--- /dev/null
+/*
+ * libshuffform.cpp
+ * Mothur
+ *
+ * Created by Pat Schloss on 4/8/09.
+ * Copyright 2009 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+#include "libshuff.h"
+
+/***********************************************************************/
+
+void swap(int& i,int& j){ int t = i; i = j; j = t; }
+
+/***********************************************************************/
+
+Libshuff::Libshuff(FullMatrix* D, int it, float step, float co) : matrix(D), iters(it), stepSize(step), cutOff(co){
+ try{
+ groupNames = matrix->getGroups();
+ groupSizes = matrix->getSizes();
+ numGroups = matrix->getNumGroups();
+
+ initializeGroups(matrix);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Libshuff class Function Libshuff. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Libshuff class function Libshuff. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+
+/***********************************************************************/
+
+void Libshuff::initializeGroups(FullMatrix* matrix){
+ try{
+ groups.resize(numGroups);
+ savedGroups.resize(numGroups);
+
+ savedGroups.resize(numGroups);
+ for(int i=0;i<numGroups;i++) {
+ groups[i].resize(groupSizes[i]);
+ savedGroups[i].resize(groupSizes[i]);
+ }
+ int index=0;
+ for(int i=0;i<numGroups;i++){
+ for(int j=0;j<groupSizes[i];j++){
+ savedGroups[i][j] = groups[i][j] = index++;
+ }
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Libshuff class Function initializeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Libshuff class function initializeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+
+/***********************************************************************/
+
+vector<vector<vector<double> > > Libshuff::getSavedMins(){
+ return savedMins;
+}
+
+/***********************************************************************/
+
+vector<double> Libshuff::getMinX(int x){
+ try{
+ vector<double> minX(groupSizes[x], 0);
+ for(int i=0;i<groupSizes[x];i++){
+ 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);
+ for(int j=0;j<groupSizes[x];j++){
+ if(i != j) {
+ double dx = matrix->get(groups[x][i], groups[x][j]);
+ if(dx < minX[i]){ minX[i] = dx; }
+ }
+ }
+ }
+ return minX;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Libshuff class Function getMinX. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Libshuff class function getMinX. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+
+/***********************************************************************/
+
+vector<double> Libshuff::getMinXY(int x, int y){
+ try{
+ vector<double> minXY(groupSizes[x], 0);
+
+ for(int i=0;i<groupSizes[x];i++){
+ minXY[i] = matrix->get(groups[x][i], groups[y][0]);
+ for(int j=0;j<groupSizes[y];j++){
+ double dxy = matrix->get(groups[x][i], groups[y][j]);
+ if(dxy<minXY[i]){ minXY[i] = dxy; }
+ }
+ }
+ return minXY;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Libshuff class Function getMinXY. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Libshuff class function getMinXY. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void Libshuff::randomizeGroups(int x, int y){
+ try{
+ int nv = groupSizes[x]+groupSizes[y];
+ vector<int> v(nv);
+
+ int index=0;
+ for(int k=0;k<groupSizes[x];k++) { v[index++] = groups[x][k]; }
+ for(int k=0;k<groupSizes[y];k++) { v[index++] = groups[y][k]; }
+
+ for(int k=nv-1;k>0;k--){
+ int z = (int)(rand() % k);
+ swap(v[z],v[k]);
+ }
+
+ index=0;
+ for(int k=0;k<groupSizes[x];k++) { groups[x][k]=v[index++]; }
+ for(int k=0;k<groupSizes[y];k++) { groups[y][k]=v[index++]; }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Libshuff class Function randomizeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Libshuff class function randomizeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void Libshuff::resetGroup(int x){
+
+ for(int k=0;k<groupSizes[x];k++) { groups[x][k] = savedGroups[x][k]; }
+
+}
+
+/***********************************************************************/
projects / mothur.git / blobdiff