cooccurrencecommand.h

   1 #ifndef COOCCURRENCECOMMAND_H
   2 #define COOCCURRENCECOMMAND_H
   3
   4 /*
   5  *  COOCCURRENCE.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 11/10/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15 #include "trialswap2.h"
  16 #include "inputdata.h"
  17 #include "sharedrabundvector.h"
  18
  19
  20 class CooccurrenceCommand : public Command {
  21
  22 public:
  23
  24         CooccurrenceCommand(string);
  25         CooccurrenceCommand();
  26         ~CooccurrenceCommand(){}
  27
  28         vector<string> setParameters();
  29         string getCommandName()                 { return "Cooccurrence";                        }
  30         string getCommandCategory()             { return "Hypothesis Testing";  }
  31
  32         string getHelpString();
  33     string getOutputPattern(string);
  34         string getCitation() { return "Ulrich W & Gotelli NJ (2010).  Null model analysis of species associations using abundance data.  Ecology  91:3384.\nhttp://www.mothur.org/wiki/Cooccurrence"; }
  35         string getDescription()         { return "calculates four metrics and tests their significance to assess whether presence-absence patterns are different than what one would expect by chance."; }
  36
  37         int execute();
  38         void help() { m->mothurOut(getHelpString()); }
  39
  40
  41 private:
  42     string metric, matrix, outputDir;
  43     string label, sharedfile, groups;
  44     bool abort, allLines;
  45     set<string> labels;
  46     vector<string> outputNames, Groups;
  47     int runs;
  48
  49     int getCooccurrence(vector<SharedRAbundVector*>&, ofstream&);
  50
  51 };
  52
  53 #endif
  54
  55