X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getotuscommand.h;fp=getotuscommand.h;h=34562fe7cf8f426048e5f1e71d568039bef1a117;hb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;hp=ec69acb4c0381c6b2b5190abf1a88ae214751647;hpb=36a867cbd85d9c276d3c8d13f25a150bbbe2466b;p=mothur.git

diff --git a/getotuscommand.h b/getotuscommand.h
index ec69acb..34562fe 100644
--- a/getotuscommand.h
+++ b/getotuscommand.h
@@ -23,18 +23,20 @@ public:
 	GetOtusCommand(string);	
 	GetOtusCommand();
 	~GetOtusCommand(){}
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();	
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "get.otus";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getHelpString();	
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
 	string accnosfile, groupfile, listfile, outputDir, groups, label;
 	bool abort;
 	vector<string> outputNames, Groups;
-	map<string, vector<string> > outputTypes;
 	GroupMap* groupMap;
 	
 	void readAccnos();