removedistscommand.h

   1 //
   2 //  removedistscommand.h
   3 //  Mothur
   4 //
   5 //  Created by Sarah Westcott on 1/29/13.
   6 //  Copyright (c) 2013 Schloss Lab. All rights reserved.
   7 //
   8
   9 #ifndef Mothur_removedistscommand_h
  10 #define Mothur_removedistscommand_h
  11
  12 #include "command.hpp"
  13
  14 class RemoveDistsCommand : public Command {
  15
  16 public:
  17
  18         RemoveDistsCommand(string);
  19         RemoveDistsCommand();
  20         ~RemoveDistsCommand(){}
  21
  22         vector<string> setParameters();
  23         string getCommandName()                 { return "remove.dists";                        }
  24         string getCommandCategory()             { return "General";                 }
  25
  26         string getHelpString();
  27     string getOutputPattern(string);
  28         string getCitation() { return "http://www.mothur.org/wiki/Remove.dists"; }
  29         string getDescription()         { return "removes distances from a phylip or column file related to groups or sequences listed in an accnos file"; }
  30
  31
  32         int execute();
  33         void help() { m->mothurOut(getHelpString()); }
  34
  35
  36 private:
  37         set<string> names;
  38         string accnosfile, phylipfile, columnfile, outputDir;
  39         bool abort;
  40         vector<string> outputNames;
  41
  42         int readPhylip();
  43         int readColumn();
  44
  45 };
  46
  47
  48 #endif