X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=blastdb.hpp;h=e2f4f57180560ae287c644a527553abde89e45e6;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=fea55c8256e561af5477356b3c5bc545b30d6960;hpb=5a1e62397b91f57d0d3aff635891df04b8999a88;p=mothur.git

diff --git a/blastdb.hpp b/blastdb.hpp
index fea55c8..e2f4f57 100644
--- a/blastdb.hpp
+++ b/blastdb.hpp
@@ -12,31 +12,36 @@
  */
 
 #include "mothur.h"
-#include "globaldata.hpp"
 
 class BlastDB : public Database {
 
 public:
-	BlastDB(float, float, float, float);
+	BlastDB(string, float, float, float, float, string, int);
+	BlastDB(string, int);
+	BlastDB(const BlastDB& bdb) : dbFileName(bdb.dbFileName), queryFileName(bdb.queryFileName), blastFileName(bdb.blastFileName), path(bdb.path),
+									count(bdb.count), gapOpen(bdb.gapOpen), gapExtend(bdb.gapExtend), match(bdb.match), misMatch(bdb.misMatch), Database(bdb) {}
 	~BlastDB();
 	
 	void generateDB();
 	void addSequence(Sequence);
 	vector<int> findClosestSequences(Sequence*, int);
-	map<int, float> findClosest(Sequence*, int); //template index -> searchscore
-
+	vector<int> findClosestMegaBlast(Sequence*, int, int);
+	
 private:
+	
+	string scrubName(string);
+	
 	string dbFileName;
 	string queryFileName;
 	string blastFileName;
 	string path;
 	
-	int count;
+	int count, threadID;
 	float gapOpen;
 	float gapExtend;
 	float match;
 	float misMatch;
-	GlobalData* globaldata;
+	
 };
 
 #endif