working on pam

[mothur.git] / nastreport.hpp

diff --git a/nastreport.hpp b/nastreport.hpp
index 424b0bbf1d9c3da79739c71efa6676c67b87abf5..c25575ae20b1a7be12a4af0586ed7734f6ec9691 100644 (file)
--- a/nastreport.hpp
+++ b/nastreport.hpp
@@ -13,23 +13,26 @@
 
 #include "mothur.h"
 
-using namespace std;
-
 /******************************************************************************************************************/
 
 class NastReport {
 
 public:
        NastReport(string);
+       NastReport();
+       ~NastReport();
        void setCandidate(Sequence*);
        void setTemplate(Sequence*);
        void setSearchParameters(string, float);
        void setAlignmentParameters(string, Alignment*);
        void setNastParameters(Nast);
        void print();
+       string getReport();
+       string getHeaders();
        
 private:
        string queryName;
+       string output;
        int queryLength;
        string templateName;
        int templateLength;
@@ -44,6 +47,7 @@ private:
        int totalGapsInQuery, totalGapsInTemplate;
        float similarityToTemplate;
        ofstream candidateReportFile;
+       MothurOut* m;
 };
 
 /******************************************************************************************************************/