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 #include "sequence.hpp"
  17
  18 class TrimSeqsCommand : public Command {
  19 public:
  20         TrimSeqsCommand();
  21         ~TrimSeqsCommand();
  22         int execute();
  23
  24 private:
  25         void getOligos();
  26         bool stripBarcode(Sequence&, string&);
  27         bool stripForward(Sequence&);
  28         bool stripReverse(Sequence&);
  29
  30         GlobalData* globaldata;
  31
  32         int totalBarcodeCount, matchBarcodeCount; // to be removed
  33         int totalFPrimerCount, matchFPrimerCount; // to be removed
  34         int totalRPrimerCount, matchRPrimerCount; // to be removed
  35
  36         bool oligos, flip;
  37         int numFPrimers, numRPrimers;
  38         vector<string> forPrimer, revPrimer;
  39         map<string, string> barcodes;
  40 };
  41
  42 #endif