X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mantelcommand.h;h=0a2c4045960911c65c4ea43213c08add648663a6;hb=2c97dd48b8e27ee0a6a86c7a082f4c504c3357c6;hp=0646b294c0a53bd327aca2a256a4eaa9ba45735b;hpb=5553e33be3a45eee6bed2ac9a5c4ca0aa0e8d5e4;p=mothur.git

diff --git a/mantelcommand.h b/mantelcommand.h
index 0646b29..0a2c404 100644
--- a/mantelcommand.h
+++ b/mantelcommand.h
@@ -17,13 +17,17 @@ class MantelCommand : public Command {
 public:
 	MantelCommand(string);
 	MantelCommand();
-	~MantelCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
+	~MantelCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "mantel";					}
+	string getCommandCategory()		{ return "Hypothesis Testing";		}
+	string getHelpString();	
+	string getCitation() { return "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/Mantel"; }
+	string getDescription()		{ return "Mantel’s test for correlation between matrices"; }
+
 	int execute();
-	void help();
+	void help() { m->mothurOut(getHelpString()); }
 	
 private:
 	
@@ -32,7 +36,6 @@ private:
 	int iters;
 	
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 };