1 #ifndef CLUSTERDOTURCOMMAND_H
2 #define CLUSTERDOTURCOMMAND_H
5 * clusterdoturcommand.h
8 * Created by westcott on 10/27/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "nameassignment.hpp"
15 #include "rabundvector.hpp"
16 #include "sabundvector.hpp"
17 #include "listvector.hpp"
20 class ClusterDoturCommand : public Command {
23 ClusterDoturCommand(string);
24 ClusterDoturCommand();
25 ~ClusterDoturCommand(){}
27 vector<string> setParameters();
28 string getCommandName() { return "cluster.classic"; }
29 string getCommandCategory() { return "Clustering"; }
30 string getHelpString();
31 string getCitation() { return "http://www.mothur.org/wiki/Cluster.classic"; }
34 void help() { m->mothurOut(getHelpString()); }
37 bool abort, hard, sim;
38 string method, fileroot, tag, outputDir, phylipfile, namefile;
40 int precision, length;
41 ofstream sabundFile, rabundFile, listFile;
42 NameAssignment* nameMap;
45 RAbundVector oldRAbund;
48 void printData(string label);
49 vector<string> outputNames;