working on chimeras

[mothur.git] / blastdb.hpp

diff --git a/blastdb.hpp b/blastdb.hpp
index dfb2a2ced94ae71623856930ee0c348802530acd..fea55c8256e561af5477356b3c5bc545b30d6960 100644 (file)
--- a/blastdb.hpp
+++ b/blastdb.hpp
@@ -15,10 +15,15 @@
 #include "globaldata.hpp"
 
 class BlastDB : public Database {
+
 public:
-       BlastDB(string, float, float, float, float);
+       BlastDB(float, float, float, float);
        ~BlastDB();
-       Sequence* findClosestSequence(Sequence*);
+       
+       void generateDB();
+       void addSequence(Sequence);
+       vector<int> findClosestSequences(Sequence*, int);
+       map<int, float> findClosest(Sequence*, int); //template index -> searchscore
 
 private:
        string dbFileName;
@@ -26,11 +31,11 @@ private:
        string blastFileName;
        string path;
        
+       int count;
        float gapOpen;
        float gapExtend;
        float match;
        float misMatch;
-       Sequence* emptySequence;
        GlobalData* globaldata;
 };