X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mantelcommand.h;h=33fa3ea21e91fa2663994947720080933fad3d61;hp=0646b294c0a53bd327aca2a256a4eaa9ba45735b;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=5553e33be3a45eee6bed2ac9a5c4ca0aa0e8d5e4

diff --git a/mantelcommand.h b/mantelcommand.h
index 0646b29..33fa3ea 100644
--- a/mantelcommand.h
+++ b/mantelcommand.h
@@ -17,13 +17,19 @@ 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 getOutputPattern(string);	
+	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 +38,6 @@ private:
 	int iters;
 	
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 };