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[mothur.git] / dlibshuff.cpp

diff --git a/dlibshuff.cpp b/dlibshuff.cpp
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+++ b/dlibshuff.cpp
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+/*
+ *  DLibshuff.cpp
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 4/8/09.
+ *  Copyright 2009 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+#include "dlibshuff.h"
+
+/***********************************************************************/
+
+DLibshuff::DLibshuff(FullMatrix* D, int it, float step, float co) : Libshuff(D, it, step, co){
+
+       numDXs = int(cutOff / stepSize);
+
+}
+
+/***********************************************************************/
+
+float DLibshuff::evaluatePair(int i, int j){
+       return dCalculate(i,j);
+}
+
+/***********************************************************************/
+
+vector<vector<double> > DLibshuff::evaluateAll(){
+       savedMins.resize(numGroups);
+       vector<vector<double> > dCXYValues(numGroups);
+       
+       for(int i=0;i<numGroups;i++){
+               savedMins[i].resize(numGroups);
+               dCXYValues[i].resize(numGroups);
+               for(int j=0;j<numGroups;j++){
+                       if(i!=j){       dCXYValues[i][j] = dCalculate(i,j);     }
+                       savedMins[i][i] = minX;
+                       savedMins[i][j] = minXY;
+               }
+       }
+       
+       return dCXYValues;
+}
+
+/***********************************************************************/
+
+double DLibshuff::dCalculate(int x, int y){
+       
+       minX = getMinX(x);
+       minXY = getMinXY(x, y);
+       
+       vector<int> nx = calcN(minX);
+       vector<int> nxy = calcN(minXY);
+
+       double sum = 0;
+
+       for(int i=0;i<numDXs;i++){
+               float h = (nx[i] - nxy[i]) / (float) groupSizes[x];
+               sum += h * h * stepSize;
+       }
+
+       return sum;
+}
+
+/***********************************************************************/
+
+vector<int> DLibshuff::calcN(vector<double> minVector){
+
+       vector<int> counts(numDXs,0);
+       
+       int precision = int(1 / stepSize);
+       
+       for(int i=0;i<minVector.size();i++){
+               int bin = int (precision * minVector[i]);
+               if(bin < numDXs){       counts[bin]++;  }
+       }
+
+       for(int i=1;i<numDXs;i++){
+               counts[i] += counts[i-1];
+       }
+       
+       return counts;
+}
+
+/***********************************************************************/