X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotypecommand.h;h=ef8b8f17e37051be4951d6dd662d0db1beb1dbaa;hb=372fb21ea66ced432b109225851a1b80ef0491a3;hp=a0411308e01121af1a56a68dd28218b421598cbc;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/phylotypecommand.h b/phylotypecommand.h
index a041130..ef8b8f1 100644
--- a/phylotypecommand.h
+++ b/phylotypecommand.h
@@ -26,20 +26,22 @@ public:
 	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;
-	string taxonomyFileName, label, outputDir, namefile;
+	string taxonomyFileName, label, outputDir, namefile, countfile;
 	set<string> labels; //holds labels to be used
 	int cutoff;
 	map<string, string> namemap;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 	
 	map<int, int> currentNodes;
 	map<int, int> parentNodes;