X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=amovacommand.h;fp=amovacommand.h;h=f50df46f70a3c6cce602ba8eeb5a4987c6dd2c95;hb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;hp=51a420064fc0e560cebb291035b1d9245febce5c;hpb=36a867cbd85d9c276d3c8d13f25a150bbbe2466b;p=mothur.git

diff --git a/amovacommand.h b/amovacommand.h
index 51a4200..f50df46 100644
--- a/amovacommand.h
+++ b/amovacommand.h
@@ -11,8 +11,6 @@
  */
 
 #include "command.hpp"
-
-//class GlobalData;
 class GroupMap;
 
 class AmovaCommand : public Command {
@@ -20,13 +18,15 @@ 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();	
+	
 	int execute();
-	void help();
+	void help() { m->mothurOut(getHelpString()); }
 	
 private:
 	double runAMOVA(ofstream&, map<string, vector<int> >, double);
@@ -34,9 +34,7 @@ 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;
 
 	string outputDir, inputDir, designFileName, phylipFileName;