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A

A - sequence.Base

B

Base - Enum in sequence

These values represents DNA nucleotides and the corresponding hash values are derived from ntHash: recursive nucleotide hashing.

buildIndex(int) - Method in class dna.DNA

Stores DNA hash values and its corresponding indices in hash table.

buildIndex(int, int, int, Map<Long, List<Integer>>) - Method in class dna.DNA

This method builds hash table using DNA hash values and its indices.

buildIndex(long) - Method in class sequence.DiskSequence

buildIndex(long) - Method in class sequence.MemorySequence

buildIndex(long) - Method in interface sequence.Sequence

Builds the index based on the length of the k-mer.

buildIndexFast(int) - Method in class dna.DNA

This method uses multi-threading to build the hash table.

buildIndexFile(int) - Method in class dna.DNA

This method calculates k-mer at every index from a DNA sequence and insert them into database.

C

C - sequence.Base

clearTable(int) - Method in class dna.DNA

Clears the table.

clearTable(int) - Method in class sequence.DiskSequence

Clears table corresponding to the length of the k-mer.

close() - Method in class sequence.DiskSequence

D

DiskSequence - Class in sequence

DiskSequence(File) - Constructor for class sequence.DiskSequence

dna - package dna

DNA - Class in dna

DNA() - Constructor for class dna.DNA

Constructor for FASTA file process.

DNA(int) - Constructor for class dna.DNA

Constructor for random generation of DNA sequence.

DNA(File) - Constructor for class dna.DNA

Constructor that takes file as an argument and saves it in class.

DNA(String) - Constructor for class dna.DNA

Constructor that takes DNA string, convert them into Base, and insert into list.

F

findIndex(Map<Long, List<Integer>>, DNA) - Method in class dna.DNA

This method searches for start indices that contains the k-mer.

findIndexFast(Map<Long, List<Integer>>, DNA) - Method in class dna.DNA

This method utilizes stream to compare k-mer from the DNA sequence and the actual k-mer and find the indices that matches.

fromString(String) - Static method in class sequence.MemorySequence

Constructs a new MemorySequence from the input sequence string that contains A, G, T, and C.

G

G - sequence.Base

getBase(long) - Method in class sequence.DiskSequence

getBase(long) - Method in class sequence.MemorySequence

getBase(long) - Method in interface sequence.Sequence

getIndex(DNA) - Method in class dna.DNA

Brute force search.

getIndexBit(DNA) - Method in class dna.DNA

Calculate hash values of sub-sequences using Rabin-Karp algorithm and bit operation.

getIndexDB(DNA) - Method in class dna.DNA

This method finds the index of the DNA hash value that matches that of the k-mer.

getIndexFast(DNA) - Method in class dna.DNA

This method utilizes multi-threading to find the matching indices of the DNA sequence to that of the actual k-mer.

getIndexFile(DNA) - Method in class dna.DNA

getIndexHash(DNA) - Method in class dna.DNA

This method calculates hash value of k-mer from the sequence using Rabin-Karp algorithm.

getIndexRange(DNA, int, int) - Method in class dna.DNA

This method uses brute force to find indices of k-mer from the sequence that matches the actual k-mer.

getMatchingPositions(Sequence) - Method in class sequence.DiskSequence

getMatchingPositions(Sequence) - Method in class sequence.MemorySequence

getMatchingPositions(Sequence) - Method in interface sequence.Sequence

Gets positions of the sequence that matches with k-mer.

getSize() - Method in class dna.DNA

getSize() - Method in class sequence.DiskSequence

getSize() - Method in class sequence.MemorySequence

getSize() - Method in interface sequence.Sequence

getValue() - Method in enum sequence.Base

I

isSame(DNA, int) - Method in class dna.DNA

Compare each character of k-mer to each character of the entire sequence.

M

main(String[]) - Static method in class dna.Main

Main - Class in dna

Main() - Constructor for class dna.Main

MemorySequence - Class in sequence

An immutable sequence that is stored completely in memory.

R

random(int) - Static method in class sequence.MemorySequence

Generates a random MemorySequence of length k.

S

sequence - package sequence

Sequence - Interface in sequence

T

T - sequence.Base

toString() - Method in class dna.DNA

toString() - Method in enum sequence.Base

toString() - Method in class sequence.DiskSequence

V

valueOf(String) - Static method in enum sequence.Base

Returns the enum constant of this type with the specified name.

values() - Static method in enum sequence.Base

Returns an array containing the constants of this enum type, in the order they are declared.

viewDB(int) - Method in class dna.DNA

Views the database.

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