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"
18 class ClassifyOtuCommand : public Command {
21 ClassifyOtuCommand(string);
22 ~ClassifyOtuCommand();
30 string listfile, namefile, taxfile, label, outputDir;
31 bool abort, allLines, probs;
33 set<string> labels; //holds labels to be used
34 vector<string> outputNames;
35 map<string, string> nameMap;
36 map<string, string> taxMap;
39 int readTaxonomyFile();
40 void removeConfidences(string&);
41 int process(ListVector*);
42 string findConsensusTaxonomy(int, ListVector*, int&); // returns the name of the "representative" taxonomy of given bin