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         ~ClassifyOtuCommand() {}
  24
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "classify.otu";                }
  27         string getCommandCategory()             { return "Phylotype Analysis";  }
  28         string getHelpString();
  29
  30         int execute();
  31         void help() { m->mothurOut(getHelpString()); }
  32
  33 private:
  34
  35         ListVector* list;
  36         InputData* input;
  37         string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis;
  38         bool abort, allLines, probs;
  39         int cutoff;
  40         set<string> labels; //holds labels to be used
  41         vector<string> outputNames;
  42         map<string, string> nameMap;
  43         map<string, string> taxMap;
  44
  45         int readNamesFile();
  46         int readTaxonomyFile();
  47         void removeConfidences(string&);
  48         int process(ListVector*);
  49         vector<string> findConsensusTaxonomy(int, ListVector*, int&, string&);  // returns the name of the "representative" taxonomy of given bin
  50
  51
  52 };
  53
  54 #endif
  55
  56