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>, map<string, int>, vector<string>, vector<string>, vector<string>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, rbarcodes, revPrimers, linker, spacer
  24         TrimOligos(int,int, int, int, map<string, int>, map<string, int>, vector<string>, vector<string>, vector<string>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, rbarcodes, revPrimers, linker, spacer
  25                 ~TrimOligos();
  26
  27                 int stripBarcode(Sequence&, int&);
  28                 int stripBarcode(Sequence&, QualityScores&, int&);
  29
  30         int stripRBarcode(Sequence&, int&);
  31         int stripRBarcode(Sequence&, QualityScores&, int&);
  32
  33                 int stripForward(Sequence&, int&);
  34                 int stripForward(Sequence&, QualityScores&, int&, bool);
  35
  36                 bool stripReverse(Sequence&);
  37                 bool stripReverse(Sequence&, QualityScores&);
  38
  39         bool stripLinker(Sequence&);
  40         bool stripLinker(Sequence&, QualityScores&);
  41
  42         bool stripSpacer(Sequence&);
  43         bool stripSpacer(Sequence&, QualityScores&);
  44
  45
  46         private:
  47                 int pdiffs, bdiffs, ldiffs, sdiffs;
  48
  49                 map<string, int> barcodes;
  50         map<string, int> rbarcodes;
  51                 map<string, int> primers;
  52                 vector<string> revPrimer;
  53         vector<string> linker;
  54         vector<string> spacer;
  55
  56                 MothurOut* m;
  57
  58                 bool compareDNASeq(string, string);
  59                 int countDiffs(string, string);
  60 };
  61
  62 #endif
  63