (Sequence Nuc) newtype EST_set = ESet [Sequence Nuc] time :: String -> IO () -> IO () showT :: Integral a => a -> String integralRandomR :: (Integral a, RandomGen g) => (a, a) -> g -> (a, g) genOffset :: Gen Offset genNonNegOffset :: Gen Offset genPositiveOffset :: Gen Offset

Documentation

data Test Source

Constructors forall t . Testable t => T String t

newtype Nucleotide Source

Constructors N Char Instances Show Nucleotide Arbitrary Nucleotide

newtype Quality Source

Constructors Q Word8 Instances Show Quality Arbitrary Quality

fromN :: Nucleotide -> Char Source

fromQ :: Quality -> Word8 Source

newtype EST Source

For testing, variable lengths Constructors E (Sequence Nuc) Instances Show EST Arbitrary EST

newtype ESTq Source

Constructors Eq (Sequence Nuc) Instances Show ESTq Arbitrary ESTq

newtype Protein Source

Constructors P (Sequence Amino) Instances Show Protein

newtype EST_short Source

For benchmarking, fixed lengths Constructors ES (Sequence Nuc) Instances Show EST_short Arbitrary EST_short

newtype EST_long Source

Constructors EL (Sequence Nuc) Instances Show EST_long Arbitrary EST_long

newtype EST_set Source

Constructors ESet [Sequence Nuc] Instances Show EST_set Arbitrary EST_set

time :: String -> IO () -> IO () Source

Take time (CPU and wall clock) and report it

showT :: Integral a => a -> String Source

Print a CPUTime difference

integralRandomR :: (Integral a, RandomGen g) => (a, a) -> g -> (a, g) Source

Shamelessly stolen from FPS

genOffset :: Gen Offset Source

Constrained position generators

genNonNegOffset :: Gen Offset Source

genPositiveOffset :: Gen Offset Source

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