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 #include "counttable.h"
  15
  16 /**************************************************************************************************/
  17
  18 class SummaryTaxCommand : public Command {
  19         public:
  20                 SummaryTaxCommand(string);
  21                 SummaryTaxCommand();
  22                 ~SummaryTaxCommand(){}
  23
  24                 vector<string> setParameters();
  25                 string getCommandName()                 { return "summary.tax";                 }
  26                 string getCommandCategory()             { return "Phylotype Analysis";          }
  27
  28         string getHelpString();
  29     string getOutputPattern(string);
  30                 string getCitation() { return "http://www.mothur.org/wiki/Summary.tax"; }
  31                 string getDescription()         { return "summarize the taxonomies of a set of sequences"; }
  32
  33                 int execute();
  34                 void help() { m->mothurOut(getHelpString()); }
  35
  36         private:
  37                 bool abort;
  38                 string taxfile, outputDir, namefile, groupfile, refTaxonomy, countfile;
  39                 vector<string> outputNames;
  40                 map<string, int> nameMap;
  41 };
  42
  43 /**************************************************************************************************/
  44
  45
  46 #endif