libshuff.h

   1 #ifndef LIBSHUFF
   2 #define LIBSHUFF
   3
   4 /*
   5  *  libshuff.h
   6  *  Mothur
   7  *
   8  *  Created by Pat Schloss on 4/8/09.
   9  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
  10  *
  11  */
  12
  13 #include "fullmatrix.h"
  14
  15 class Libshuff {
  16
  17 public:
  18         Libshuff(FullMatrix*, int, float, float);
  19         virtual vector<vector<double> > evaluateAll() = 0;
  20         virtual float evaluatePair(int,int) = 0;
  21         void randomizeGroups(int, int);
  22         void resetGroup(int);
  23         vector<vector<vector<double> > > getSavedMins();
  24
  25 protected:
  26         void initializeGroups(FullMatrix*);
  27         vector<double> getMinX(int);
  28         vector<double> getMinXY(int, int);
  29
  30         vector<vector<vector<double> > > savedMins;
  31
  32
  33         FullMatrix* matrix;
  34         vector<int> groupSizes;
  35         vector<string> groupNames;
  36         vector<vector<int> > groups;
  37         vector<vector<int> > savedGroups;
  38         vector<double> minX;
  39         vector<double> minXY;
  40         float cutOff;
  41         int iters;
  42         float stepSize;
  43
  44         int numGroups;
  45         MothurOut* m;
  46 };
  47
  48 #endif