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         ~HeatMapSimCommand();
  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         InputData* input;
  38         vector<SharedRAbundVector*> lookup;
  39         vector<Calculator*> heatCalculators;
  40         ValidCalculators* validCalculator;
  41         HeatMapSim* heatmap;
  42         OptionParser* parser;
  43         map<string, string> parameters;
  44         map<string, string>::iterator it;
  45         bool abort, allLines;
  46         set<string> labels; //holds labels to be used
  47         string format, groups, label, calc, phylipfile, columnfile, namefile, outputDir;
  48         vector<string> Estimators, Groups, outputNames;
  49         map<string, vector<string> > outputTypes;
  50
  51         int runCommandShared();
  52         int runCommandDist();
  53
  54
  55 };
  56
  57 #endif
  58