countseqscommand.h

   1 #ifndef COuNTSEQSCOMMAND_H
   2 #define COuNTSEQSCOMMAND_H
   3
   4 /*
   5  *  countseqscommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 6/1/11.
   9  *  Copyright 2011 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14
  15 class CountSeqsCommand : public Command {
  16
  17 public:
  18
  19         CountSeqsCommand(string);
  20         CountSeqsCommand();
  21         ~CountSeqsCommand(){}
  22
  23         vector<string> setParameters();
  24         string getCommandName()                 { return "count.seqs";                          }
  25         string getCommandCategory()             { return "Sequence Processing";         }
  26
  27         string getHelpString();
  28     string getOutputPattern(string);
  29         string getCitation() { return "http://www.mothur.org/wiki/Count.seqs"; }
  30         string getDescription()         { return "counts the number of sequences represented by each unique sequence in a namesfile"; }
  31
  32         int execute();
  33         void help() { m->mothurOut(getHelpString()); }
  34
  35
  36 private:
  37         string namefile, groupfile, outputDir, groups;
  38         bool abort, large;
  39         vector<string> Groups, outputNames;
  40
  41     int processSmall(string);
  42     int processLarge(string);
  43     map<int, string> processNameFile(string);
  44     map<int, string> getGroupNames(string, set<string>&);
  45
  46 };
  47
  48 #endif
  49
  50