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diff --git a/kmerdb.cpp b/kmerdb.cpp
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-/*
- *  kmerdb.cpp
- *  
- *
- *  Created by Pat Schloss on 12/16/08.
- *  Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- *	This class is a child class of the Database class, which stores the template sequences as a kmer table and provides
- *	a method of searching the kmer table for the sequence with the most kmers in common with a query sequence.
- *	kmerLocations is the primary storage variable that is a two-dimensional vector where each row represents the
- *	different number of kmers and each column contains the index to sequences that use that kmer.
- *
- *	Construction of an object of this type will first look for an appropriately named database file and if it is found
- *	then will read in the database file (readKmerDB), otherwise it will generate one and store the data in memory
- *	(generateKmerDB)
- *
- *	The search method used here is roughly the same as that used in the SimRank program that is found at the
- *	greengenes website.  The default kmer size is 7.  The speed complexity is between O(L) and O(LN).  When I use 7mers
- *	on average a kmer is found in ~100 other sequences with a database of ~5000 sequences.  If this is the case then the
- *	time would be on the order of O(0.1LN) -> fast.
- *
-
- */
-
-#include "sequence.hpp"
-#include "kmer.hpp"
-#include "database.hpp"
-#include "kmerdb.hpp"
-
-/**************************************************************************************************/
-
-KmerDB::KmerDB(string fastaFileName, int kSize) : Database(), kmerSize(kSize) {
-	try { 
-	
-		kmerDBName = fastaFileName.substr(0,fastaFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
-		
-		int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 16777216, 67108864 };
-		count = 0;
-		
-		maxKmer = power4s[kmerSize];
-		kmerLocations.resize(maxKmer+1);
-		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "KmerDB", "KmerDB");
-		exit(1);
-	}	
-
-}
-/**************************************************************************************************/
-KmerDB::KmerDB() : Database() {}
-/**************************************************************************************************/
-
-KmerDB::~KmerDB(){}
-
-/**************************************************************************************************/
-
-vector<int> KmerDB::findClosestSequences(Sequence* candidateSeq, int num){
-	try {
-		if (num > numSeqs) { m->mothurOut("[WARNING]: you requested " + toString(num) + " closest sequences, but the template only contains " + toString(numSeqs) + ", adjusting."); m->mothurOutEndLine(); num = numSeqs; }
-		
-		vector<int> topMatches;
-		Kmer kmer(kmerSize);
-		searchScore = 0;
-		Scores.clear();
-		
-		vector<int> matches(numSeqs, 0);						//	a record of the sequences with shared kmers
-		vector<int> timesKmerFound(kmerLocations.size()+1, 0);	//	a record of the kmers that we have already found
-		
-		int numKmers = candidateSeq->getNumBases() - kmerSize + 1;	
-	
-		for(int i=0;i<numKmers;i++){
-			int kmerNumber = kmer.getKmerNumber(candidateSeq->getUnaligned(), i);		//	go through the query sequence and get a kmer number
-			if(timesKmerFound[kmerNumber] == 0){				//	if we haven't seen it before...
-				for(int j=0;j<kmerLocations[kmerNumber].size();j++){//increase the count for each sequence that also has
-					matches[kmerLocations[kmerNumber][j]]++;	//	that kmer
-				}
-			}
-			timesKmerFound[kmerNumber] = 1;						//	ok, we've seen the kmer now
-		}
-		
-		if (num != 1) {
-			vector<seqMatch> seqMatches; seqMatches.resize(numSeqs);
-			for(int i=0;i<numSeqs;i++){		
-				seqMatches[i].seq = i;
-				seqMatches[i].match = matches[i];
-			}
-			
-			//sorts putting largest matches first
-			sort(seqMatches.begin(), seqMatches.end(), compareSeqMatches);
-			
-			searchScore = seqMatches[0].match;
-			searchScore = 100 * searchScore / (float) numKmers;		//	return the Sequence object corresponding to the db
-		
-			//save top matches
-			for (int i = 0; i < num; i++) {
-				topMatches.push_back(seqMatches[i].seq);
-				float thisScore = 100 * seqMatches[i].match / (float) numKmers;
-				Scores.push_back(thisScore);
-			}
-		}else{
-			int bestIndex = 0;
-			int bestMatch = -1;
-			for(int i=0;i<numSeqs;i++){	
-				
-				if (matches[i] > bestMatch) {
-					bestIndex = i;
-					bestMatch = matches[i];
-				}
-			}
-			
-			searchScore = bestMatch;
-			searchScore = 100 * searchScore / (float) numKmers;		//	return the Sequence object corresponding to the db
-			topMatches.push_back(bestIndex);
-			Scores.push_back(searchScore);
-		}
-		return topMatches;		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "KmerDB", "findClosestSequences");
-		exit(1);
-	}	
-}
-
-/**************************************************************************************************/
-
-void KmerDB::generateDB(){
-	try {
-		
-		ofstream kmerFile;										//	once we have the kmerLocations folder print it out
-		m->openOutputFile(kmerDBName, kmerFile);					//	to a file
-		
-		//output version
-		kmerFile << "#" << m->getVersion() << endl;
-		
-		for(int i=0;i<maxKmer;i++){								//	step through all of the possible kmer numbers
-			kmerFile << i << ' ' << kmerLocations[i].size();	//	print the kmer number and the number of sequences with
-			for(int j=0;j<kmerLocations[i].size();j++){			//	that kmer.  then print out the indices of the sequences
-				kmerFile << ' ' << kmerLocations[i][j];			//	with that kmer.
