nastreport.hpp

   1 #ifndef NASTREPORT_HPP
   2 #define NASTREPORT_HPP
   3
   4
   5 /*
   6  *  nastreport.hpp
   7  *
   8  *
   9  *  Created by Pat Schloss on 12/19/08.
  10  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
  11  *
  12  */
  13
  14 #include "mothur.h"
  15
  16 using namespace std;
  17
  18 /******************************************************************************************************************/
  19
  20 class NastReport {
  21
  22 public:
  23         NastReport(string);
  24         void setCandidate(Sequence*);
  25         void setTemplate(Sequence*);
  26         void setSearchParameters(string, float);
  27         void setAlignmentParameters(string, Alignment*);
  28         void setNastParameters(Nast);
  29         void print();
  30
  31 private:
  32         string queryName;
  33         int queryLength;
  34         string templateName;
  35         int templateLength;
  36         string searchMethod;
  37         float searchScore;
  38         string alignmentMethod;
  39         int candidateStartPosition, candidateEndPosition;
  40         int templateStartPosition, templateEndPosition;
  41
  42         int pairwiseAlignmentLength;
  43         int longestInsert;
  44         int totalGapsInQuery, totalGapsInTemplate;
  45         float similarityToTemplate;
  46         ofstream candidateReportFile;
  47 };
  48
  49 /******************************************************************************************************************/
  50
  51 #endif