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[mothur.git] / distancedb.hpp

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+#ifndef DISTANCEDB_HPP
+#define DISTANCEDB_HPP
+
+/*
+ *  distancedb.hpp
+ *  
+ *
+ *  Created by westcott on 1/27/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "mothur.h"
+#include "dist.h"
+
+class DistanceDB : public Database {
+       
+public:
+       
+       DistanceDB();
+       ~DistanceDB() { delete distCalculator; }
+       
+       void generateDB() {} //doesn't generate a search db 
+       void addSequence(Sequence); 
+       string getName(int i) { return data[i].getName(); } 
+       vector<int> findClosestSequences(Sequence*, int);  // returns indexes of n closest sequences to query
+       
+       #ifdef USE_MPI  
+       int MPISend(int) {return 0;}
+       int MPIRecv(int) {return 0;}
+       #endif
+       
+private:
+       vector<Sequence> data;
+       Dist* distCalculator;
+       
+       int templateSeqsLength;
+       bool templateAligned;
+       
+       bool isAligned(string);
+       
+};
+
+#endif