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diff --git a/suffixdb.cpp b/suffixdb.cpp
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--- a/suffixdb.cpp
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-/*
- *  suffixdb.cpp
- *  
- *
- *  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 objecct
- *	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 "database.hpp"
-#include "sequence.hpp"
-#include "suffixtree.hpp"
-#include "suffixdb.hpp"
-
-/**************************************************************************************************/
-
-SuffixDB::SuffixDB(int numSeqs) : Database() {
-	suffixForest.resize(numSeqs);
-	count = 0;
-}
-/**************************************************************************************************/
-
-SuffixDB::SuffixDB() : Database() {
-	count = 0;
-}
-
-/**************************************************************************************************/
-//assumes sequences have been added using addSequence
-vector<int> SuffixDB::findClosestSequences(Sequence* candidateSeq, int num){
-	try {
-		vector<int> topMatches;
-		string processedSeq = candidateSeq->convert2ints();		//	the candidate sequence needs to be a string of ints
-		
-		vector<seqMatch> seqMatches;
-		for(int i=0;i<suffixForest.size();i++){					//	scan through the forest and see what the minimum
-			int count = suffixForest[i].countSuffixes(processedSeq);	//	return score is and keep track of the
-			seqMatch temp(i, count);
-			seqMatches.push_back(temp);
-		}
-		
-		//sorts putting smallest matches first
-		sort(seqMatches.begin(), seqMatches.end(), compareSeqMatchesReverse);
-		
-		searchScore = seqMatches[0].match;
-		searchScore = 100 * (1. - searchScore / (float)processedSeq.length());
-		
-		//save top matches
-		for (int i = 0; i < num; i++) {
-			topMatches.push_back(seqMatches[i].seq);
-		}
-
-		//	return the Sequence object that has the minimum score
-		return topMatches;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SuffixDB", "findClosestSequences");
-		exit(1);
-	}	
-}
-/**************************************************************************************************/
-//adding the sequences generates the db
-void SuffixDB::addSequence(Sequence seq) {
-	try {
-		suffixForest[count].loadSequence(seq);		
-		count++;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SuffixDB", "addSequence");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-
-SuffixDB::~SuffixDB(){														
-	for (int i = (suffixForest.size()-1); i >= 0; i--) {  suffixForest.pop_back();  }
-}
-/**************************************************************************************************/