calhoun.seq
Class KmerHasher

java.lang.Object
  calhoun.seq.KmerHasher

All Implemented Interfaces:

java.io.Serializable

public class KmerHasher
extends java.lang.Object
implements java.io.Serializable

Class for computing kmer hashes. You instantiate the class with the length of the kmer to hash and the alphabet to use. The hashing functions then compute hashes for individual kmers. This class does not stored any hashes, which are just ints.

See Also:

Serialized Form

Nested Class Summary

static interface

KmerHasher.CharacterHash

Field Summary

static KmerHasher.CharacterHash	ACGTN Character hash function to use with DNA bases which included the ambiguity code "N".
static KmerHasher.CharacterHash	ACGTNcomp Character hash function to use with DNA bases which included the ambiguity code "N".
static KmerHasher.CharacterHash	ACGTother Character hash function to use with DNA bases which included the ambiguity code "N".
static KmerHasher.CharacterHash	ACGTotherRC Character hash function to use with DNA bases which included the ambiguity code "N".
static KmerHasher.CharacterHash	DNA Character hash function to use with DNA bases.
static KmerHasher.CharacterHash	LETTERS Character hash function to use with any letters.

Constructor Summary

KmerHasher(KmerHasher.CharacterHash charHash, int length)
Creates a hash from a given character hash and length.

Method Summary

int	hash(char c)
int	hash(char[] chr) Computes a hash given a character array.
int	hash(char[] chr, int start) Computes a hash given a character array.
int	hash(java.lang.String str, int pos) Computes hash given a 0-based position on the string.
boolean	hashable(char a)
int	range()
static java.lang.String	reverseComplement(java.lang.String forward)
int	reverseShiftHash(char chr, int hash) Updates an existing hash.
int	shiftHash(char chr, int hash) Updates an existing hash.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DNA

public static KmerHasher.CharacterHash DNA

Character hash function to use with DNA bases. Upper and lower case get hashed to the same value. Handles only the 4 nucleotides (ACTG). No other characters allowed.

ACGTN

public static KmerHasher.CharacterHash ACGTN

Character hash function to use with DNA bases which included the ambiguity code "N". Upper and lower case get hashed to the same value. Handles only the 4 nucleotides (ACTG). No other characters allowed.

ACGTNcomp

public static KmerHasher.CharacterHash ACGTNcomp

Character hash function to use with DNA bases which included the ambiguity code "N". Upper and lower case get hashed to the same value. Handles only the 4 nucleotides (ACTG). No other characters allowed.

ACGTother

public static KmerHasher.CharacterHash ACGTother

Character hash function to use with DNA bases which included the ambiguity code "N". Upper and lower case get hashed to the same value. Handles only the 4 nucleotides (ACTG). No other characters allowed.

ACGTotherRC

public static KmerHasher.CharacterHash ACGTotherRC

Character hash function to use with DNA bases which included the ambiguity code "N". Upper and lower case get hashed to the same value. Handles only the 4 nucleotides (ACTG). No other characters allowed.

LETTERS

public static KmerHasher.CharacterHash LETTERS

Character hash function to use with any letters. Upper and lower case get hashed to the same value.

Constructor Detail

KmerHasher

public KmerHasher(KmerHasher.CharacterHash charHash,
                  int length)

Creates a hash from a given character hash and length.

Method Detail

reverseComplement

public static java.lang.String reverseComplement(java.lang.String forward)

range

public int range()

hash

public int hash(java.lang.String str,
                int pos)

Computes hash given a 0-based position on the string.

hash

public int hash(char[] chr)

Computes a hash given a character array. The array must be the exact size of the hash

hash

public int hash(char[] chr,
                int start)

Computes a hash given a character array. Starts at the given index into the array

shiftHash

public int shiftHash(char chr,
                     int hash)

Updates an existing hash. Drops the first character and adds in the new one to the end. hash("BCDE", 0) == shiftHash("E", hash("ABCD", 0))

reverseShiftHash

public int reverseShiftHash(char chr,
                            int hash)

Updates an existing hash. Drops the first character and adds in the new one to the end. hash("ABCD", 0) == reverseShiftHash("A", hash("BCDE", 0))

hash

public int hash(char c)

hashable

public boolean hashable(char a)