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         ~SummaryCommand();
  27         vector<string> getRequiredParameters();
  28         vector<string> getValidParameters();
  29         vector<string> getRequiredFiles();
  30         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  31         int execute();
  32         void help();
  33
  34 private:
  35         GlobalData* globaldata;
  36         ReadOTUFile* read;
  37         vector<Calculator*> sumCalculators;
  38         InputData* input;
  39         ValidCalculators* validCalculator;
  40         SAbundVector* sabund;
  41         int abund, size;
  42
  43         bool abort, allLines, groupMode;
  44         set<string> labels; //holds labels to be used
  45         string label, calc, outputDir;
  46         vector<string>  Estimators;
  47         vector<string> inputFileNames, outputNames;
  48         map<string, vector<string> > outputTypes;
  49         vector<string> groups;
  50
  51         vector<string> parseSharedFile(string);
  52         string createGroupSummaryFile(int, int, vector<string>&);
  53
  54
  55 };
  56 #endif