X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=anosimcommand.h;h=6e5aba0e65980914e6c25e6e0e55fadc4b0136b9;hb=bd27c2b0612942815b7417c79f7ee41f669a2a34;hp=ab724007237d508e1b2dabf1bba521c5c38f7497;hpb=7b287636ea67fb2254b119c21b4057a177d3ce19;p=mothur.git

diff --git a/anosimcommand.h b/anosimcommand.h
index ab72400..6e5aba0 100644
--- a/anosimcommand.h
+++ b/anosimcommand.h
@@ -20,18 +20,23 @@ class AnosimCommand : public Command {
 public:
 	AnosimCommand(string);
 	AnosimCommand();
-	~AnosimCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
+	~AnosimCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "anosim";					}
+	string getCommandCategory()		{ return "Hypothesis Testing";		}
+    
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "Clarke, K. R. (1993). Non-parametric multivariate analysis of changes in community structure. _Australian Journal of Ecology_ 18, 117-143.\nhttp://www.mothur.org/wiki/Anosim"; }
+	string getDescription()		{ return "analysis of similarity"; }
+	
 	int execute();
-	void help();
+	void help() { m->mothurOut(getHelpString()); }
 	
 private:
 	bool abort;
 	GroupMap* designMap;
-	map<string, vector<string> > outputTypes;
 	string outputDir, inputDir, designFileName, phylipFileName;
 	
 	vector<vector<double> > convertToRanks(vector<vector<double> >);