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         ~LibShuffCommand(){};
  26         vector<string> getRequiredParameters();
  27         vector<string> getValidParameters();
  28         vector<string> getRequiredFiles();
  29         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  30         int execute();
  31         void help();
  32
  33 private:
  34         vector<string> groupNames;
  35
  36         void setGroups();
  37         int printCoverageFile();
  38         int printSummaryFile();
  39
  40         GlobalData* globaldata;
  41         FullMatrix* matrix;
  42         Libshuff* form;
  43         float cutOff, step;
  44         int numGroups, numComp, iters;
  45         string coverageFile, summaryFile;
  46         vector<vector<int> > pValueCounts;
  47         vector<vector<double> > savedDXYValues;
  48         vector<vector<vector<double> > > savedMinValues;
  49
  50         bool abort;
  51         string outputFile, groups, userform, savegroups, outputDir;
  52         vector<string> Groups, outputNames; //holds groups to be used
  53         map<string, vector<string> > outputTypes;
  54 };
  55
  56 #endif