added path search for lookup file in shhh.seqs

[mothur.git] / suffixtree.hpp

diff --git a/suffixtree.hpp b/suffixtree.hpp
index 387d4bdca798f423d4d86a123c5a552321412048..805b9b0fda003cbeade1ce5ea875cb994ab3c960 100644 (file)
--- 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;
        
 };