getlistcountcommand.h

   1 #ifndef GETLISTCOUNTCOMMAND_H
   2 #define GETLISTCOUNTCOMMAND_H
   3 /*
   4  *  getlistcountcommand.h
   5  *  Mothur
   6  *
   7  *  Created by westcott on 10/12/09.
   8  *  Copyright 2009 Schloss Lab. All rights reserved.
   9  *
  10  */
  11
  12 #include "command.hpp"
  13 #include "inputdata.h"
  14 #include "listvector.hpp"
  15
  16 /**********************************************************/
  17
  18 class GetListCountCommand : public Command {
  19
  20 public:
  21         GetListCountCommand(string);
  22         GetListCountCommand();
  23         ~GetListCountCommand(){}
  24
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "get.otulist";                         }
  27         string getCommandCategory()             { return "OTU-Based Approaches";        }
  28         string getCitation() { return "http://www.mothur.org/wiki/Get.otulist"; }
  29         string getDescription()         { return "lists each OTU number and the sequence contained in that OTU"; }
  30
  31
  32         string getHelpString();
  33     string getOutputPattern(string);
  34
  35         int execute();
  36         void help() { m->mothurOut(getHelpString()); }
  37
  38
  39 private:
  40         ListVector* list;
  41         InputData* input;
  42
  43         bool abort, allLines;
  44         set<string> labels; //holds labels to be used
  45         string label, listfile, outputDir, sort;
  46         ofstream out;
  47         vector<string> outputNames;
  48
  49         void process(ListVector*);
  50 };
  51 /**********************************************************/
  52
  53 #endif