getrepseqscommand.h

   1 #ifndef GETREPSEQSCOMMAND_H
   2 #define GETREPSEQSCOMMAND_H
   3 /*
   4  *  getrepseqscommand.h
   5  *  Mothur
   6  *
   7  *  Created by Sarah Westcott on 5/19/09.
   8  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   9  *
  10  */
  11
  12
  13 #include "command.hpp"
  14 #include "inputdata.h"
  15 #include "listvector.hpp"
  16 #include "readotu.h"
  17 #include "fastamap.h"
  18 #include "groupmap.h"
  19
  20
  21 class GlobalData;
  22
  23 class GetRepSeqsCommand : public Command {
  24
  25 public:
  26         GetRepSeqsCommand();
  27         ~GetRepSeqsCommand();
  28         int execute();
  29
  30 private:
  31         GlobalData* globaldata;
  32         ListVector* list;
  33         ReadOTUFile* read;
  34         GroupMap* groupMap;
  35         InputData* input;
  36         FastaMap* fasta;
  37         string filename, fastafile, namesfile;
  38         map<string, ofstream*> filehandles;
  39         map<string, ofstream*>::iterator it;
  40         map<string, bool> used;  //group, if it had any unique otus
  41         map<string, bool>::iterator it2;
  42         map<string, string> seq;
  43         map<string, string>::iterator it3;
  44         ifstream in, inNames;
  45
  46         void readNamesFile();
  47         void removeFiles(string);
  48 };
  49
  50 #endif