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"
14 #include "sharedrabundvector.h"
15 #include "listvector.hpp"
17 class GetLineageCommand : public Command {
21 GetLineageCommand(string);
23 ~GetLineageCommand(){}
25 vector<string> setParameters();
26 string getCommandName() { return "get.lineage"; }
27 string getCommandCategory() { return "Phylotype Analysis"; }
29 string getHelpString();
30 string getOutputPattern(string);
31 string getCitation() { return "http://www.mothur.org/wiki/Get.lineage"; }
32 string getDescription() { return "gets 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()); }
41 vector<string> outputNames, listOfTaxons;
42 string fastafile, namefile, groupfile, alignfile, countfile, listfile, taxfile, outputDir, taxons, sharedfile, constaxonomy, label;
44 vector<SharedRAbundVector*> lookup;
59 vector< map<string, float> > getTaxons(string);