added alignment code

[mothur.git] / distancedb.hpp

diff --git a/distancedb.hpp b/distancedb.hpp
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+#ifndef DISTANCEDB_HPP
+#define DISTANCEDB_HPP
+
+/*
+ *  distancedb.hpp
+ *  
+ *
+ *  Created by Pat Schloss on 12/29/08.
+ *  Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+
+using namespace std;
+
+#include "mothur.h"
+
+class DistanceDB : public Database {
+       
+public:
+       DistanceDB(string, string);
+       Sequence* findClosestSequence(Sequence*);
+       
+private:
+
+       struct hit{
+               string seqName;
+               int indexNumber;
+               float simScore;
+       };
+       vector<hit> mostSimSequenceVector;
+//     ifstream inputData;
+       int searchIndex;
+};
+
+#endif