added cluster.classic command

[mothur.git] / heatmapcommand.h

diff --git a/heatmapcommand.h b/heatmapcommand.h
index f75c06425e7b6af1232809fb8a2f1f98c20d98aa..a85d510074c55a73adc25b07f16a8a81bdd4a30c 100644 (file)
--- a/heatmapcommand.h
+++ b/heatmapcommand.h
@@ -13,32 +13,43 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "sharedlistvector.h"
 #include "heatmap.h"
-#include "sharedutilities.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;
-       SharedUtil* util;
+       ReadOTUFile* read;
        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;
+       vector<string> Groups, outputNames;
+       map<string, vector<string> > outputTypes;
+       int numOTU, fontSize;
+
 
 };