added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / suffixtree.hpp

diff --git a/suffixtree.hpp b/suffixtree.hpp
index 387d4bdca798f423d4d86a123c5a552321412048..492db54772ddcc1b2e2d60ea46c1700529453e22 100644 (file)
--- a/suffixtree.hpp
+++ b/suffixtree.hpp
@@ -27,8 +27,6 @@
 
 #include "mothur.h"
 
-using namespace std;
-
 class SuffixNode;
 
 //********************************************************************************************************************
@@ -39,11 +37,13 @@ public:
        SuffixTree();
        ~SuffixTree();
 //     SuffixTree(string, string);
+       SuffixTree(const SuffixTree&);
 
-       void loadSequence(Sequence*);
+       void loadSequence(Sequence);
        string getSeqName();
        void print();   
        int countSuffixes(string, int&);
+       int countSuffixes(string);      
 
 private:       
        void addPrefix(int);
@@ -61,6 +61,7 @@ private:
        int nodeCounter;
        string seqName;
        string sequence;
+       MothurOut* m;
        
 };