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 "sequence.hpp"
  16
  17 class TrimSeqsCommand : public Command {
  18 public:
  19         TrimSeqsCommand(string);
  20         ~TrimSeqsCommand();
  21         int execute();
  22         void help();
  23
  24 private:
  25
  26         struct linePair {
  27                 int start;
  28                 int num;
  29                 linePair(long int i, int j) : start(i), num(j) {}
  30         };
  31
  32         void getOligos(vector<string>&);
  33         bool stripQualThreshold(Sequence&, ifstream&);
  34         bool cullQualAverage(Sequence&, ifstream&);
  35         bool stripBarcode(Sequence&, int&);
  36         bool stripForward(Sequence&);
  37         bool stripReverse(Sequence&);
  38         bool cullLength(Sequence&);
  39         bool cullHomoP(Sequence&);
  40         bool cullAmbigs(Sequence&);
  41         bool compareDNASeq(string, string);
  42
  43         bool abort;
  44         string fastaFile, oligoFile, qFileName, outputDir;
  45
  46         bool flip, allFiles, qtrim;
  47         int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors;
  48         vector<string> forPrimer, revPrimer, outputNames;
  49         map<string, int> barcodes;
  50         vector<string> groupVector;
  51
  52         vector<int> processIDS;   //processid
  53         vector<linePair*> lines;
  54         vector<linePair*> qLines;
  55
  56         int driverCreateTrim(string, string, string, string, string, vector<string>, linePair*, linePair*);
  57         int createProcessesCreateTrim(string, string, string, string, string, vector<string>);
  58         int setLines(string, vector<linePair*>&);
  59
  60 };
  61
  62 #endif