catchallcommand.h

   1 #ifndef CATCHALLCOMMAND_H
   2 #define CATCHALLCOMMAND_H
   3
   4 /*
   5  *  catchallcommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 5/11/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "inputdata.h"
  15 #include "sabundvector.hpp"
  16
  17 /*
  18  citation goes here
  19  */
  20
  21 /****************************************************************************/
  22
  23 class CatchAllCommand : public Command {
  24
  25 public:
  26
  27         CatchAllCommand(string);
  28         CatchAllCommand();
  29         ~CatchAllCommand() {}
  30
  31         vector<string> setParameters();
  32         string getCommandName()                 { return "catchall";                    }
  33         string getCommandCategory()             { return "OTU-Based Approaches";        }
  34         string getOutputFileNameTag(string, string);
  35         string getHelpString();
  36         string getCitation() { return "Bunge, J. (2011). Estimating the number of species with CatchAll. Forthcoming in Proceedings of the Pacific Symposium on Biocomputing 2011.\nhttp://www.northeastern.edu/catchall/index.html http://www.mothur.org/wiki/Catchall"; }
  37         string getDescription()         { return "estimate number of species"; }
  38
  39         int execute();
  40         void help() { m->mothurOut(getHelpString()); }
  41
  42 private:
  43         string outputDir, sharedfile, sabundfile, format, path, savedOutputDir;
  44         bool abort, allLines;
  45         set<string> labels;
  46         vector<string> outputNames;
  47         vector<string> groups;
  48
  49         string process(SAbundVector*, string);
  50         int createSummaryFile(string, string, ofstream&);
  51         vector<string> parseSharedFile(string);
  52         string combineSummmary(vector<string>&);
  53 };
  54
  55 /****************************************************************************/
  56
  57 #endif
  58
  59