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 "coverage.h"
  15 #include "fullmatrix.h"
  16
  17 using namespace std;
  18
  19 class GlobalData;
  20
  21 class LibShuffCommand : public Command {
  22
  23         public:
  24                 LibShuffCommand();
  25                 ~LibShuffCommand();
  26                 int execute();
  27
  28         private:
  29                 vector< vector< vector<float> > > cValues; // vector<vector of coverage scores, one for each comparison.> -one for each distance level.
  30                 vector< vector<float> > deltaValues; // vector< vector of delta scores, one for each comparison.> -one at each distance
  31                 vector<float> sumDelta; //sum of delta scores, one for each comparison.
  32                 vector<float> sumDeltaSig; //number of random  matrixes with that delta value or ??
  33                 vector< vector<float> > rsumDelta; //vector< vector<sumdelta scores for a given comparison> >
  34                 vector<string> groupComb;
  35                 vector<float> dist;
  36
  37
  38                 void setGroups();
  39                 int findIndex(float, int);
  40                 void printCoverageFile();
  41                 void printSummaryFile();
  42
  43                 GlobalData* globaldata;
  44                 Coverage* coverage;
  45                 FullMatrix* matrix;
  46                 float cutOff, step;
  47                 int numGroups, numComp, iters;
  48                 string coverageFile, summaryFile, form;
  49                 ofstream out, outSum;
  50
  51
  52 };
  53
  54 #endif