X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=suffixdb.hpp;h=ca1ff42a11c6bcbd689e0e49e2cdfb36604e0807;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=f211aa7ba7f612613419c54e551cb0755d2dffc7;hpb=02909d6cae9963ba00dc746969a370fa8ca934fc;p=mothur.git

diff --git a/suffixdb.hpp b/suffixdb.hpp
index f211aa7..ca1ff42 100644
--- a/suffixdb.hpp
+++ b/suffixdb.hpp
@@ -20,18 +20,29 @@
 
 #include "mothur.h"
 #include "database.hpp"
-
-class SuffixTree;
+#include "suffixtree.hpp"
+//class SuffixTree;
 
 class SuffixDB : public Database {
 	
 public:
-	SuffixDB(string);
+	SuffixDB(int);
+	SuffixDB();
+	SuffixDB(const SuffixDB& sdb) : count(sdb.count), Database(sdb) {
+		for (int i = 0; i < sdb.suffixForest.size(); i++) {
+			SuffixTree temp(sdb.suffixForest[i]);
+			suffixForest.push_back(temp);
+		}
+	}
 	~SuffixDB();
-	Sequence findClosestSequence(Sequence*);
+	
+	void generateDB() {}; //adding sequences generates the db
+	void addSequence(Sequence);
+	vector<int> findClosestSequences(Sequence*, int);
 
 private:
 	vector<SuffixTree> suffixForest;
+	int count;
 };
 
 #endif