parselistscommand.h

   1 #ifndef PARSELISTCOMMAND_H
   2 #define PARSELISTCOMMAND_H
   3 /*
   4  *  parselistcommand.h
   5  *  Mothur
   6  *
   7  *  Created by westcott on 2/24/10.
   8  *  Copyright 2010 Schloss Lab. All rights reserved.
   9  *
  10  */
  11
  12 #include "command.hpp"
  13 #include "groupmap.h"
  14 #include "inputdata.h"
  15 #include "listvector.hpp"
  16
  17 /***************************************************************************************/
  18
  19 class ParseListCommand : public Command {
  20
  21 public:
  22         ParseListCommand(string);
  23         ParseListCommand();
  24         ~ParseListCommand() {}
  25
  26         vector<string> setParameters();
  27         string getCommandName()                 { return "parse.list";                          }
  28         string getCommandCategory()             { return "OTU-Based Approaches";        }
  29         string getHelpString();
  30         string getCitation() { return "http://www.mothur.org/wiki/Parse.list"; }
  31         string getDescription()         { return "parses a list file by group"; }
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36 private:
  37         int parse(ListVector*);
  38
  39         ListVector* list;
  40         GroupMap* groupMap;
  41         InputData* input;
  42
  43         ofstream out;
  44         string outputDir, listfile, groupfile, label;
  45         set<string> labels;
  46         bool abort, allLines;
  47         vector<string> outputNames;
  48
  49         map<string, ofstream*> filehandles;
  50         map<string, ofstream*>::iterator it3;
  51
  52 };
  53
  54 /***************************************************************************************/
  55
  56 #endif
  57