X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=indicatorcommand.h;h=578aa95cbd6ebd773e6595c875ef487fe4a6861b;hb=4de093e3b92bdab1579565cb2873553412f6671e;hp=0ec100aecba915fb304e72146d06cbe2376ce8aa;hpb=3247d888e7aafc4a65ec9062a94dfd166c2c5b1d;p=mothur.git

diff --git a/indicatorcommand.h b/indicatorcommand.h
index 0ec100a..578aa95 100644
--- a/indicatorcommand.h
+++ b/indicatorcommand.h
@@ -13,7 +13,6 @@
 #include "command.hpp"
 #include "readtree.h"
 #include "treemap.h"
-#include "globaldata.hpp"
 #include "sharedrabundvector.h"
 #include "sharedrabundfloatvector.h"
 #include "inputdata.h"
@@ -22,22 +21,24 @@ class IndicatorCommand : public Command {
 public:
 	IndicatorCommand(string);
 	IndicatorCommand();
-	~IndicatorCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
+	~IndicatorCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "indicator";				}
+	string getCommandCategory()		{ return "Hypothesis Testing";		}
+	string getHelpString();	
+	string getCitation() { return "Dufrene M, Legendre P (1997). Species assemblages and indicator species: The need for a flexible asymmetrical approach. Ecol Monogr 67: 345-66.\n McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Indicator"; }
+	
 	int execute();
-	void help();
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	GlobalData* globaldata;
 	ReadTree* read;
 	TreeMap* treeMap;
-	string treefile, sharedfile, relabundfile, groups, label, inputFileName, outputDir;
+	GroupMap* designMap;
+	string treefile, sharedfile, relabundfile, groups, label, inputFileName, outputDir, designfile;
 	bool abort;
 	vector<string> outputNames, Groups;
-	map<string, vector<string> > outputTypes;
 	vector<SharedRAbundVector*> lookup;
 	vector<SharedRAbundFloatVector*> lookupFloat;