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 #include "readotu.h"
  16
  17 class GlobalData;
  18
  19 /**********************************************************/
  20
  21 class GetListCountCommand : public Command {
  22
  23 public:
  24         GetListCountCommand(string);
  25         GetListCountCommand();
  26         ~GetListCountCommand();
  27         vector<string> getRequiredParameters();
  28         vector<string> getValidParameters();
  29         vector<string> getRequiredFiles();
  30         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  31         int execute();
  32         void help();
  33
  34 private:
  35         GlobalData* globaldata;
  36         ListVector* list;
  37         ReadOTUFile* read;
  38         InputData* input;
  39
  40         bool abort, allLines;
  41         set<string> labels; //holds labels to be used
  42         string label, listfile, outputDir, sort;
  43         ofstream out;
  44         vector<string> outputNames;
  45         map<string, vector<string> > outputTypes;
  46
  47         void process(ListVector*);
  48 };
  49 /**********************************************************/
  50
  51 #endif