#include "command.hpp"
#include "inputdata.h"
-#include "readmatrix.hpp"
#include "sharedlistvector.h"
#include "heatmap.h"
-#include "sharedutilities.h"
-
-
-class GlobalData;
+#include "rabundvector.hpp"
class HeatMapCommand : public Command {
public:
+ HeatMapCommand(string);
HeatMapCommand();
- ~HeatMapCommand();
- int execute();
+ ~HeatMapCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "heatmap.bin"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ 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;
- ReadMatrix* read;
- SharedUtil* util;
InputData* input;
- SharedListVector* SharedList;
- SharedOrderVector* order;
- OrderVector* ordersingle;
+ RAbundVector* rabund;
+ vector<SharedRAbundVector*> lookup;
+ vector<SharedRAbundFloatVector*> lookupFloat;
HeatMap* heatmap;
- string format;
+
+ bool abort, allLines;
+ set<string> labels; //holds labels to be used
+ string format, groups, sorted, scale, label, outputDir, sharedfile, relabundfile, listfile, rabundfile, sabundfile, inputfile;
+ vector<string> Groups, outputNames;
+ int numOTU, fontSize;
+
};