X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotypecommand.h;h=ecc7376ecb7ea1a312af1e374ae76fb089e08add;hb=133dddf9ffde5059e3ea8290a2e7742843e3f2b7;hp=0322daf423ab716022e2146b6d4f352911fed693;hpb=7a2154809d332281cf4006943a9bd94b8208c837;p=mothur.git

diff --git a/phylotypecommand.h b/phylotypecommand.h
index 0322daf..ecc7376 100644
--- a/phylotypecommand.h
+++ b/phylotypecommand.h
@@ -20,19 +20,33 @@ class PhylotypeCommand : public Command {
 	
 public:
 	PhylotypeCommand(string);	
-	~PhylotypeCommand();
-	int execute(); 
-	void help();	
+	PhylotypeCommand();
+	~PhylotypeCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "phylotype";		}
+	string getCommandCategory()		{ return "Clustering";		}
+	string getHelpString();	
+	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;
+	string taxonomyFileName, label, outputDir, namefile;
 	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;
 	map<int, int>::iterator itCurrent;
+	
+	int readNamesFile();
 
 };