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         vector<string> getRequiredParameters();
  25         vector<string> getValidParameters();
  26         vector<string> getRequiredFiles();
  27         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  28         int execute();
  29         void help();
  30
  31 private:
  32
  33         ListVector* list;
  34         InputData* input;
  35         string listfile, namefile, taxfile, label, outputDir;
  36         bool abort, allLines, probs;
  37         int cutoff;
  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;
  43
  44         int readNamesFile();
  45         int readTaxonomyFile();
  46         void removeConfidences(string&);
  47         int process(ListVector*);
  48         string findConsensusTaxonomy(int, ListVector*, int&);   // returns the name of the "representative" taxonomy of given bin
  49
  50
  51 };
  52
  53 #endif
  54
  55