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(int,int, int, int, map<string, int>, map<string, int>, vector<string>, vector<string>, vector<string>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimers, linker, spacer
  24                 ~TrimOligos();
  25
  26                 int stripBarcode(Sequence&, int&);
  27                 int stripBarcode(Sequence&, QualityScores&, int&);
  28
  29                 int stripForward(Sequence&, int&);
  30                 int stripForward(Sequence&, QualityScores&, int&, bool);
  31
  32                 bool stripReverse(Sequence&);
  33                 bool stripReverse(Sequence&, QualityScores&);
  34
  35         bool stripLinker(Sequence&);
  36         bool stripLinker(Sequence&, QualityScores&);
  37
  38         bool stripSpacer(Sequence&);
  39         bool stripSpacer(Sequence&, QualityScores&);
  40
  41
  42         private:
  43                 int pdiffs, bdiffs, ldiffs, sdiffs;
  44
  45                 map<string, int> barcodes;
  46                 map<string, int> primers;
  47                 vector<string> revPrimer;
  48         vector<string> linker;
  49         vector<string> spacer;
  50
  51                 MothurOut* m;
  52
  53                 bool compareDNASeq(string, string);
  54                 int countDiffs(string, string);
  55 };
  56
  57 #endif
  58