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 "globaldata.hpp"
16 #include "rabundvector.hpp"
17 #include "sabundvector.hpp"
18 #include "listvector.hpp"
21 class ClusterDoturCommand : public Command {
24 ClusterDoturCommand(string);
25 ClusterDoturCommand();
26 ~ClusterDoturCommand();
27 vector<string> getRequiredParameters();
28 vector<string> getValidParameters();
29 vector<string> getRequiredFiles();
30 map<string, vector<string> > getOutputFiles() { return outputTypes; }
36 string method, fileroot, tag, outputDir, phylipfile, namefile;
38 int precision, length;
39 ofstream sabundFile, rabundFile, listFile;
40 NameAssignment* nameMap;
43 RAbundVector oldRAbund;
46 void printData(string label);
47 vector<string> outputNames;
48 map<string, vector<string> > outputTypes;