qualityscores.h

   1 #ifndef QUALITYSCORES
   2 #define QUALITYSCORES
   3
   4 /*
   5  *  qualityscores.h
   6  *  Mothur
   7  *
   8  *  Created by Pat Schloss on 7/12/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 //DataStructure for a quality file.
  14
  15
  16 #include "mothur.h"
  17 #include "mothurout.h"
  18 #include "sequence.hpp"
  19
  20 /**************************************************************************************************/
  21
  22 class QualityScores {
  23 public:
  24         QualityScores();
  25     QualityScores(string n, vector<int> qs);
  26         QualityScores(ifstream&);
  27         string getName();
  28         int getLength(){    return (int)qScores.size();  }
  29         vector<int> getQualityScores() { return qScores; }
  30         void printQScores(ofstream&);
  31         void trimQScores(int, int);
  32         void flipQScores();
  33         bool stripQualThreshold(Sequence&, double);
  34         bool stripQualRollingAverage(Sequence&, double, bool);
  35         bool stripQualWindowAverage(Sequence&, int, int, double, bool);
  36         bool cullQualAverage(Sequence&, double, bool);
  37         void updateQScoreErrorMap(map<char, vector<int> >&, string, int, int, int);
  38         void updateForwardMap(vector<vector<int> >&, int, int, int);
  39         void updateReverseMap(vector<vector<int> >&, int, int, int);
  40     void setName(string n);
  41     void setScores(vector<int> qs) { qScores = qs; seqLength = qScores.size(); }
  42     vector<int> getScores() { return qScores; }
  43
  44 private:
  45
  46         double calculateAverage(bool);
  47         MothurOut* m;
  48         vector<int> qScores;
  49
  50         string seqName;
  51         int seqLength;
  52
  53     string getSequenceName(ifstream&);
  54 };
  55
  56 /**************************************************************************************************/
  57
  58 #endif