Package dna

Class DNA

java.lang.Object

dna.DNA

public class DNA
extends Object

Constructor Summary

Constructors

Constructor	Description
DNA()	Constructor for FASTA file process.
DNA(int n)	Constructor for random generation of DNA sequence.
DNA(File file)	Constructor that takes file as an argument and saves it in class.
DNA(String dnaString)	Constructor that takes DNA string, convert them into Base, and insert into list.

Method Summary

Modifier and Type	Method	Description
Map<Long,List<Integer>>	buildIndex(int k)	Stores DNA hash values and its corresponding indices in hash table.
void	buildIndex(int start, int end, int k, Map<Long,List<Integer>> map)	This method builds hash table using DNA hash values and its indices.
Map<Long,List<Integer>>	buildIndexFast(int k)	This method uses multi-threading to build the hash table.
void	buildIndexFile(int k)	This method calculates k-mer at every index from a DNA sequence and insert them into database.
void	clearTable(int k)	Clears the table.
List<Integer>	findIndex(Map<Long,List<Integer>> map, DNA kmer)	This method searches for start indices that contains the k-mer.
List<Integer>	findIndexFast(Map<Long,List<Integer>> map, DNA kmer)	This method utilizes stream to compare k-mer from the DNA sequence and the actual k-mer and find the indices that matches.
List<Integer>	getIndex(DNA kmer)	Brute force search.
List<Integer>	getIndexBit(DNA kmer)	Calculate hash values of sub-sequences using Rabin-Karp algorithm and bit operation.
List<Long>	getIndexDB(DNA kmer)	This method finds the index of the DNA hash value that matches that of the k-mer.
List<Integer>	getIndexFast(DNA kmer)	This method utilizes multi-threading to find the matching indices of the DNA sequence to that of the actual k-mer.
List<Long>	getIndexFile(DNA kmer)
List<Integer>	getIndexHash(DNA kmer)	This method calculates hash value of k-mer from the sequence using Rabin-Karp algorithm.
List<Integer>	getIndexRange(DNA kmer, int start, int end)	This method uses brute force to find indices of k-mer from the sequence that matches the actual k-mer.
int	getSize()
boolean	isSame(DNA kmer, int index)	Compare each character of k-mer to each character of the entire sequence.
String	toString()
void	viewDB(int k)	Views the database.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

DNA

public DNA()

Constructor for FASTA file process.

DNA

public DNA(String dnaString)

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

Parameters:

dnaString - DNA sequence

DNA

public DNA(int n)

Constructor for random generation of DNA sequence.

Parameters:

n - of random sequence to be generated

DNA

public DNA(File file)

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

Parameters:

file - FASTA file

Method Detail

buildIndexFile

public void buildIndexFile(int k)
                    throws Exception

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

Parameters:

k - length of the k-mer

Throws:

Exception - if errors occur on database end, throws exception

clearTable

public void clearTable(int k)
                throws Exception

Clears the table.

Parameters:

k - length of the k-mer

Throws:

Exception - if the table cannot be cleared

viewDB

public void viewDB(int k)
            throws Exception

Views the database.

Parameters:

k - length of the k-mer

Throws:

Exception - when there is no database

getIndexDB

public List<Long> getIndexDB(DNA kmer)
                      throws Exception

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

Parameters:

kmer - The sequence of the k-mer

Returns:

the list with target indices

Throws:

Exception - when an error occurs during reading the input file or the database.

toString

public String toString()

Overrides:

toString in class Object

getIndex

public List<Integer> getIndex(DNA kmer)

Brute force search.

Parameters:

kmer - sequence of the k-mer

Returns:

list of first index of the sequence when the k-mer finds its match in the sequence

getIndexFile

public List<Long> getIndexFile(DNA kmer)

Parameters:

kmer - sequence of the k-mer

Returns:

the list with indices of k-mer from the sequence that matches the actual k-mer

getIndexRange

public List<Integer> getIndexRange(DNA kmer,
                                   int start,
                                   int end)

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

Parameters:

kmer - sequence of the k-mer

start - start index of the sequence

end - end index of the sequence

Returns:

the list with target indices

isSame

public boolean isSame(DNA kmer,
                      int index)

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

Parameters:

kmer - the sequence of the actual k-mer

index - index from the DNA sequence

Returns:

true if the k-mer finds its match in the sequence

getIndexHash

public List<Integer> getIndexHash(DNA kmer)

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

Parameters:

kmer - sequence of the actual k-mer

Returns:

list with indices of k-mer from the sequence that matches the hash value of the actual k-mer

getIndexBit

public List<Integer> getIndexBit(DNA kmer)

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

Parameters:

kmer - sequence of the actual k-mer

Returns:

list of indices of matching sub k-mer from the DNA sequence

buildIndex

public Map<Long,List<Integer>> buildIndex(int k)

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

Parameters:

k - length of the k-mer

Returns:

hash table with DNA hash values and list of target indices

buildIndex

public void buildIndex(int start,
                       int end,
                       int k,
                       Map<Long,List<Integer>> map)

This method builds hash table using DNA hash values and its indices. If there are duplicate DNA hash values in the map, this method simply adds the corresponding index to the existing list. Otherwise, it inserts the DNA hash value into the map and a new list with the current index.

Parameters:

start - start index

end - end index

k - length of the k-mer

map - hash table with DNA hash values and its corresponding indices

buildIndexFast

public Map<Long,List<Integer>> buildIndexFast(int k)

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

Parameters:

k - length of the k-mer

Returns:

map with specific hash value with corresponding index in a list

findIndexFast

public List<Integer> findIndexFast(Map<Long,List<Integer>> map,
                                   DNA kmer)

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

Parameters:

map - the hash table with DNA hash values and its corresponding list of indices

kmer - the sequence of the actual k-mer

Returns:

the list of indices that matches between k-mer from the DNA sequence and the actual k-mer

getSize

public int getSize()

Returns:

size of the base

findIndex

public List<Integer> findIndex(Map<Long,List<Integer>> map,
                               DNA kmer)

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

Parameters:

map - map with hash value with corresponding indices in a list

kmer - target k-mer

Returns:

list of indices

getIndexFast

public List<Integer> getIndexFast(DNA kmer)

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

Parameters:

kmer - the sequence of the k-mer

Returns:

the list with matching indices