Revert to previous commit

[mothur.git] / slibshuff.cpp

diff --git a/slibshuff.cpp b/slibshuff.cpp
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+++ b/slibshuff.cpp
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+/*
+ *  slibshuff.cpp
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 4/8/09.
+ *  Copyright 2009 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+#include "slibshuff.h"
+
+/***********************************************************************/
+
+SLibshuff::SLibshuff(FullMatrix* D, int it, float co) : Libshuff(D, it, 0, co){}
+
+/***********************************************************************/
+
+float SLibshuff::evaluatePair(int i, int j){
+       return sCalculate(i,j);
+}
+
+/***********************************************************************/
+
+vector<vector<double> > SLibshuff::evaluateAll(){
+       try{
+               savedMins.resize(numGroups);
+               vector<vector<double> > dCXYValues(numGroups);
+
+               for(int i=0;i<numGroups;i++){
+                       dCXYValues[i].resize(numGroups);
+                       savedMins[i].resize(numGroups);
+                       for(int j=0;j<numGroups;j++){
+                               if(i!=j){
+                                       dCXYValues[i][j] = sCalculate(i,j);     
+                                       savedMins[i][j] = minXY;
+                               }
+
+                               if(savedMins[i][i].size() == 0){
+                                       savedMins[i][i] = minX;
+                               }
+
+                       }
+               }               
+               return dCXYValues;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SLibshuff", "evaluateAll");
+               exit(1);
+       }
+}
+
+/***********************************************************************/
+
+double SLibshuff::sCalculate(int x, int y){
+       try{
+               double sum = 0.0,t=0.0;
+               
+               minX = getMinX(x);
+               
+               if (m->control_pressed) { return sum; }
+               
+               minXY = getMinXY(x,y);
+               
+               if (m->control_pressed) { return sum; }
+
+               sort(minX.begin(), minX.end());
+               
+               if (m->control_pressed) { return sum; }
+               
+               sort(minXY.begin(), minXY.end());
+               
+               if (m->control_pressed) { return sum; }
+
+               int ix=0,iy=0;
+               while( (ix < groupSizes[x]) && (iy < groupSizes[x]) ) {
+                       double h = (ix-iy)/double(groupSizes[x]);
+                       
+                       if(minX[ix] < minXY[iy]) {
+                               sum += (minX[ix] - t)*h*h;
+                               t = minX[ix++];
+                       }
+                       else {
+                               sum += (minXY[iy] - t)*h*h;
+                               t = minXY[iy++];
+                       }
+                       
+               }
+               
+               if(ix < groupSizes[x]) {
+                       
+                       while(ix < groupSizes[x]) {
+                               double h = (ix-iy)/double(groupSizes[x]);
+                               sum += (minX[ix] - t)*h*h;
+                               t = minX[ix++];
+                       }
+                       
+               }
+               else {
+                       
+                       while(iy < groupSizes[x]) {
+                               double h = (ix-iy)/double(groupSizes[x]);
+                               sum += (minXY[iy] - t)*h*h;
+                               t = minXY[iy++];
+                       }
+                       
+               }
+               
+               return sum;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SLibshuff", "sCalculate");
+               exit(1);
+       }
+}
+
+/***********************************************************************/