1 #ifndef GETLINEAGECOMMAND_H
2 #define GETLINEAGECOMMAND_H
8 * Created by westcott on 9/24/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
15 class GetLineageCommand : public Command {
19 GetLineageCommand(string);
21 ~GetLineageCommand(){}
23 vector<string> setParameters();
24 string getCommandName() { return "get.lineage"; }
25 string getCommandCategory() { return "Phylotype Analysis"; }
26 string getHelpString();
29 void help() { m->mothurOut(getHelpString()); }
34 vector<string> outputNames;
35 string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
44 string removeConfidences(string);
45 vector< map<string, float> > getTaxons(string);