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
  35         string getHelpString();
  36     string getOutputPattern(string);
  37         string getCitation() { return "Bunge J, Woodard L, Bohning D, Foster JA, Connolly S, Allen HK (2012). Estimating population diversity with CatchAll. Bioinformatics  28:1045.\nhttp://www.northeastern.edu/catchall/index.html\nhttp://www.mothur.org/wiki/Catchall"; }
  38         string getDescription()         { return "estimate number of species"; }
  39
  40         int execute();
  41         void help() { m->mothurOut(getHelpString()); }
  42
  43 private:
  44         string outputDir, sharedfile, sabundfile, format, path, savedOutputDir;
  45         bool abort, allLines;
  46         set<string> labels;
  47         vector<string> outputNames;
  48         vector<string> groups;
  49
  50         string process(SAbundVector*, string);
  51         int createSummaryFile(string, string, ofstream&);
  52         vector<string> parseSharedFile(string);
  53         string combineSummmary(vector<string>&);
  54 };
  55
  56 /****************************************************************************/
  57
  58 #endif
  59
  60