working on pam

[mothur.git] / suffixdb.hpp

diff --git a/suffixdb.hpp b/suffixdb.hpp
index 15114cf9a103707b67486864fd0d8b40f96e95c7..3796801a73c852bd61b6785d453d1cce825a0e66 100644 (file)
--- a/suffixdb.hpp
+++ b/suffixdb.hpp
@@ -20,17 +20,22 @@
 
 #include "mothur.h"
 #include "database.hpp"
-
-class SuffixTree;
+#include "suffixtree.hpp"
 
 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);
 
 private:
        vector<SuffixTree> suffixForest;
+       int count;
 };
 
 #endif