5 * Created by Pat Schloss on 4/8/09.
6 * Copyright 2009 Patrick D. Schloss. All rights reserved.
12 /***********************************************************************/
14 void swap(int& i,int& j){ int t = i; i = j; j = t; }
16 /***********************************************************************/
18 Libshuff::Libshuff(FullMatrix* D, int it, float step, float co) : matrix(D), iters(it), stepSize(step), cutOff(co){
20 m = MothurOut::getInstance();
21 groupNames = matrix->getGroups();
22 groupSizes = matrix->getSizes();
23 numGroups = matrix->getNumGroups();
24 initializeGroups(matrix);
27 m->errorOut(e, "Libshuff", "Libshuff");
32 /***********************************************************************/
34 void Libshuff::initializeGroups(FullMatrix* matrix){
36 groups.resize(numGroups);
37 savedGroups.resize(numGroups);
39 savedGroups.resize(numGroups);
40 for(int i=0;i<numGroups;i++) {
41 groups[i].resize(groupSizes[i]);
42 savedGroups[i].resize(groupSizes[i]);
45 for(int i=0;i<numGroups;i++){
47 for(int j=0;j<groupSizes[i];j++){
48 savedGroups[i][j] = groups[i][j] = index++;
53 m->errorOut(e, "Libshuff", "initializeGroups");
58 /***********************************************************************/
60 vector<vector<vector<double> > > Libshuff::getSavedMins(){
64 /***********************************************************************/
66 vector<double> Libshuff::getMinX(int x){
68 vector<double> minX(groupSizes[x], 0);
69 for(int i=0;i<groupSizes[x];i++){
70 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
71 //minX[i] = matrix->get(groups[x][i], groups[x][0]);
72 for(int j=0;j<groupSizes[x];j++){
74 double dx = matrix->get(groups[x][i], groups[x][j]);
75 if(dx < minX[i]){ minX[i] = dx; }
82 m->errorOut(e, "Libshuff", "getMinX");
87 /***********************************************************************/
89 vector<double> Libshuff::getMinXY(int x, int y){
91 vector<double> minXY(groupSizes[x], 0);
93 for(int i=0;i<groupSizes[x];i++){
94 minXY[i] = matrix->get(groups[x][i], groups[y][0]);
95 for(int j=0;j<groupSizes[y];j++){
96 double dxy = matrix->get(groups[x][i], groups[y][j]);
97 if(dxy<minXY[i]){ minXY[i] = dxy; }
102 catch(exception& e) {
103 m->errorOut(e, "Libshuff", "getMinXY");
108 /***********************************************************************/
110 void Libshuff::randomizeGroups(int x, int y){
112 int nv = groupSizes[x]+groupSizes[y];
116 for(int k=0;k<groupSizes[x];k++) { v[index++] = groups[x][k]; }
117 for(int k=0;k<groupSizes[y];k++) { v[index++] = groups[y][k]; }
119 for(int k=nv-1;k>0;k--){
120 int z = (int)(rand() % k);
125 for(int k=0;k<groupSizes[x];k++) { groups[x][k]=v[index++]; }
126 for(int k=0;k<groupSizes[y];k++) { groups[y][k]=v[index++]; }
128 catch(exception& e) {
129 m->errorOut(e, "Libshuff", "randomizeGroups");
134 /***********************************************************************/
136 void Libshuff::resetGroup(int x){
138 for(int k=0;k<groupSizes[x];k++) { groups[x][k] = savedGroups[x][k]; }
142 /***********************************************************************/