trimflowscommand.h

   1 #ifndef TRIMFLOWSCOMMAND_H
   2 #define TRIMFLOWSCOMMAND_H
   3
   4 /*
   5  *  trimflowscommand.h
   6  *  Mothur
   7  *
   8  *  Created by Pat Schloss on 12/22/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14 #include "command.hpp"
  15 #include "sequence.hpp"
  16 #include "flowdata.h"
  17 #include "groupmap.h"
  18
  19 class TrimFlowsCommand : public Command {
  20 public:
  21         TrimFlowsCommand(string);
  22         TrimFlowsCommand();
  23         ~TrimFlowsCommand();
  24         vector<string> getRequiredParameters();
  25         vector<string> getValidParameters();
  26         vector<string> getRequiredFiles();
  27         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  28         int execute();
  29         void help();
  30
  31 private:
  32         bool abort;
  33
  34         struct linePair {
  35                 unsigned long int start;
  36                 unsigned long int end;
  37                 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
  38         };
  39         int comboStarts;
  40         vector<int> processIDS;   //processid
  41         vector<linePair*> lines;
  42
  43         vector<unsigned long int> getFlowFileBreaks();
  44         int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >);
  45         int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
  46
  47
  48         map<string, vector<string> > outputTypes;
  49         vector<string> outputNames;
  50         set<string> filesToRemove;
  51
  52
  53
  54         void getOligos(vector<vector<string> >&);               //a rewrite of what is in trimseqscommand.h
  55         int stripBarcode(Sequence&, int&);                              //largely redundant with trimseqscommand.h
  56         int stripForward(Sequence&, int&);                              //largely redundant with trimseqscommand.h
  57         bool stripReverse(Sequence&);                                   //largely redundant with trimseqscommand.h
  58         bool compareDNASeq(string, string);                             //largely redundant with trimseqscommand.h
  59         int countDiffs(string, string);                                 //largely redundant with trimseqscommand.h
  60
  61         bool allFiles;
  62         int processors;
  63         int numFPrimers, numRPrimers;
  64         int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
  65         int numFlows;
  66         float signal, noise;
  67         bool fasta;
  68         string flowOrder;
  69
  70         string flowFileName, oligoFileName, outputDir;
  71
  72
  73         map<string, int> barcodes;
  74         map<string, int> primers;
  75         vector<string> revPrimer;
  76
  77         vector<string> primerNameVector;        //needed here?
  78         vector<string> barcodeNameVector;       //needed here?
  79
  80         map<string, int> combos;                        //needed here?
  81         map<string, int> groupToIndex;          //needed here?
  82
  83 };
  84
  85
  86 #endif