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 ~Libshuff() {}
  20         virtual vector<vector<double> > evaluateAll() = 0;
  21         virtual float evaluatePair(int,int) = 0;
  22         void randomizeGroups(int, int);
  23         void resetGroup(int);
  24         vector<vector<vector<double> > > getSavedMins();
  25
  26 protected:
  27         void initializeGroups(FullMatrix*);
  28         vector<double> getMinX(int);
  29         vector<double> getMinXY(int, int);
  30
  31         vector<vector<vector<double> > > savedMins;
  32
  33
  34         FullMatrix* matrix;
  35         vector<int> groupSizes;
  36         vector<string> groupNames;
  37         vector<vector<int> > groups;
  38         vector<vector<int> > savedGroups;
  39         vector<double> minX;
  40         vector<double> minXY;
  41         float cutOff;
  42         int iters;
  43         float stepSize;
  44
  45         int numGroups;
  46         MothurOut* m;
  47 };
  48
  49 #endif