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"; }
26 string getHelpString();
27 string getCitation() { return "http://www.mothur.org/wiki/Remove.lineage"; }
28 string getDescription() { return "removes sequences from a list, fasta, name, group, alignreport or taxonomy file from a given taxonomy or set of taxonomies"; }
31 void help() { m->mothurOut(getHelpString()); }
35 vector<string> outputNames, listOfTaxons;
36 string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
45 string removeConfidences(string);
46 vector< map<string, float> > getTaxons(string);