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();
33 void help() { m->mothurOut(getHelpString()); }
36 bool abort, hard, sim;
37 string method, fileroot, tag, outputDir, phylipfile, namefile;
39 int precision, length;
40 ofstream sabundFile, rabundFile, listFile;
41 NameAssignment* nameMap;
44 RAbundVector oldRAbund;
47 void printData(string label);
48 vector<string> outputNames;