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 struct oligosPair {
  19         string forward;
  20         string reverse;
  21
  22         oligosPair() { forward = ""; reverse = "";  }
  23         oligosPair(string f, string r) : forward(f), reverse(r) {}
  24         ~oligosPair() {}
  25 };
  26
  27 class TrimOligos {
  28
  29         public:
  30         TrimOligos(int,int, map<string, int>, map<string, int>, vector<string>); //pdiffs, bdiffs, primers, barcodes, revPrimers
  31         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
  32         TrimOligos(int,int, int, int, map<int, oligosPair>, map<int, oligosPair>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes
  33                 ~TrimOligos();
  34
  35                 int stripBarcode(Sequence&, int&);
  36                 int stripBarcode(Sequence&, QualityScores&, int&);
  37         int stripBarcode(Sequence&, Sequence&, QualityScores&, QualityScores&, int&);
  38         int stripBarcode(Sequence&, Sequence&, int&);
  39
  40                 int stripForward(Sequence&, int&);
  41                 int stripForward(Sequence&, QualityScores&, int&, bool);
  42         int stripForward(Sequence&, Sequence&, QualityScores&, QualityScores&, int&);
  43         int stripForward(Sequence&, Sequence&, int&);
  44
  45                 bool stripReverse(Sequence&);
  46                 bool stripReverse(Sequence&, QualityScores&);
  47
  48         bool stripLinker(Sequence&);
  49         bool stripLinker(Sequence&, QualityScores&);
  50
  51         bool stripSpacer(Sequence&);
  52         bool stripSpacer(Sequence&, QualityScores&);
  53
  54         //seq, primerStart, primerEnd
  55         bool findForward(Sequence&, int&, int&);
  56         bool findReverse(Sequence&, int&, int&);
  57
  58         string reverseOligo(string);
  59         string getTrashCode() { return trashCode; }
  60
  61
  62         private:
  63                 int pdiffs, bdiffs, ldiffs, sdiffs;
  64         bool paired;
  65         string trashCode;
  66
  67                 map<string, int> barcodes;
  68                 map<string, int> primers;
  69                 vector<string> revPrimer;
  70         vector<string> linker;
  71         vector<string> spacer;
  72         map<string, vector<int> > ifbarcodes;
  73         map<string, vector<int> > ifprimers;
  74         map<string, vector<int> > irbarcodes;
  75         map<string, vector<int> > irprimers;
  76         map<int, oligosPair> ipbarcodes;
  77         map<int, oligosPair> ipprimers;
  78
  79         int maxFBarcodeLength, maxRBarcodeLength, maxFPrimerLength, maxRPrimerLength, maxLinkerLength, maxSpacerLength;
  80
  81                 MothurOut* m;
  82
  83                 bool compareDNASeq(string, string);
  84                 int countDiffs(string, string);
  85
  86         int stripPairedBarcode(Sequence& seq, QualityScores& qual, int& group);
  87         int stripPairedPrimers(Sequence& seq, QualityScores& qual, int& group, bool);
  88 };
  89
  90 #endif
  91