added set.logfile command

[mothur.git] / suffixdb.hpp

diff --git a/suffixdb.hpp b/suffixdb.hpp
index 15114cf9a103707b67486864fd0d8b40f96e95c7..4dc7e0fadd0cc1575250da05029d3ef32b388894 100644 (file)
--- a/suffixdb.hpp
+++ b/suffixdb.hpp
@@ -26,11 +26,22 @@ class SuffixTree;
 class SuffixDB : public Database {
        
 public:
-       SuffixDB(string);
-       Sequence* findClosestSequence(Sequence*);
+       SuffixDB(int);
+       SuffixDB();
+       ~SuffixDB();
+       
+       void generateDB() {}; //adding sequences generates the db
+       void addSequence(Sequence);
+       vector<int> findClosestSequences(Sequence*, int);
+       
+       #ifdef USE_MPI  
+       int MPISend(int); //just sends numSeqs
+       int MPIRecv(int);
+       #endif
 
 private:
        vector<SuffixTree> suffixForest;
+       int count;
 };
 
 #endif