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#ifndef SUFFIXDB_HPP
#define SUFFIXDB_HPP
/*
* suffixdb.hpp
*
*
* Created by Pat Schloss on 12/16/08.
* Copyright 2008 Patrick D. Schloss. All rights reserved.
*
* This is a child class of the Database abstract datatype. The class is basically a database of suffix trees and an
* encapsulation of the method for finding the most similar tree to an inputted sequence. the suffixForest object
* is a vector of SuffixTrees, with each template sequence being represented by a different SuffixTree. The class also
* provides a method to take an unaligned sequence and find the closest sequence in the suffixForest. The search
* method is inspired by the article and Perl source code provided at http://www.ddj.com/web-development/184416093. I
* would estimate that the time complexity is O(LN) for each search, which is slower than the kmer searching, but
* faster than blast
*
*/
#include "mothur.h"
#include "searchdatabase.hpp"
#include "suffixtree.hpp"
class SuffixDB : public SearchDatabase {
public:
SuffixDB(int);
SuffixDB();
~SuffixDB();
void generateDB(){}; //adding sequences generates the db
void addSequence(Sequence);
vector<int> findClosestSequences(Sequence*, int, vector<float>&) const;
private:
vector<SuffixTree> suffixForest;
int count;
};
#endif
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