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(int,int, int, int, map<int, oligosPair>, map<int, oligosPair>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes
  25                 ~TrimOligos();
  26
  27                 int stripBarcode(Sequence&, int&);
  28                 int stripBarcode(Sequence&, QualityScores&, int&);
  29         int stripBarcode(Sequence&, Sequence&, QualityScores&, QualityScores&, int&);
  30         int stripBarcode(Sequence&, Sequence&, int&);
  31
  32                 int stripForward(Sequence&, int&);
  33                 int stripForward(Sequence&, QualityScores&, int&, bool);
  34         int stripForward(Sequence&, Sequence&, QualityScores&, QualityScores&, int&);
  35         int stripForward(Sequence&, Sequence&, int&);
  36
  37                 bool stripReverse(Sequence&);
  38                 bool stripReverse(Sequence&, QualityScores&);
  39
  40         bool stripLinker(Sequence&);
  41         bool stripLinker(Sequence&, QualityScores&);
  42
  43         bool stripSpacer(Sequence&);
  44         bool stripSpacer(Sequence&, QualityScores&);
  45
  46         //seq, primerStart, primerEnd
  47         bool findForward(Sequence&, int&, int&);
  48         bool findReverse(Sequence&, int&, int&);
  49
  50         string reverseOligo(string);
  51
  52         private:
  53                 int pdiffs, bdiffs, ldiffs, sdiffs;
  54         bool paired;
  55
  56                 map<string, int> barcodes;
  57                 map<string, int> primers;
  58                 vector<string> revPrimer;
  59         vector<string> linker;
  60         vector<string> spacer;
  61         map<string, vector<int> > ifbarcodes;
  62         map<string, vector<int> > ifprimers;
  63         map<string, vector<int> > irbarcodes;
  64         map<string, vector<int> > irprimers;
  65         map<int, oligosPair> ipbarcodes;
  66         map<int, oligosPair> ipprimers;
  67
  68         int maxFBarcodeLength, maxRBarcodeLength, maxFPrimerLength, maxRPrimerLength, maxLinkerLength, maxSpacerLength;
  69
  70                 MothurOut* m;
  71
  72                 bool compareDNASeq(string, string);
  73                 int countDiffs(string, string);
  74
  75         int stripPairedBarcode(Sequence& seq, QualityScores& qual, int& group);
  76         int stripPairedPrimers(Sequence& seq, QualityScores& qual, int& group, bool);
  77         int stripPairedBarcode(Sequence& seq,  int& group);
  78         int stripPairedPrimers(Sequence& seq,  int& group);
  79
  80 };
  81
  82 #endif
  83