changes while testing

[mothur.git] / suffixtree.hpp

diff --git a/suffixtree.hpp b/suffixtree.hpp
index 387d4bdca798f423d4d86a123c5a552321412048..d2b69e42325777d508a23000b0bc0924e0cc34f9 100644 (file)
--- 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;
        
 };