getsabundcommand.h

   1 #ifndef GETSABUNDCOMMAND_H
   2 #define GETSABUNDCOMMAND_H
   3
   4 /*
   5  *  getsabundcommand.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 6/2/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15 #include "inputdata.h"
  16 #include "sabundvector.hpp"
  17
  18 class GetSAbundCommand : public Command {
  19 public:
  20         GetSAbundCommand(string);
  21         GetSAbundCommand();
  22         ~GetSAbundCommand() {}
  23
  24         vector<string> setParameters();
  25         string getCommandName()                 { return "get.sabund";                          }
  26         string getCommandCategory()             { return "OTU-Based Approaches";        }
  27
  28         string getHelpString();
  29     string getOutputPattern(string);
  30         string getCitation() { return "http://www.mothur.org/wiki/Get.sabund"; }
  31         string getDescription()         { return "creates a sabund file"; }
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36 private:
  37         string filename, format, inputfile, listfile, rabundfile, outputDir, countfile;
  38         ofstream out;
  39         vector<string> outputNames;
  40
  41         bool abort, allLines;
  42         set<string> labels; //holds labels to be used
  43         string label;
  44
  45     int processList(ofstream& out);
  46     int createRabund(CountTable& ct, ListVector*& list, RAbundVector*& rabund);
  47
  48 };
  49
  50 #endif