slibshuff.cpp

   1 /*
   2  *  slibshuff.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 4/8/09.
   6  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "slibshuff.h"
  11
  12 /***********************************************************************/
  13
  14 SLibshuff::SLibshuff(FullMatrix* D, int it, float co) : Libshuff(D, it, 0, co){}
  15
  16 /***********************************************************************/
  17
  18 float SLibshuff::evaluatePair(int i, int j){
  19         return sCalculate(i,j);
  20 }
  21
  22 /***********************************************************************/
  23
  24 vector<vector<double> > SLibshuff::evaluateAll(){
  25         try{
  26                 savedMins.resize(numGroups);
  27
  28                 vector<vector<double> > dCXYValues(numGroups);
  29
  30                 for(int i=0;i<numGroups;i++){
  31                         dCXYValues[i].resize(numGroups);
  32                         savedMins[i].resize(numGroups);
  33                         for(int j=0;j<numGroups;j++){
  34                                 if(i!=j){
  35                                         dCXYValues[i][j] = sCalculate(i,j);
  36                                         savedMins[i][j] = minXY;
  37                                 }
  38
  39                                 if(savedMins[i][i].size() == 0){
  40                                         savedMins[i][i] = minX;
  41                                 }
  42
  43                         }
  44                 }
  45                 return dCXYValues;
  46         }
  47         catch(exception& e) {
  48                 cout << "Standard Error: " << e.what() << " has occurred in the SLibshuff class Function evaluateAll. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  49                 exit(1);
  50         }
  51         catch(...) {
  52                 cout << "An unknown error has occurred in the SLibshuff class function evaluateAll. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  53                 exit(1);
  54         }
  55
  56 }
  57
  58 /***********************************************************************/
  59
  60 double SLibshuff::sCalculate(int x, int y){
  61         try{
  62                 minX = getMinX(x);
  63                 minXY = getMinXY(x,y);
  64
  65                 sort(minX.begin(), minX.end());
  66                 sort(minXY.begin(), minXY.end());
  67
  68                 double sum = 0.0,t=0.0;
  69                 int ix=0,iy=0;
  70                 while( (ix < groupSizes[x]) && (iy < groupSizes[x]) ) {
  71                         double h = (ix-iy)/double(groupSizes[x]);
  72
  73                         if(minX[ix] < minXY[iy]) {
  74                                 sum += (minX[ix] - t)*h*h;
  75                                 t = minX[ix++];
  76                         }
  77                         else {
  78                                 sum += (minXY[iy] - t)*h*h;
  79                                 t = minXY[iy++];
  80                         }
  81
  82                 }
  83
  84                 if(ix < groupSizes[x]) {
  85
  86                         while(ix < groupSizes[x]) {
  87                                 double h = (ix-iy)/double(groupSizes[x]);
  88                                 sum += (minX[ix] - t)*h*h;
  89                                 t = minX[ix++];
  90                         }
  91
  92                 }
  93                 else {
  94
  95                         while(iy < groupSizes[x]) {
  96                                 double h = (ix-iy)/double(groupSizes[x]);
  97                                 sum += (minXY[iy] - t)*h*h;
  98                                 t = minXY[iy++];
  99                         }
 100
 101                 }
 102
 103                 return sum;
 104         }
 105         catch(exception& e) {
 106                 cout << "Standard Error: " << e.what() << " has occurred in the SLibshuff class Function sCalculate. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 107                 exit(1);
 108         }
 109         catch(...) {
 110                 cout << "An unknown error has occurred in the SLibshuff class function sCalculate. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 111                 exit(1);
 112         }
 113
 114 }
 115
 116 /***********************************************************************/