1 #ifndef REMOVELINEAGECOMMAND_H
2 #define REMOVELINEAGECOMMAND_H
5 * removelineagecommand.h
8 * Created by westcott on 9/24/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
15 class RemoveLineageCommand : public Command {
19 RemoveLineageCommand(string);
20 RemoveLineageCommand();
21 ~RemoveLineageCommand(){};
22 vector<string> getRequiredParameters();
23 vector<string> getValidParameters();
24 vector<string> getRequiredFiles();
25 map<string, vector<string> > getOutputFiles() { return outputTypes; }
31 vector<string> outputNames;
32 map<string, vector<string> > outputTypes;
33 string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
42 string removeConfidences(string);
43 vector< map<string, int> > getTaxons(string);