#include "command.hpp"
#include "inputdata.h"
-#include "readotu.h"
#include "validcalculator.h"
#include "heatmapsim.h"
-
-class GlobalData;
+#include "nameassignment.hpp"
class HeatMapSimCommand : public Command {
public:
HeatMapSimCommand(string);
- ~HeatMapSimCommand();
- int execute();
- void help();
+ HeatMapSimCommand();
+ ~HeatMapSimCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "heatmap.sim"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Heatmap.sim"; }
+ string getDescription() { return "generate a heatmap indicating the pairwise distance between multiple samples using a variety of calculators"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
- GlobalData* globaldata;
- ReadOTUFile* read;
InputData* input;
vector<SharedRAbundVector*> lookup;
vector<Calculator*> heatCalculators;
- ValidCalculators* validCalculator;
HeatMapSim* heatmap;
OptionParser* parser;
- map<string, string> parameters;
- map<string, string>::iterator it;
bool abort, allLines;
set<string> labels; //holds labels to be used
- string format, groups, label, calc, phylipfile, columnfile, namefile;
- vector<string> Estimators, Groups;
+ string format, groups, label, calc, sharedfile, phylipfile, columnfile, namefile, outputDir, inputfile;
+ vector<string> Estimators, Groups, outputNames;
+ int fontsize;
int runCommandShared();
int runCommandDist();