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         void setCandidate(Sequence*);
  24         void setTemplate(Sequence*);
  25         void setSearchParameters(string, float);
  26         void setAlignmentParameters(string, Alignment*);
  27         void setNastParameters(Nast);
  28         void print();
  29
  30 private:
  31         string queryName;
  32         int queryLength;
  33         string templateName;
  34         int templateLength;
  35         string searchMethod;
  36         float searchScore;
  37         string alignmentMethod;
  38         int candidateStartPosition, candidateEndPosition;
  39         int templateStartPosition, templateEndPosition;
  40
  41         int pairwiseAlignmentLength;
  42         int longestInsert;
  43         int totalGapsInQuery, totalGapsInTemplate;
  44         float similarityToTemplate;
  45         ofstream candidateReportFile;
  46 };
  47
  48 /******************************************************************************************************************/
  49
  50 #endif