Date of Award
Fall 2011
Degree Type
Thesis
Degree Name
Master of Science (MSc)
Department
Computing and Software
Supervisor
Frantisek Franek
Co-Supervisor
Antoine Deza, Emil Sekerinski
Language
English
Committee Member
Antoine Deza, Emil Sekerinski
Abstract
In the first part of this thesis we present a C++ implementation of an improved O(n log n) algorithm to compute runs, number of primitively rooted distinct squares, and maximal repetitions, based on Crochemore's partitioning algorithm. This is a joint work with Mei Jiang and extends her work on the problem. In the second part we present a C++ implementation of a linear algorithm to compute runs based on the Main's, and Kolpakov and Kucherov's algorithms following the strategy:
1. Compute suffix array and LCP array in linear time;
2. Using the suffix array and LCP array, compute Lempel-Ziv factorization in linear time;
3. Using the Lempel-Ziv factorization, compute in linear time some of the runs that include all the leftmost runs following Main's algorithm;
4. Using Kolpakov and Kucherov's approach, compute in linear time the rest of all the runs.
For our linear time implementation, we partially relied on Jonathan Fischer's Java implementation.
Recommended Citation
Weng, Chia-Chun, "Implementing Efficient Algorithms for Computing Runs" (2011). Open Access Dissertations and Theses. Paper 6266.
http://digitalcommons.mcmaster.ca/opendissertations/6266
McMaster University Library