1 #ifndef CLASSIFYOTUSCOMMAND_H
2 #define CLASSIFYOTUSCOMMAND_H
8 * Created by westcott on 6/1/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "listvector.hpp"
15 #include "inputdata.h"
16 #include "counttable.h"
19 class ClassifyOtuCommand : public Command {
22 ClassifyOtuCommand(string);
24 ~ClassifyOtuCommand() {}
26 vector<string> setParameters();
27 string getCommandName() { return "classify.otu"; }
28 string getCommandCategory() { return "Phylotype Analysis"; }
29 string getOutputFileNameTag(string, string);
30 string getHelpString();
31 string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219.\nhttp://www.mothur.org/wiki/Classify.otu"; }
32 string getDescription() { return "find the concensus taxonomy for each OTU"; }
35 void help() { m->mothurOut(getHelpString()); }
42 string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis, countfile;
43 bool abort, allLines, probs;
45 set<string> labels; //holds labels to be used
46 vector<string> outputNames;
47 map<string, string> nameMap;
48 map<string, string> taxMap;
50 int process(ListVector*);
51 string addUnclassifieds(string, int);
52 vector<string> findConsensusTaxonomy(int, ListVector*, int&, string&); // returns the name of the "representative" taxonomy of given bin