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();
  24                 ~LibShuffCommand(){};
  25                 int execute();
  26
  27         private:
  28                 vector<string> groupNames;
  29
  30                 void setGroups();
  31                 void printCoverageFile();
  32                 void printSummaryFile();
  33
  34                 GlobalData* globaldata;
  35                 FullMatrix* matrix;
  36                 Libshuff* form;
  37                 float cutOff, step;
  38                 int numGroups, numComp, iters;
  39                 string coverageFile, summaryFile;
  40                 vector<vector<int> > pValueCounts;
  41                 vector<vector<double> > savedDXYValues;
  42                 vector<vector<vector<double> > > savedMinValues;
  43 };
  44
  45 #endif