summarysharedcommand.h

   1 #ifndef SUMMARYSHAREDCOMMAND_H
   2 #define SUMMARYSHAREDCOMMAND_H
   3 /*
   4  *  summarysharedcommand.h
   5  *  Dotur
   6  *
   7  *  Created by Sarah Westcott on 1/2/09.
   8  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   9  *
  10  */
  11
  12
  13 #include "command.hpp"
  14 #include "sharedrabundvector.h"
  15 #include "inputdata.h"
  16 #include "calculator.h"
  17 #include "readotu.h"
  18 #include "validcalculator.h"
  19
  20 class GlobalData;
  21
  22 class SummarySharedCommand : public Command {
  23
  24 public:
  25         SummarySharedCommand(string);
  26         ~SummarySharedCommand();
  27         int execute();
  28         void help();
  29
  30 private:
  31         GlobalData* globaldata;
  32         ReadOTUFile* read;
  33         vector<Calculator*> sumCalculators;
  34         InputData* input;
  35         ValidCalculators* validCalculator;
  36
  37         bool abort, allLines, mult, all;
  38         set<string> labels; //holds labels to be used
  39         string label, calc, groups;
  40         vector<string>  Estimators, Groups;
  41         vector<SharedRAbundVector*> lookup;
  42         string outputFileName, format, outAllFileName, outputDir;
  43         ofstream outputFileHandle, outAll;
  44         void process(vector<SharedRAbundVector*>);
  45
  46 };
  47
  48 #endif