1 #ifndef PHYLOTYPECOMMAND_H
2 #define PHYLOTYPECOMMAND_H
9 * Created by westcott on 11/20/09.
10 * Copyright 2009 Schloss Lab. All rights reserved.
14 #include "taxonomyequalizer.h"
15 #include "command.hpp"
17 /*************************************************************************/
19 class PhylotypeCommand : public Command {
22 PhylotypeCommand(string);
25 vector<string> getRequiredParameters();
26 vector<string> getValidParameters();
27 vector<string> getRequiredFiles();
28 map<string, vector<string> > getOutputFiles() { return outputTypes; }
34 string taxonomyFileName, label, outputDir, namefile;
35 set<string> labels; //holds labels to be used
37 map<string, string> namemap;
38 vector<string> outputNames;
39 map<string, vector<string> > outputTypes;
41 map<int, int> currentNodes;
42 map<int, int> parentNodes;
43 map<int, int>::iterator itCurrent;
50 /*************************************************************************/