X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=distancedb.hpp;h=2624d6d6440190520e02af09c43264bf365c9f33;hp=dc4c9a6b46f8ee28b8db5b24b8b0bd083f03d033;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=526a868606faa50caf86e7399f7554c0335b39e5

diff --git a/distancedb.hpp b/distancedb.hpp
index dc4c9a6..2624d6d 100644
--- a/distancedb.hpp
+++ b/distancedb.hpp
@@ -5,32 +5,41 @@
  *  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.
  *
  */
 
 
-using namespace std;
-
 #include "mothur.h"
+#include "dist.h"
 
 class DistanceDB : public Database {
 	
 public:
-	DistanceDB(string, string);
-	Sequence* findClosestSequence(Sequence*);
+	
+	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;
-//	ifstream inputData;
-	int searchIndex;
+	vector<Sequence> data;
+	Dist* distCalculator;
+	
+	int templateSeqsLength;
+	bool templateAligned;
+	
+	bool isAligned(string);
+	
 };
 
 #endif