X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=homovacommand.h;h=22741e979ec9b0847ca660f5ab41eab49fe715d5;hp=11f3c07fcebb96ddfe7a473aac8ccb0f234e167d;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=7b287636ea67fb2254b119c21b4057a177d3ce19

diff --git a/homovacommand.h b/homovacommand.h
index 11f3c07..22741e9 100644
--- a/homovacommand.h
+++ b/homovacommand.h
@@ -21,13 +21,19 @@ class HomovaCommand : public Command {
 public:
 	HomovaCommand(string);
 	HomovaCommand();
-	~HomovaCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
+	~HomovaCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "homova";					}
+	string getCommandCategory()		{ return "Hypothesis Testing";		}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "Stewart CN, Excoffier L (1996). Assessing population genetic structure and variability with RAPD data: Application to Vaccinium macrocarpon (American Cranberry). J Evol Biol 9: 153-71. \nhttp://www.mothur.org/wiki/Homova"; }
+	string getDescription()		{ return "homova"; }
+
 	int execute();
-	void help();
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	double runHOMOVA(ofstream& , map<string, vector<int> >, double);
@@ -36,8 +42,7 @@ private:
 	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;