worked on trim.seqs - added in the groupfiles for allfiles=t, cleaned up the outputNa...

[mothur.git] / blastdb.hpp

diff --git a/blastdb.hpp b/blastdb.hpp
index f0f17f9ce58bc8ee2b466cc9be6b95ddf53e207a..2e7423dcba612f332d7ef2f2657fac9aa16f1b79 100644 (file)
--- a/blastdb.hpp
+++ b/blastdb.hpp
@@ -15,22 +15,28 @@
 #include "globaldata.hpp"
 
 class BlastDB : public Database {
+
 public:
-       BlastDB(string, float, float, float, float);
+       BlastDB(float, float, float, float);
+       BlastDB();
        ~BlastDB();
-       Sequence findClosestSequence(Sequence*);
-
+       
+       void generateDB();
+       void addSequence(Sequence);
+       vector<int> findClosestSequences(Sequence*, int);
+       vector<int> findClosestMegaBlast(Sequence*, int);
+       
 private:
        string dbFileName;
        string queryFileName;
        string blastFileName;
        string path;
        
+       int count;
        float gapOpen;
        float gapExtend;
        float match;
        float misMatch;
-       Sequence emptySequence;
        GlobalData* globaldata;
 };