collectsharedcommand.h

   1 #ifndef COLLECTSHAREDCOMMAND_H
   2 #define COLLECTSHAREDCOMMAND_H
   3 /*
   4  *  collectsharedcommand.h
   5  *  Dotur
   6  *
   7  *  Created by Sarah Westcott on 1/2/09.
   8  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   9  *
  10  */
  11
  12
  13 #include "command.hpp"
  14 #include "sharedordervector.h"
  15 #include "inputdata.h"
  16 #include "collect.h"
  17 #include "display.h"
  18 #include "validcalculator.h"
  19 #include "sharedutilities.h"
  20
  21
  22 class CollectSharedCommand : public Command {
  23
  24 public:
  25         CollectSharedCommand(string);
  26         CollectSharedCommand();
  27         ~CollectSharedCommand();
  28
  29         vector<string> setParameters();
  30         string getCommandName()                 { return "collect.shared";                      }
  31         string getCommandCategory()             { return "OTU-Based Approaches";        }
  32         string getHelpString();
  33         string getCitation() { return "Schloss PD, Handelsman J (2006). Introducing SONS, A tool that compares the membership of microbial communities. Appl Environ Microbiol 72: 6773-9. \nhttp://www.mothur.org/wiki/Collect.shared"; }
  34         string getDescription()         { return "generates collector's curves for calculators, which describe the similarity between communities or their shared richness"; }
  35
  36         int execute();
  37         void help() { m->mothurOut(getHelpString()); }
  38
  39
  40 private:
  41         SharedOrderVector* order;
  42         InputData* input;
  43         Collect* cCurve;
  44         vector<Display*> cDisplays;
  45         float freq;
  46
  47         bool abort, allLines, all;
  48         set<string> labels; //holds labels to be used
  49         string label, calc, groups, outputDir, sharedfile;
  50         vector<string>  Estimators, Groups, outputNames;
  51 };
  52
  53 #endif