X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=amovacommand.h;h=98d19ddfc249d550c5d6d5b7c33cf036642393a0;hp=51a420064fc0e560cebb291035b1d9245febce5c;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=7b287636ea67fb2254b119c21b4057a177d3ce19

diff --git a/amovacommand.h b/amovacommand.h
index 51a4200..98d19dd 100644
--- a/amovacommand.h
+++ b/amovacommand.h
@@ -11,8 +11,6 @@
  */
 
 #include "command.hpp"
-
-//class GlobalData;
 class GroupMap;
 
 class AmovaCommand : public Command {
@@ -20,13 +18,19 @@ class AmovaCommand : public Command {
 public:
 	AmovaCommand(string);
 	AmovaCommand();
-	~AmovaCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
+	~AmovaCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "amova";					}
+	string getCommandCategory()		{ return "Hypothesis Testing";		}
+	
+	string getHelpString();	
+    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();
+	void help() { m->mothurOut(getHelpString()); }
 	
 private:
 	double runAMOVA(ofstream&, map<string, vector<int> >, double);
@@ -34,10 +38,8 @@ private:
 	double calcSSTotal(map<string, vector<int> >&);
 	map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
 
-	
 	bool abort;
-	map<string, vector<string> > outputTypes;
-	vector<string> outputNames;
+	vector<string> outputNames, Sets;
 
 	string outputDir, inputDir, designFileName, phylipFileName;
 	GroupMap* designMap;