changes while testing

[mothur.git] / heatmapsimcommand.h

diff --git a/heatmapsimcommand.h b/heatmapsimcommand.h
index 595f918f442352aea7dd94d6e62065b28398c6ca..f421fdc5bf2c3ff8aed22a197afc3309a86b4e34 100644 (file)
--- a/heatmapsimcommand.h
+++ b/heatmapsimcommand.h
@@ -12,35 +12,44 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "validcalculator.h"
 #include "heatmapsim.h"
-
-class GlobalData;
+#include "nameassignment.hpp"
 
 class HeatMapSimCommand : public Command {
 
 public:
        HeatMapSimCommand(string);
-       ~HeatMapSimCommand();
-       int execute();
-       void help();
+       HeatMapSimCommand();
+       ~HeatMapSimCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "heatmap.sim";                         }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Heatmap.sim"; }
+       string getDescription()         { return "generate a heatmap indicating the pairwise distance between multiple samples using a variety of calculators"; }
+
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
-       GlobalData* globaldata;
-       ReadOTUFile* read;
        InputData* input;
        vector<SharedRAbundVector*> lookup;
        vector<Calculator*> heatCalculators;
-       ValidCalculators* validCalculator;
        HeatMapSim* heatmap;
        OptionParser* parser;
-       map<string, string> parameters;
-       map<string, string>::iterator it;
        bool abort, allLines;
        set<string> labels; //holds labels to be used
-       string format, groups, label, calc;
-       vector<string> Estimators, Groups;
+       string format, groups, label, calc, sharedfile, phylipfile, columnfile, countfile, namefile, outputDir, inputfile;
+       vector<string> Estimators, Groups, outputNames;
+       int fontsize;
+       
+       int runCommandShared();
+       int runCommandDist();
 
 
 };