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 getOutputFileNameTag(string, string);
  30         string getHelpString();
  31         string getCitation() { return "http://www.mothur.org/wiki/Parse.list"; }
  32         string getDescription()         { return "parses a list file by group"; }
  33
  34         int execute();
  35         void help() { m->mothurOut(getHelpString()); }
  36
  37 private:
  38         int parse(ListVector*);
  39
  40         ListVector* list;
  41         GroupMap* groupMap;
  42         InputData* input;
  43
  44         ofstream out;
  45         string outputDir, listfile, groupfile, label;
  46         set<string> labels;
  47         bool abort, allLines;
  48         vector<string> outputNames;
  49
  50         map<string, ofstream*> filehandles;
  51         map<string, ofstream*>::iterator it3;
  52
  53 };
  54
  55 /***************************************************************************************/
  56
  57 #endif
  58