X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=suffixtree.hpp;h=d2b69e42325777d508a23000b0bc0924e0cc34f9;hp=387d4bdca798f423d4d86a123c5a552321412048;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=526a868606faa50caf86e7399f7554c0335b39e5

diff --git a/suffixtree.hpp b/suffixtree.hpp
index 387d4bd..d2b69e4 100644
--- a/suffixtree.hpp
+++ b/suffixtree.hpp
@@ -27,8 +27,6 @@
 
 #include "mothur.h"
 
-using namespace std;
-
 class SuffixNode;
 
 //********************************************************************************************************************
@@ -38,12 +36,12 @@ class SuffixTree {
 public:
 	SuffixTree();
 	~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 +59,7 @@ private:
 	int nodeCounter;
 	string seqName;
 	string sequence;
+	MothurOut* m;
 	
 };