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         vector<string> getRequiredParameters();
  26         vector<string> getValidParameters();
  27         vector<string> getRequiredFiles();
  28         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  29         int execute();
  30         void help();
  31
  32 private:
  33         int parse(ListVector*);
  34
  35         ListVector* list;
  36         GroupMap* groupMap;
  37         InputData* input;
  38
  39         ofstream out;
  40         string outputDir, listfile, groupfile, label;
  41         set<string> labels;
  42         bool abort, allLines;
  43         vector<string> outputNames;
  44         map<string, vector<string> > outputTypes;
  45
  46         map<string, ofstream*> filehandles;
  47         map<string, ofstream*>::iterator it3;
  48
  49 };
  50
  51 /***************************************************************************************/
  52
  53 #endif
  54