Ανάπτυξη βιβλιοθήκης αλγορίθμων για ταίριασμα αλφαριθμητικών υποστηριζόμενη από οπτικοποίηση και σύγκριση των αποδόσεών τους με benchmarks σε βιολογικά δεδομένα

Abstract

String searching, the act of finding a string in an even larger text, is an important and well-studied field in computer science, with applications ranging from simple tasks such as finding words in a text editor or performing a spell check, to more complex ones like system intrusion detection systems and DNA sequence matching. Their importance creates the need for easily understandable, efficient implementations of those algorithms. This thesis attempts to provide an in-depth insight in the 35 string search algorithms presented by Charras and Lecroq, by presenting their underlying functionality, implementing them according to the object-oriented paradigm in the Java programming language, comparing them on a custom, Java-based benchmark suite on huge biological sequence data and animating them by implementing a visualization suite.