X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=blastdb.hpp;h=50a8379b68ec89130b7df1892aab4538daa77a1e;hb=372fb21ea66ced432b109225851a1b80ef0491a3;hp=dfb2a2ced94ae71623856930ee0c348802530acd;hpb=36a8526766106bce1412e530e99f9c699dd59105;p=mothur.git

diff --git a/blastdb.hpp b/blastdb.hpp
index dfb2a2c..50a8379 100644
--- a/blastdb.hpp
+++ b/blastdb.hpp
@@ -12,26 +12,34 @@
  */
 
 #include "mothur.h"
-#include "globaldata.hpp"
 
 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;
-	GlobalData* globaldata;
+	
 };
 
 #endif