X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotypecommand.h;h=7fe10af58dde8ae842be2496376b3569df49bd29;hb=55bbd10379db27def51cec72a8819d775f73e45b;hp=e45e21b74a9ae58a6beef19a9a484344364c31de;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/phylotypecommand.h b/phylotypecommand.h
index e45e21b..7fe10af 100644
--- a/phylotypecommand.h
+++ b/phylotypecommand.h
@@ -21,13 +21,19 @@ class PhylotypeCommand : public Command {
 public:
 	PhylotypeCommand(string);	
 	PhylotypeCommand();
-	~PhylotypeCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute(); 
-	void help();	
+	~PhylotypeCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "phylotype";		}
+	string getCommandCategory()		{ return "Clustering";		}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Phylotype"; }
+	string getDescription()		{ return "cluster your sequences into OTUs based on their classifications"; }
+
+	int execute();
+	void help() { m->mothurOut(getHelpString()); }
 	
 private:
 	bool abort, allLines;