degapseqscommand.h

   1 #ifndef DEGAPSEQSCOMMAND_H
   2 #define DEGAPSEQSCOMMAND_H
   3
   4 /*
   5  *  degapseqscommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 6/21/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15
  16 class DegapSeqsCommand : public Command {
  17 public:
  18         DegapSeqsCommand(string);
  19         DegapSeqsCommand();
  20         ~DegapSeqsCommand();
  21         vector<string> getRequiredParameters();
  22         vector<string> getValidParameters();
  23         vector<string> getRequiredFiles();
  24         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  25         int execute();
  26         void help();
  27
  28 private:
  29
  30         bool abort;
  31         string fastafile, outputDir;
  32         vector<string> outputNames;
  33         vector<string> fastaFileNames;
  34         map<string, vector<string> > outputTypes;
  35 };
  36
  37 #endif
  38