summarytaxcommand.h

   1 #ifndef SUMMARYTAXCOMMAND_H
   2 #define SUMMARYTAXCOMMAND_H
   3
   4 /*
   5  *  summarytaxcommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 9/23/11.
   9  *  Copyright 2011 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14
  15 /**************************************************************************************************/
  16
  17 class SummaryTaxCommand : public Command {
  18         public:
  19                 SummaryTaxCommand(string);
  20                 SummaryTaxCommand();
  21                 ~SummaryTaxCommand(){}
  22
  23                 vector<string> setParameters();
  24                 string getCommandName()                 { return "summary.tax";                 }
  25                 string getCommandCategory()             { return "Phylotype Analysis";          }
  26                 string getOutputFileNameTag(string, string);
  27         string getHelpString();
  28                 string getCitation() { return "http://www.mothur.org/wiki/Summary.tax"; }
  29                 string getDescription()         { return "summarize the taxonomies of a set of sequences"; }
  30
  31                 int execute();
  32                 void help() { m->mothurOut(getHelpString()); }
  33
  34         private:
  35                 bool abort;
  36                 string taxfile, outputDir, namefile, groupfile, refTaxonomy;
  37                 vector<string> outputNames;
  38                 map<string, int> nameMap;
  39 };
  40
  41 /**************************************************************************************************/
  42
  43
  44 #endif