* distancedb.hpp
*
*
- * Created by Pat Schloss on 12/29/08.
- * Copyright 2008 Patrick D. Schloss. All rights reserved.
+ * 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(string, string);
- vector<int> findClosestSequences(Sequence*, int);
+
+ 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:
-
- struct hit{
- string seqName;
- int indexNumber;
- float simScore;
- };
-
- vector<hit> mostSimSequenceVector;
- int searchIndex;
+ vector<Sequence> data;
+ Dist* distCalculator;
+
+ int templateSeqsLength;
+ bool templateAligned;
+
+ bool isAligned(string);
+
};
#endif