deuniqueseqscommand.h

   1 #ifndef DEUNIQUESEQSCOMMAND_H
   2 #define DEUNIQUESEQSCOMMAND_H
   3 /*
   4  *  deuniqueseqscommand.h
   5  *  Mothur
   6  *
   7  *  Created by westcott on 10/19/10.
   8  *  Copyright 2010 Schloss Lab. All rights reserved.
   9  *
  10  */
  11
  12 #include "command.hpp"
  13
  14 /* This command is the reverse of unique.seqs */
  15
  16 class DeUniqueSeqsCommand : public Command {
  17
  18 public:
  19         DeUniqueSeqsCommand(string);
  20         DeUniqueSeqsCommand();
  21         ~DeUniqueSeqsCommand() {}
  22         vector<string> getRequiredParameters();
  23         vector<string> getValidParameters();
  24         vector<string> getRequiredFiles();
  25         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  26         int execute();
  27         void help();
  28
  29 private:
  30
  31         string fastaFile, nameFile, outputDir;
  32         vector<string> outputNames;
  33         map<string, vector<string> > outputTypes;
  34         bool abort;
  35
  36         map<string, string> nameMap;
  37
  38         int readNamesFile();
  39
  40 };
  41
  42 #endif
  43