X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=blastdb.hpp;h=50a8379b68ec89130b7df1892aab4538daa77a1e;hp=a952897f05e496e09a6faaacf7c4de97d49bd132;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=526a868606faa50caf86e7399f7554c0335b39e5

diff --git a/blastdb.hpp b/blastdb.hpp
index a952897..50a8379 100644
--- a/blastdb.hpp
+++ b/blastdb.hpp
@@ -14,21 +14,32 @@
 #include "mothur.h"
 
 class BlastDB : public Database {
+
 public:
-	BlastDB(string, float, float, float, float);
+	BlastDB(string, float, float, float, float, string, int);
+	BlastDB(string, int);
 	~BlastDB();
-	Sequence* findClosestSequence(Sequence*);
-
+	
+	void generateDB();
+	void addSequence(Sequence);
+	vector<int> findClosestSequences(Sequence*, int);
+	vector<int> findClosestMegaBlast(Sequence*, int, int);
+	
 private:
+	
+	string scrubName(string);
+	
 	string dbFileName;
 	string queryFileName;
 	string blastFileName;
+	string path;
 	
+	int count, threadID;
 	float gapOpen;
 	float gapExtend;
 	float match;
 	float misMatch;
-	Sequence* emptySequence;
+	
 };
 
 #endif