added alignment code

[mothur.git] / nastreport.hpp

diff --git a/nastreport.hpp b/nastreport.hpp
new file mode 100644 (file)
index 0000000..424b0bb
--- /dev/null
+++ b/nastreport.hpp
@@ -0,0 +1,51 @@
+#ifndef NASTREPORT_HPP
+#define NASTREPORT_HPP
+
+
+/*
+ *  nastreport.hpp
+ *  
+ *
+ *  Created by Pat Schloss on 12/19/08.
+ *  Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+#include "mothur.h"
+
+using namespace std;
+
+/******************************************************************************************************************/
+
+class NastReport {
+
+public:
+       NastReport(string);
+       void setCandidate(Sequence*);
+       void setTemplate(Sequence*);
+       void setSearchParameters(string, float);
+       void setAlignmentParameters(string, Alignment*);
+       void setNastParameters(Nast);
+       void print();
+       
+private:
+       string queryName;
+       int queryLength;
+       string templateName;
+       int templateLength;
+       string searchMethod;
+       float searchScore;
+       string alignmentMethod;
+       int candidateStartPosition, candidateEndPosition;
+       int templateStartPosition, templateEndPosition;
+
+       int pairwiseAlignmentLength;
+       int longestInsert;
+       int totalGapsInQuery, totalGapsInTemplate;
+       float similarityToTemplate;
+       ofstream candidateReportFile;
+};
+
+/******************************************************************************************************************/
+
+#endif