1 #ifndef PHYLOTYPECOMMAND_H
2 #define PHYLOTYPECOMMAND_H
9 * Created by westcott on 11/20/09.
10 * Copyright 2009 Schloss Lab. All rights reserved.
14 #include "taxonomyequalizer.h"
15 #include "command.hpp"
17 /*************************************************************************/
19 class PhylotypeCommand : public Command {
22 PhylotypeCommand(string);
26 vector<string> setParameters();
27 string getCommandName() { return "phylotype"; }
28 string getCommandCategory() { return "Clustering"; }
29 string getHelpString();
30 string getCitation() { return "http://www.mothur.org/wiki/Phylotype"; }
31 string getDescription() { return "cluster your sequences into OTUs based on their classifications"; }
34 void help() { m->mothurOut(getHelpString()); }
38 string taxonomyFileName, label, outputDir, namefile;
39 set<string> labels; //holds labels to be used
41 map<string, string> namemap;
42 vector<string> outputNames;
43 map<string, vector<string> > outputTypes;
45 map<int, int> currentNodes;
46 map<int, int> parentNodes;
47 map<int, int>::iterator itCurrent;
54 /*************************************************************************/