Table 1 Time complexity of different applications
Application | output size | standard CGR | quadtree CGR | Suffix Tree |
|---|---|---|---|---|
LCE | 1 | O(1) | O(1) | O(1) |
k-mismatch | N | O(kN) | O(kN) | O(kN) |
Exact palindromes | N | O(N) | O(N) | O(N) |
k-mismatch palindromes | N | O(kN) | O(kN) | O(kN) |
Exact tandem repeats | z | O(N log N + z) | O(N log N + z) | O(N log N + z) |
k-mismatch tandem repeats | z | O(kN log N + z) | O(kN log N + z) | O(kN log N + z) |
Longest common suffix | 1 | O(1) | O(1) | O(1) |
Exact match (MATCHES) | occ | O(N) | O(L + occ) | O(L + occ) |
Occurrences (COUNT) | 1 | O(N) | O(L + occ) | O(L + occ) |
Longest common substring | 1 | O(N log N) | O(N log N) | O(N) |