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 /******************************************************************************************************************/
  17
  18 class NastReport {
  19
  20 public:
  21         NastReport(string);
  22         NastReport();
  23         ~NastReport();
  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         string getReport();
  31         string getHeaders();
  32
  33 private:
  34         string queryName;
  35         string output;
  36         int queryLength;
  37         string templateName;
  38         int templateLength;
  39         string searchMethod;
  40         float searchScore;
  41         string alignmentMethod;
  42         int candidateStartPosition, candidateEndPosition;
  43         int templateStartPosition, templateEndPosition;
  44
  45         int pairwiseAlignmentLength;
  46         int longestInsert;
  47         int totalGapsInQuery, totalGapsInTemplate;
  48         float similarityToTemplate;
  49         ofstream candidateReportFile;
  50         MothurOut* m;
  51 };
  52
  53 /******************************************************************************************************************/
  54
  55 #endif