bio-0.4.6: A bioinformatics librarySource codeContentsIndex
Bio.Sequence.HashWord
Synopsis
data HashF k = HF {
hash :: SeqData -> Offset -> Maybe k
hashes :: SeqData -> [(k, Offset)]
ksort :: [k] -> [k]
}
genkeys :: HashF k -> HashF k
contigous :: Integral k => Int -> HashF k
rcontig :: Integral k => Int -> HashF k
compact :: SeqData -> [SeqData]
rcpacked :: Integral k => Int -> HashF k
type Shape = String
gapped :: Integral k => Shape -> HashF k
isN :: Char -> Bool
n2k :: Integral k => Int -> SeqData -> k
n2i' :: Num a => a -> SeqData -> a
k2n :: Integral k => Int -> k -> SeqData
val :: Num t => Char -> t
unval :: Num a => a -> Char
complement :: Char -> Char
Documentation
data HashF k Source
This is a struct for containing a set of hashing functions
Constructors
HF
hash :: SeqData -> Offset -> Maybe kcalculates the hash at a given offset in the sequence
hashes :: SeqData -> [(k, Offset)]calculate all hashes from a sequence, and their indices
ksort :: [k] -> [k]for sorting hashes
genkeys :: HashF k -> HashF kSource
Adds a default hashes function to a HashF, when hash is defined.
contigous :: Integral k => Int -> HashF kSource
Contigous constructs an int/eger from a contigous k-word.
rcontig :: Integral k => Int -> HashF kSource
Like contigous, but returns the same hash for a word and its reverse complement.
compact :: SeqData -> [SeqData]Source
rcpacked :: Integral k => Int -> HashF kSource
Like rcontig, but ignoring monomers (i.e. arbitrarily long runs of a single nucelotide are treated the same a single nucleotide.
type Shape = StringSource
gapped :: Integral k => Shape -> HashF kSource
isN :: Char -> BoolSource
n2k :: Integral k => Int -> SeqData -> kSource
n2i' :: Num a => a -> SeqData -> aSource
k2n :: Integral k => Int -> k -> SeqDataSource
val :: Num t => Char -> tSource
unval :: Num a => a -> CharSource
complement :: Char -> CharSource
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