Revert to previous commit

[mothur.git] / libshuff.cpp

diff --git a/libshuff.cpp b/libshuff.cpp
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+/*
+ *  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{
+               m = MothurOut::getInstance();
+               groupNames = matrix->getGroups();
+               groupSizes = matrix->getSizes();
+               numGroups = matrix->getNumGroups();
+               initializeGroups(matrix);
+       }
+       catch(exception& e) {
+               m->errorOut(e, "Libshuff", "Libshuff");
+               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) {
+               m->errorOut(e, "Libshuff", "initializeGroups");
+               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); //get the first value in row i of this block
+                       //minX[i] = matrix->get(groups[x][i], groups[x][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) {
+               m->errorOut(e, "Libshuff", "getMinX");
+               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) {
+               m->errorOut(e, "Libshuff", "getMinXY");
+               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) {
+               m->errorOut(e, "Libshuff", "randomizeGroups");
+               exit(1);
+       }
+}
+
+/***********************************************************************/
+
+void Libshuff::resetGroup(int x){
+       
+       for(int k=0;k<groupSizes[x];k++)        {       groups[x][k] = savedGroups[x][k];       }
+       
+}
+
+/***********************************************************************/