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
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "trim.flows";  }
  27         string getCommandCategory()             { return "Hidden";              }
  28         string getHelpString();
  29         string getCitation() { return "no citation"; }
  30
  31         int execute();
  32         void help() { m->mothurOut(getHelpString()); }
  33
  34 private:
  35         bool abort;
  36
  37         struct linePair {
  38                 unsigned long int start;
  39                 unsigned long int end;
  40                 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
  41         };
  42         int comboStarts;
  43         vector<int> processIDS;   //processid
  44         vector<linePair*> lines;
  45
  46         vector<unsigned long int> getFlowFileBreaks();
  47         int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >);
  48         int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
  49
  50         vector<string> outputNames;
  51         set<string> filesToRemove;
  52
  53         void getOligos(vector<vector<string> >&);               //a rewrite of what is in trimseqscommand.h
  54         int stripBarcode(Sequence&, int&);                              //largely redundant with trimseqscommand.h
  55         int stripForward(Sequence&, int&);                              //largely redundant with trimseqscommand.h
  56         bool stripReverse(Sequence&);                                   //largely redundant with trimseqscommand.h
  57         bool compareDNASeq(string, string);                             //largely redundant with trimseqscommand.h
  58         int countDiffs(string, string);                                 //largely redundant with trimseqscommand.h
  59
  60         bool allFiles;
  61         int processors;
  62         int numFPrimers, numRPrimers;
  63         int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
  64         int numFlows;
  65         float signal, noise;
  66         bool fasta;
  67         string flowOrder;
  68
  69         string flowFileName, oligoFileName, outputDir;
  70
  71
  72         map<string, int> barcodes;
  73         map<string, int> primers;
  74         vector<string> revPrimer;
  75
  76         vector<string> primerNameVector;        //needed here?
  77         vector<string> barcodeNameVector;       //needed here?
  78
  79         map<string, int> combos;                        //needed here?
  80         map<string, int> groupToIndex;          //needed here?
  81
  82 };
  83
  84
  85 #endif