heatmapcommand.h

   1 #ifndef HEATMAPCOMMAND_H
   2 #define HEATMAPCOMMAND_H
   3
   4 /*
   5  *  heatmapcommand.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 3/25/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15 #include "inputdata.h"
  16 #include "readotu.h"
  17 #include "sharedlistvector.h"
  18 #include "heatmap.h"
  19 #include "rabundvector.hpp"
  20
  21 class GlobalData;
  22
  23 class HeatMapCommand : public Command {
  24
  25 public:
  26         HeatMapCommand(string);
  27         HeatMapCommand();
  28         ~HeatMapCommand();
  29         vector<string> getRequiredParameters();
  30         vector<string> getValidParameters();
  31         vector<string> getRequiredFiles();
  32         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  33         int execute();
  34         void help();
  35
  36 private:
  37         GlobalData* globaldata;
  38         ReadOTUFile* read;
  39         InputData* input;
  40         SharedListVector* SharedList;
  41         RAbundVector* rabund;
  42         vector<SharedRAbundVector*> lookup;
  43         vector<SharedRAbundFloatVector*> lookupFloat;
  44         HeatMap* heatmap;
  45
  46         bool abort, allLines;
  47         set<string> labels; //holds labels to be used
  48         string format, groups, sorted, scale, label, outputDir;
  49         vector<string> Groups, outputNames;
  50         map<string, vector<string> > outputTypes;
  51         int numOTU, fontSize;
  52
  53
  54 };
  55
  56 #endif
  57