-			}
-			kmerFile << endl;
-		}
-		kmerFile.close();
-		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "KmerDB", "generateDB");
-		exit(1);
-	}	
-	
-}
-/**************************************************************************************************/
-void KmerDB::addSequence(Sequence seq) {
-	try {
-		Kmer kmer(kmerSize);
-		
-		string unaligned = seq.getUnaligned();	//	...take the unaligned sequence...
-		int numKmers = unaligned.length() - kmerSize + 1;
-			
-		vector<int> seenBefore(maxKmer+1,0);
-		for(int j=0;j<numKmers;j++){						//	...step though the sequence and get each kmer...
-			int kmerNumber = kmer.getKmerNumber(unaligned, j);
-			if(seenBefore[kmerNumber] == 0){
-				kmerLocations[kmerNumber].push_back(count);		//	...insert the sequence index into kmerLocations for
-			}												//	the appropriate kmer number
-			seenBefore[kmerNumber] = 1;
-		}													
-	
-		count++;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "KmerDB", "addSequence");
-		exit(1);
-	}	
-}
-/**************************************************************************************************/
-
-void KmerDB::readKmerDB(ifstream& kmerDBFile){
-	try {
-					
-		kmerDBFile.seekg(0);									//	start at the beginning of the file
-		
-		//read version
-		string line = m->getline(kmerDBFile); m->gobble(kmerDBFile);
-		
-		string seqName;
-		int seqNumber;
-
-		for(int i=0;i<maxKmer;i++){
-			int numValues = 0;	
-			kmerDBFile >> seqName >> numValues;
-			
-			for(int j=0;j<numValues;j++){						//	for each kmer number get the...
-				kmerDBFile >> seqNumber;						//		1. number of sequences with the kmer number
-				kmerLocations[i].push_back(seqNumber);			//		2. sequence indices
-			}
-		}
-		kmerDBFile.close();
-		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "KmerDB", "readKmerDB");
-		exit(1);
-	}	
-}
-
-/**************************************************************************************************/
-int KmerDB::getCount(int kmer) {
-	try {
-		if (kmer < 0) { return 0; }  //if user gives negative number
-		else if (kmer > maxKmer) {	return 0;	}  //or a kmer that is bigger than maxkmer
-		else {	return kmerLocations[kmer].size();	}  // kmer is in vector range
-	}
-	catch(exception& e) {
-		m->errorOut(e, "KmerDB", "getCount");
-		exit(1);
-	}	
-}
-/**************************************************************************************************/
-int KmerDB::getReversed(int kmerNumber) {
-	try {
-		Kmer kmer(kmerSize);
-		
-		if (kmerNumber < 0) { return 0; }  //if user gives negative number
-		else if (kmerNumber > maxKmer) {	return 0;	}  //or a kmer that is bigger than maxkmer
-		else {	return kmer.getReverseKmerNumber(kmerNumber);	}  // kmer is in vector range
-	}
-	catch(exception& e) {
-		m->errorOut(e, "KmerDB", "getReversed");
-		exit(1);
-	}	
-}
-/**************************************************************************************************/
-vector<int> KmerDB::getSequencesWithKmer(int kmer) {
-	try {
-		
-		vector<int> seqs;
-	
-		if (kmer < 0) { }  //if user gives negative number
-		else if (kmer > maxKmer) {	}  //or a kmer that is bigger than maxkmer
-		else {	seqs = kmerLocations[kmer];	}
-		
-		return seqs;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "KmerDB", "getSequencesWithKmer");
-		exit(1);
-	}	
-}
-/**************************************************************************************************/
-
-
-/**************************************************************************************************/
-
-