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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 k | calculates 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 k | Source

Adds a default hashes function to a `HashF`, when hash is defined.

contigous :: Integral k => Int -> HashF k | Source

Contigous constructs an int/eger from a contigous k-word.

rcontig :: Integral k => Int -> HashF k | Source

Like `contigous`, but returns the same hash for a word and its reverse complement.

compact :: SeqData -> [SeqData] | Source

rcpacked :: Integral k => Int -> HashF k | Source

Like `rcontig`, but ignoring monomers (i.e. arbitrarily long runs of a single nucelotide are treated the same a single nucleotide.

type Shape = String | Source

gapped :: Integral k => Shape -> HashF k | Source

isN :: Char -> Bool | Source

n2k :: Integral k => Int -> SeqData -> k | Source

n2i' :: Num a => a -> SeqData -> a | Source

k2n :: Integral k => Int -> k -> SeqData | Source

val :: Num t => Char -> t | Source

unval :: Num a => a -> Char | Source

complement :: Char -> Char | Source

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