changed random forest output filename

[mothur.git] / heatmapcommand.h

diff --git a/heatmapcommand.h b/heatmapcommand.h
index a85d510074c55a73adc25b07f16a8a81bdd4a30c..fc5165ed65b9aa63e56de900acafcede5cc4d43c 100644 (file)
--- a/heatmapcommand.h
+++ b/heatmapcommand.h
@@ -13,31 +13,34 @@
 
 #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();
-       ~HeatMapCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~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;
-       ReadOTUFile* read;
        InputData* input;
-       SharedListVector* SharedList;
        RAbundVector* rabund;
        vector<SharedRAbundVector*> lookup;
        vector<SharedRAbundFloatVector*> lookupFloat;
@@ -45,9 +48,8 @@ private:
 
        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;
-       map<string, vector<string> > outputTypes;
        int numOTU, fontSize;