libshuff.cpp

   1 /*
   2  *  libshuffform.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 "libshuff.h"
  11
  12 /***********************************************************************/
  13
  14 void swap(int& i,int& j){       int t = i;  i = j;  j = t;      }
  15
  16 /***********************************************************************/
  17
  18 Libshuff::Libshuff(FullMatrix* D, int it, float step, float co) : matrix(D), iters(it), stepSize(step), cutOff(co){
  19         try{
  20                 groupNames = matrix->getGroups();
  21                 groupSizes = matrix->getSizes();
  22                 numGroups = matrix->getNumGroups();
  23                 initializeGroups(matrix);
  24         }
  25         catch(exception& e) {
  26                 errorOut(e, "Libshuff", "Libshuff");
  27                 exit(1);
  28         }
  29 }
  30
  31 /***********************************************************************/
  32
  33 void Libshuff::initializeGroups(FullMatrix* matrix){
  34         try{
  35                 groups.resize(numGroups);
  36                 savedGroups.resize(numGroups);
  37
  38                 savedGroups.resize(numGroups);
  39                 for(int i=0;i<numGroups;i++) {
  40                         groups[i].resize(groupSizes[i]);
  41                         savedGroups[i].resize(groupSizes[i]);
  42                 }
  43                 int index=0;
  44                 for(int i=0;i<numGroups;i++){
  45
  46                         for(int j=0;j<groupSizes[i];j++){
  47                                 savedGroups[i][j] = groups[i][j] = index++;
  48                         }
  49                 }
  50         }
  51         catch(exception& e) {
  52                 errorOut(e, "Libshuff", "initializeGroups");
  53                 exit(1);
  54         }
  55 }
  56
  57 /***********************************************************************/
  58
  59 vector<vector<vector<double> > > Libshuff::getSavedMins(){
  60         return savedMins;
  61 }
  62
  63 /***********************************************************************/
  64
  65 vector<double> Libshuff::getMinX(int x){
  66         try{
  67                 vector<double> minX(groupSizes[x], 0);
  68                 for(int i=0;i<groupSizes[x];i++){
  69                         minX[i] = (groupSizes[x] > 1 ? (i==0 ? matrix->get(groups[x][0], groups[x][1]) : matrix->get(groups[x][i], groups[x][0])) : 0.0); //get the first value in row i of this block
  70                         //minX[i] = matrix->get(groups[x][i], groups[x][0]);
  71                         for(int j=0;j<groupSizes[x];j++){
  72                                 if(i != j)      {
  73                                         double dx = matrix->get(groups[x][i], groups[x][j]);
  74                                         if(dx < minX[i]){       minX[i] = dx;   }
  75                                 }
  76                         }
  77                 }
  78                 return minX;
  79         }
  80         catch(exception& e) {
  81                 errorOut(e, "Libshuff", "getMinX");
  82                 exit(1);
  83         }
  84 }
  85
  86 /***********************************************************************/
  87
  88 vector<double> Libshuff::getMinXY(int x, int y){
  89         try{
  90                 vector<double> minXY(groupSizes[x], 0);
  91
  92                 for(int i=0;i<groupSizes[x];i++){
  93                         minXY[i] = matrix->get(groups[x][i], groups[y][0]);
  94                         for(int j=0;j<groupSizes[y];j++){
  95                                 double dxy = matrix->get(groups[x][i], groups[y][j]);
  96                                 if(dxy<minXY[i]){       minXY[i] = dxy; }
  97                         }
  98                 }
  99                 return minXY;
 100         }
 101         catch(exception& e) {
 102                 errorOut(e, "Libshuff", "getMinXY");
 103                 exit(1);
 104         }
 105 }
 106
 107 /***********************************************************************/
 108
 109 void Libshuff::randomizeGroups(int x, int y){
 110         try{
 111                 int nv = groupSizes[x]+groupSizes[y];
 112                 vector<int> v(nv);
 113
 114                 int index=0;
 115                 for(int k=0;k<groupSizes[x];k++)        {       v[index++] = groups[x][k];      }
 116                 for(int k=0;k<groupSizes[y];k++)        {       v[index++] = groups[y][k];      }
 117
 118                 for(int k=nv-1;k>0;k--){
 119                         int z = (int)(rand() % k);
 120                         swap(v[z],v[k]);
 121                 }
 122
 123                 index=0;
 124                 for(int k=0;k<groupSizes[x];k++)        {       groups[x][k]=v[index++];        }
 125                 for(int k=0;k<groupSizes[y];k++)        {       groups[y][k]=v[index++];        }
 126         }
 127         catch(exception& e) {
 128                 errorOut(e, "Libshuff", "randomizeGroups");
 129                 exit(1);
 130         }
 131 }
 132
 133 /***********************************************************************/
 134
 135 void Libshuff::resetGroup(int x){
 136
 137         for(int k=0;k<groupSizes[x];k++)        {       groups[x][k] = savedGroups[x][k];       }
 138
 139 }
 140
 141 /***********************************************************************/