#include "command.hpp"
#include "inputdata.h"
-#include "readotu.h"
#include "sharedlistvector.h"
#include "heatmap.h"
#include "rabundvector.hpp"
-class GlobalData;
class HeatMapCommand : public Command {
public:
HeatMapCommand(string);
- ~HeatMapCommand();
- int execute();
- void help();
+ HeatMapCommand();
+ ~HeatMapCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "heatmap.bin"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getOutputFileNameTag(string, string);
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Heatmap.bin"; }
+ string getDescription() { return "generate a heatmap where the color represents the relative abundanceof an OTU"; }
+
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
- GlobalData* globaldata;
- ReadOTUFile* read;
InputData* input;
- SharedListVector* SharedList;
RAbundVector* rabund;
vector<SharedRAbundVector*> lookup;
+ vector<SharedRAbundFloatVector*> lookupFloat;
HeatMap* heatmap;
bool abort, allLines;
set<string> labels; //holds labels to be used
- string format, groups, sorted, scale, label, outputDir;
+ string format, groups, sorted, scale, label, outputDir, sharedfile, relabundfile, listfile, rabundfile, sabundfile, inputfile;
vector<string> Groups, outputNames;
+ int numOTU, fontSize;
};