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);
23 ~ClassifyOtuCommand();
24 vector<string> getRequiredParameters();
25 vector<string> getValidParameters();
26 vector<string> getRequiredFiles();
27 map<string, vector<string> > getOutputFiles() { return outputTypes; }
35 string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis;
36 bool abort, allLines, probs;
38 set<string> labels; //holds labels to be used
39 vector<string> outputNames;
40 map<string, string> nameMap;
41 map<string, string> taxMap;
42 map<string, vector<string> > outputTypes;
45 int readTaxonomyFile();
46 void removeConfidences(string&);
47 int process(ListVector*);
48 vector<string> findConsensusTaxonomy(int, ListVector*, int&, string&); // returns the name of the "representative" taxonomy of given bin