chopseqscommand.h

   1 #ifndef CHOPSEQSCOMMAND_H
   2 #define CHOPSEQSCOMMAND_H
   3
   4 /*
   5  *  chopseqscommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 5/10/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15 #include "sequence.hpp"
  16
  17 class ChopSeqsCommand : public Command {
  18
  19         public:
  20
  21                 ChopSeqsCommand(string);
  22                 ChopSeqsCommand();
  23                 ~ChopSeqsCommand(){};
  24                 vector<string> getRequiredParameters();
  25                 vector<string> getValidParameters();
  26                 vector<string> getRequiredFiles();
  27                 map<string, vector<string> > getOutputFiles() { return outputTypes; }
  28                 int execute();
  29                 void help();
  30
  31         private:
  32                 string fastafile, outputDir, keep;
  33                 bool abort, countGaps, Short;
  34                 int numbases;
  35                 vector<string> outputNames;
  36                 map<string, vector<string> > outputTypes;
  37
  38                 string getChopped(Sequence);
  39
  40
  41 };
  42
  43 #endif
  44
  45