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#ifndef ALIGNMENTDB_H
#define ALIGNMENTDB_H
/*
* alignmentdb.h
* Mothur
*
* Created by westcott on 11/4/09.
* Copyright 2009 Schloss Lab. All rights reserved.
*
*/
#include "mothur.h"
#include "sequence.hpp"
#include "searchdatabase.hpp"
#include "utils.hpp"
#include "currentfile.h"
/**************************************************************************************************/
class AlignmentDB {
public:
AlignmentDB(string, string, int, float, float, float, float, int, bool); //reads fastafile passed in and stores sequences
AlignmentDB(string);
~AlignmentDB();
Sequence findClosestSequence(Sequence*, float&) const; //sequence to align, searchScore
int getLongestBase() { return longest; }
private:
int numSeqs, longest, threadID;
string method;
SearchDatabase* search;
vector<Sequence> templateSequences;
Sequence emptySequence;
MothurOut* m;
CurrentFile* current;
};
/**************************************************************************************************/
#endif
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