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(){};
23 vector<string> setParameters();
24 string getCommandName() { return "remove.lineage"; }
25 string getCommandCategory() { return "Phylotype Analysis"; }
27 string getHelpString();
28 string getOutputPattern(string);
29 string getCitation() { return "http://www.mothur.org/wiki/Remove.lineage"; }
30 string getDescription() { return "removes sequences from a list, fasta, name, group, alignreport or taxonomy file from a given taxonomy or set of taxonomies"; }
33 void help() { m->mothurOut(getHelpString()); }
37 vector<string> outputNames, listOfTaxons;
38 string fastafile, namefile, groupfile, alignfile, listfile, countfile, taxfile, outputDir, taxons;
48 vector< map<string, float> > getTaxons(string);