X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=slibshuff.cpp;fp=slibshuff.cpp;h=92998e66ac1eadb442b5b0afc0cfee33835f902a;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/slibshuff.cpp b/slibshuff.cpp
new file mode 100644
index 0000000..92998e6
--- /dev/null
+++ b/slibshuff.cpp
@@ -0,0 +1,116 @@
+/*
+ *  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);
+	}
+}
+
+/***********************************************************************/