changed random forest output filename

[mothur.git] / heatmapcommand.h

diff --git a/heatmapcommand.h b/heatmapcommand.h
index 5eeae265471785c8d582e7b250c76046554711e7..fc5165ed65b9aa63e56de900acafcede5cc4d43c 100644 (file)
--- a/heatmapcommand.h
+++ b/heatmapcommand.h
@@ -13,32 +13,45 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readmatrix.hpp"
 #include "sharedlistvector.h"
 #include "heatmap.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 getOutputPattern(string);   
+       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;
        InputData* input;
-       SharedListVector* SharedList;
-       SharedOrderVector* order;
-       OrderVector* ordersingle;
+       RAbundVector* rabund;
+       vector<SharedRAbundVector*> lookup;
+       vector<SharedRAbundFloatVector*> lookupFloat;
        HeatMap* heatmap;
-       string format;
-       
-       void setGroups();
+
+       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;
+
 
 };