working on pam

[mothur.git] / nastreport.hpp

diff --git a/nastreport.hpp b/nastreport.hpp
index 2be289c2345df9929949ddc725936adb7ee0c1ab..c25575ae20b1a7be12a4af0586ed7734f6ec9691 100644 (file)
--- a/nastreport.hpp
+++ b/nastreport.hpp
@@ -19,6 +19,7 @@ class NastReport {
 
 public:
        NastReport(string);
+       NastReport();
        ~NastReport();
        void setCandidate(Sequence*);
        void setTemplate(Sequence*);
@@ -26,9 +27,12 @@ public:
        void setAlignmentParameters(string, Alignment*);
        void setNastParameters(Nast);
        void print();
+       string getReport();
+       string getHeaders();
        
 private:
        string queryName;
+       string output;
        int queryLength;
        string templateName;
        int templateLength;
@@ -43,6 +47,7 @@ private:
        int totalGapsInQuery, totalGapsInTemplate;
        float similarityToTemplate;
        ofstream candidateReportFile;
+       MothurOut* m;
 };
 
 /******************************************************************************************************************/