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 "validcalculator.h"
  16 #include "heatmapsim.h"
  17 #include "nameassignment.hpp"
  18
  19 class HeatMapSimCommand : public Command {
  20
  21 public:
  22         HeatMapSimCommand(string);
  23         HeatMapSimCommand();
  24         ~HeatMapSimCommand(){}
  25
  26         vector<string> setParameters();
  27         string getCommandName()                 { return "heatmap.sim";                         }
  28         string getCommandCategory()             { return "OTU-Based Approaches";        }
  29
  30         string getHelpString();
  31     string getOutputPattern(string);
  32         string getCitation() { return "http://www.mothur.org/wiki/Heatmap.sim"; }
  33         string getDescription()         { return "generate a heatmap indicating the pairwise distance between multiple samples using a variety of calculators"; }
  34
  35         int execute();
  36         void help() { m->mothurOut(getHelpString()); }
  37
  38
  39 private:
  40         InputData* input;
  41         vector<SharedRAbundVector*> lookup;
  42         vector<Calculator*> heatCalculators;
  43         HeatMapSim* heatmap;
  44         OptionParser* parser;
  45         bool abort, allLines;
  46         set<string> labels; //holds labels to be used
  47         string format, groups, label, calc, sharedfile, phylipfile, columnfile, countfile, namefile, outputDir, inputfile;
  48         vector<string> Estimators, Groups, outputNames;
  49         int fontsize;
  50
  51         int runCommandShared();
  52         int runCommandDist();
  53
  54
  55 };
  56
  57 #endif
  58