added modify names parameter to set.dir

[mothur.git] / distancedb.hpp

diff --git a/distancedb.hpp b/distancedb.hpp
index dc4c9a6b46f8ee28b8db5b24b8b0bd083f03d033..2624d6d6440190520e02af09c43264bf365c9f33 100644 (file)
--- 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