summarycommand.h

   1 #ifndef SUMMARYCOMMAND_H
   2 #define SUMMARYCOMMAND_H
   3 /*
   4  *  summarycommand.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 #include "command.hpp"
  13 #include "sabundvector.hpp"
  14 #include "inputdata.h"
  15 #include "calculator.h"
  16 #include "readotu.h"
  17 #include "validcalculator.h"
  18
  19 class GlobalData;
  20
  21 class SummaryCommand : public Command {
  22
  23 public:
  24         SummaryCommand(string);
  25         ~SummaryCommand();
  26         int execute();
  27         void help();
  28
  29 private:
  30         GlobalData* globaldata;
  31         ReadOTUFile* read;
  32         vector<Calculator*> sumCalculators;
  33         InputData* input;
  34         ValidCalculators* validCalculator;
  35         SAbundVector* sabund;
  36         int abund, size;
  37
  38         bool abort, allLines;
  39         set<string> labels; //holds labels to be used
  40         string label, calc;
  41         vector<string>  Estimators;
  42         vector<string> inputFileNames;
  43         vector<string> groups;
  44
  45         vector<string> parseSharedFile(string);
  46
  47
  48 };
  49 #endif