X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=phylotypecommand.h;h=ef8b8f17e37051be4951d6dd662d0db1beb1dbaa;hp=e45e21b74a9ae58a6beef19a9a484344364c31de;hb=615301e57c25e241356a9c2380648d117709458d;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281

diff --git a/phylotypecommand.h b/phylotypecommand.h
index e45e21b..ef8b8f1 100644
--- a/phylotypecommand.h
+++ b/phylotypecommand.h
@@ -21,22 +21,27 @@ 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;
-	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;