trimseqscommand.h

   1 #ifndef TRIMSEQSCOMMAND_H
   2 #define TRIMSEQSCOMMAND_H
   3
   4 /*
   5  *  trimseqscommand.h
   6  *  Mothur
   7  *
   8  *  Created by Pat Schloss on 6/6/09.
   9  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14 #include "command.hpp"
  15 #include "globaldata.hpp"
  16
  17 class TrimSeqsCommand : public Command {
  18 public:
  19         TrimSeqsCommand();
  20         ~TrimSeqsCommand();
  21         int execute();
  22
  23 private:
  24         void getOligos();
  25         bool stripBarcode(Sequence&, string&);
  26         bool stripForward(Sequence&);
  27         bool stripReverse(Sequence&);
  28
  29         GlobalData* globaldata;
  30
  31         int totalBarcodeCount, matchBarcodeCount;
  32         int totalFPrimerCount, matchFPrimerCount;
  33         int totalRPrimerCount, matchRPrimerCount;
  34
  35
  36         bool oligos, flip;
  37         int forwardPrimerMismatch, reversePrimerMismatch, barcodeMismatch;
  38         int numFPrimers, numRPrimers;
  39         vector<string> forPrimer, revPrimer;
  40         map<string, string> barcodes;
  41
  42 };
  43
  44 #endif