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"; }
30 string getHelpString();
31 string getOutputPattern(string);
32 string getCitation() { return "http://www.mothur.org/wiki/Phylotype"; }
33 string getDescription() { return "cluster your sequences into OTUs based on their classifications"; }
36 void help() { m->mothurOut(getHelpString()); }
40 string taxonomyFileName, label, outputDir, namefile, countfile;
41 set<string> labels; //holds labels to be used
43 map<string, string> namemap;
44 vector<string> outputNames;
46 map<int, int> currentNodes;
47 map<int, int> parentNodes;
48 map<int, int>::iterator itCurrent;
55 /*************************************************************************/