X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=suffixtree.hpp;h=805b9b0fda003cbeade1ce5ea875cb994ab3c960;hb=5d6d303e481489e226fdf8d6c5385b99b50718bc;hp=387d4bdca798f423d4d86a123c5a552321412048;hpb=526a868606faa50caf86e7399f7554c0335b39e5;p=mothur.git

diff --git a/suffixtree.hpp b/suffixtree.hpp
index 387d4bd..805b9b0 100644
--- a/suffixtree.hpp
+++ b/suffixtree.hpp
@@ -27,8 +27,6 @@
 
 #include "mothur.h"
 
-using namespace std;
-
 class SuffixNode;
 
 //********************************************************************************************************************
@@ -40,10 +38,11 @@ public:
 	~SuffixTree();
 //	SuffixTree(string, string);
 
-	void loadSequence(Sequence*);
+	void loadSequence(Sequence);
 	string getSeqName();
 	void print();	
 	int countSuffixes(string, int&);
+	int countSuffixes(string);	
 
 private:	
 	void addPrefix(int);
@@ -61,6 +60,7 @@ private:
 	int nodeCounter;
 	string seqName;
 	string sequence;
+	MothurOut* m;
 	
 };