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