8 * Created by Pat Schloss on 12/16/08.
9 * Copyright 2008 Patrick D. Schloss. All rights reserved.
11 * This is a child class of the Database abstract datatype. The class is basically a database of suffix trees and an
12 * encapsulation of the method for finding the most similar tree to an inputted sequence. the suffixForest object
13 * is a vector of SuffixTrees, with each template sequence being represented by a different SuffixTree. The class also
14 * provides a method to take an unaligned sequence and find the closest sequence in the suffixForest. The search
15 * method is inspired by the article and Perl source code provided at http://www.ddj.com/web-development/184416093. I
16 * would estimate that the time complexity is O(LN) for each search, which is slower than the kmer searching, but
22 #include "database.hpp"
26 class SuffixDB : public Database {
31 Sequence findClosestSequence(Sequence*);
34 vector<SuffixTree> suffixForest;