X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=amovacommand.h;h=98d19ddfc249d550c5d6d5b7c33cf036642393a0;hp=ff82ac65f2d24ff122240d75fb326db2e03ff0c2;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77

diff --git a/amovacommand.h b/amovacommand.h
index ff82ac6..98d19dd 100644
--- a/amovacommand.h
+++ b/amovacommand.h
@@ -23,8 +23,11 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "amova";					}
 	string getCommandCategory()		{ return "Hypothesis Testing";		}
+	
 	string getHelpString();	
-	string getCitation() { return "Referenced: Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46. http://www.mothur.org/wiki/Amova"; }
+    string getOutputPattern(string);	
+    string getCitation() { return "Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.\nhttp://www.mothur.org/wiki/Amova"; }
+	string getDescription()		{ return "analysis of molecular variance"; }
 	
 	int execute();
 	void help() { m->mothurOut(getHelpString()); }
@@ -36,7 +39,7 @@ private:
 	map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
 
 	bool abort;
-	vector<string> outputNames;
+	vector<string> outputNames, Sets;
 
 	string outputDir, inputDir, designFileName, phylipFileName;
 	GroupMap* designMap;