X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=dlibshuff.cpp;fp=dlibshuff.cpp;h=9db8872abfdab387ed6a71398e570442fee6022d;hp=0000000000000000000000000000000000000000;hb=197c6d3303439582502840980d6a85cf3aab2314;hpb=3329385a816a97bdde934d98a615865c29eaacad

diff --git a/dlibshuff.cpp b/dlibshuff.cpp
new file mode 100644
index 0000000..9db8872
--- /dev/null
+++ b/dlibshuff.cpp
@@ -0,0 +1,85 @@
+/*
+ *  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;
+}
+
+/***********************************************************************/