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
  30         string getHelpString();
  31     string getOutputPattern(string);
  32         string getCitation() { return "http://www.mothur.org/wiki/Parse.list"; }
  33         string getDescription()         { return "parses a list file by group"; }
  34
  35         int execute();
  36         void help() { m->mothurOut(getHelpString()); }
  37
  38 private:
  39         int parse(ListVector*);
  40
  41         ListVector* list;
  42         GroupMap* groupMap;
  43     CountTable ct;
  44
  45         ofstream out;
  46         string outputDir, listfile, groupfile, label, countfile;
  47         set<string> labels;
  48         bool abort, allLines;
  49         vector<string> outputNames;
  50
  51         map<string, ofstream*> filehandles;
  52         map<string, ofstream*>::iterator it3;
  53
  54 };
  55
  56 /***************************************************************************************/
  57
  58 #endif
  59