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"; }
31 string getHelpString();
32 string getOutputPattern(string);
33 string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219.\nSchloss PD, Handelsman J (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-6.\nhttp://www.mothur.org/wiki/Cluster.classic\n";}
34 string getDescription() { return "cluster your sequences into OTUs using DOTUR’s method"; }
37 void help() { m->mothurOut(getHelpString()); }
40 bool abort, hard, sim;
41 string method, fileroot, tag, outputDir, phylipfile, namefile, countfile;
43 int precision, length;
44 ofstream sabundFile, rabundFile, listFile;
45 NameAssignment* nameMap;
48 RAbundVector oldRAbund;
51 void printData(string label);
52 vector<string> outputNames;