libshuffcommand.h

   1 #ifndef LIBSHUFFCOMMAND_H
   2 #define LIBSHUFFCOMMAND_H
   3
   4 /*
   5  *  libshuffcommand.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 3/9/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "fullmatrix.h"
  15 #include "libshuff.h"
  16 #include "groupmap.h"
  17
  18
  19 class LibShuffCommand : public Command {
  20
  21 public:
  22         LibShuffCommand(string);
  23         LibShuffCommand();
  24         ~LibShuffCommand(){};
  25
  26         vector<string> setParameters();
  27         string getCommandName()                 { return "libshuff";                            }
  28         string getCommandCategory()             { return "Hypothesis Testing";          }
  29         string getHelpString();
  30         string getCitation() { return "http://www.mothur.org/wiki/Libshuff"; }
  31
  32         int execute();
  33         void help() { m->mothurOut(getHelpString()); }
  34
  35 private:
  36         vector<string> groupNames;
  37
  38         void setGroups();
  39         int printCoverageFile();
  40         int printSummaryFile();
  41
  42         GroupMap* groupMap;
  43         FullMatrix* matrix;
  44         Libshuff* form;
  45         float cutOff, step;
  46         int numGroups, numComp, iters;
  47         string coverageFile, summaryFile, phylipfile, groupfile;
  48         vector<vector<int> > pValueCounts;
  49         vector<vector<double> > savedDXYValues;
  50         vector<vector<vector<double> > > savedMinValues;
  51
  52         bool abort, sim;
  53         string outputFile, groups, userform, savegroups, outputDir;
  54         vector<string> Groups, outputNames; //holds groups to be used
  55 };
  56
  57 #endif