trimoligos.h

   1 #ifndef TRIMOLIGOS_H
   2 #define TRIMOLIGOS_H
   3
   4 /*
   5  *  trimoligos.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 9/1/11.
   9  *  Copyright 2011 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14 #include "mothurout.h"
  15 #include "sequence.hpp"
  16 #include "qualityscores.h"
  17
  18
  19 class TrimOligos {
  20
  21         public:
  22                 TrimOligos(int,int, map<string, int>, map<string, int>, vector<string>); //pdiffs, bdiffs, primers, barcodes, revPrimers
  23                 ~TrimOligos();
  24
  25                 int stripBarcode(Sequence&, int&);
  26                 int stripBarcode(Sequence&, QualityScores&, int&);
  27
  28                 int stripForward(Sequence&, int&);
  29                 int stripForward(Sequence&, QualityScores&, int&);
  30
  31                 bool stripReverse(Sequence&);
  32                 bool stripReverse(Sequence&, QualityScores&);
  33
  34
  35         private:
  36                 int pdiffs, bdiffs;
  37
  38                 map<string, int> barcodes;
  39                 map<string, int> primers;
  40                 vector<string> revPrimer;
  41
  42                 MothurOut* m;
  43
  44                 bool compareDNASeq(string, string);
  45                 int countDiffs(string, string);
  46 };
  47
  48 #endif
  49