heatmapsimcommand.h

   1 #ifndef HEATMAPSIMCOMMAND_H
   2 #define HEATMAPSIMCOMMAND_H
   3
   4 /*
   5  *  heatmapsimcommand.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 6/8/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "inputdata.h"
  15 #include "readotu.h"
  16 #include "validcalculator.h"
  17 #include "heatmapsim.h"
  18
  19 class GlobalData;
  20
  21 class HeatMapSimCommand : public Command {
  22
  23 public:
  24         HeatMapSimCommand(string);
  25         ~HeatMapSimCommand();
  26         int execute();
  27         void help();
  28
  29 private:
  30         GlobalData* globaldata;
  31         ReadOTUFile* read;
  32         InputData* input;
  33         vector<SharedRAbundVector*> lookup;
  34         vector<Calculator*> heatCalculators;
  35         ValidCalculators* validCalculator;
  36         HeatMapSim* heatmap;
  37         OptionParser* parser;
  38         map<string, string> parameters;
  39         map<string, string>::iterator it;
  40         bool abort, allLines;
  41         set<string> labels; //holds labels to be used
  42         string format, groups, label, calc, phylipfile, columnfile, namefile;
  43         vector<string> Estimators, Groups;
  44
  45         int runCommandShared();
  46         int runCommandDist();
  47
  48
  49 };
  50
  51 #endif
  52