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
  17
  18 class GlobalData;
  19
  20 class LibShuffCommand : public Command {
  21
  22 public:
  23         LibShuffCommand(string);
  24         ~LibShuffCommand(){};
  25         int execute();
  26         void help();
  27
  28 private:
  29         vector<string> groupNames;
  30
  31         void setGroups();
  32         void printCoverageFile();
  33         void printSummaryFile();
  34
  35         GlobalData* globaldata;
  36         FullMatrix* matrix;
  37         Libshuff* form;
  38         float cutOff, step;
  39         int numGroups, numComp, iters;
  40         string coverageFile, summaryFile;
  41         vector<vector<int> > pValueCounts;
  42         vector<vector<double> > savedDXYValues;
  43         vector<vector<vector<double> > > savedMinValues;
  44
  45         bool abort;
  46         string outputFile, groups, userform, savegroups, outputDir;
  47         vector<string> Groups; //holds groups to be used
  48 };
  49
  50 #endif