1 #ifndef OTUHIERARCHYCOMMAND_H
2 #define OTUHIERARCHYCOMMAND_H
4 * otuhierarchycommand.h
7 * Created by westcott on 1/19/10.
8 * Copyright 2010 Schloss Lab. All rights reserved.
12 #include "command.hpp"
13 #include "listvector.hpp"
15 //**********************************************************************************************************************
17 class OtuHierarchyCommand : public Command {
20 OtuHierarchyCommand(string);
21 OtuHierarchyCommand();
22 ~OtuHierarchyCommand(){}
24 vector<string> setParameters();
25 string getCommandName() { return "otu.hierarchy"; }
26 string getCommandCategory() { return "OTU-Based Approaches"; }
28 string getHelpString();
29 string getOutputPattern(string);
30 string getCitation() { return "http://www.mothur.org/wiki/Otu.hierarchy"; }
31 string getDescription() { return "relates OTUs at different distances"; }
35 void help() { m->mothurOut(getHelpString()); }
40 set<string> labels; //holds labels to be used
41 string label, listFile, outputDir, output;
42 vector<string> outputNames;
44 vector<ListVector> getListVectors();
48 //**********************************************************************************************************************