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"
14 #include "sharedrabundvector.h"
15 #include "listvector.hpp"
18 class RemoveLineageCommand : public Command {
22 RemoveLineageCommand(string);
23 RemoveLineageCommand();
24 ~RemoveLineageCommand(){};
26 vector<string> setParameters();
27 string getCommandName() { return "remove.lineage"; }
28 string getCommandCategory() { return "Phylotype Analysis"; }
30 string getHelpString();
31 string getOutputPattern(string);
32 string getCitation() { return "http://www.mothur.org/wiki/Remove.lineage"; }
33 string getDescription() { return "removes sequences from a list, fasta, name, group, alignreport or taxonomy file from a given taxonomy or set of taxonomies"; }
36 void help() { m->mothurOut(getHelpString()); }
40 vector<string> outputNames, listOfTaxons;
41 string fastafile, namefile, groupfile, alignfile, listfile, countfile, taxfile, outputDir, taxons, sharedfile, constaxonomy, label;
43 vector<SharedRAbundVector*> lookup;
58 vector< map<string, float> > getTaxons(string);