classifyotucommand.h

   1 #ifndef CLASSIFYOTUSCOMMAND_H
   2 #define CLASSIFYOTUSCOMMAND_H
   3
   4 /*
   5  *  classifyotucommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 6/1/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "listvector.hpp"
  15 #include "inputdata.h"
  16
  17
  18 class ClassifyOtuCommand : public Command {
  19
  20 public:
  21         ClassifyOtuCommand(string);
  22         ~ClassifyOtuCommand();
  23         int execute();
  24         void help();
  25
  26 private:
  27
  28         ListVector* list;
  29         InputData* input;
  30         string listfile, namefile, taxfile, label, outputDir;
  31         bool abort, allLines, probs;
  32         int cutoff;
  33         set<string> labels; //holds labels to be used
  34         vector<string> outputNames;
  35         map<string, string> nameMap;
  36         map<string, string> taxMap;
  37
  38         int readNamesFile();
  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
  43
  44
  45 };
  46
  47 #endif
  48
  49