#include "command.hpp"
#include "inputdata.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
#include "sharedlistvector.h"
-
+#include "heatmap.h"
+#include "rabundvector.hpp"
class GlobalData;
-
class HeatMapCommand : public Command {
public:
+ HeatMapCommand(string);
HeatMapCommand();
~HeatMapCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
+ void help();
private:
GlobalData* globaldata;
- ReadMatrix* read;
+ ReadOTUFile* read;
InputData* input;
SharedListVector* SharedList;
- SharedOrderVector* order;
- OrderVector* ordersingle;
- string format;
+ 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;
+ vector<string> Groups, outputNames;
+ map<string, vector<string> > outputTypes;
+ int numOTU, fontSize;
+
};