List<Integer> |
DNA.findIndex(Map<Long,List<Integer>> map,
DNA kmer) |
This method searches for start indices that contains the k-mer.
|
List<Integer> |
DNA.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> |
DNA.getIndex(DNA kmer) |
Brute force search.
|
List<Integer> |
DNA.getIndexBit(DNA kmer) |
Calculate hash values of sub-sequences using Rabin-Karp algorithm and bit operation.
|
List<Long> |
DNA.getIndexDB(DNA kmer) |
This method finds the index of the DNA hash value that matches that of the k-mer.
|
List<Integer> |
DNA.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> |
DNA.getIndexFile(DNA kmer) |
|
List<Integer> |
DNA.getIndexHash(DNA kmer) |
This method calculates hash value of k-mer from the sequence using Rabin-Karp algorithm.
|
List<Integer> |
DNA.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.
|
boolean |
DNA.isSame(DNA kmer,
int index) |
Compare each character of k-mer to each character of the entire sequence.
|