X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedmorisitahorn.cpp;h=28ff4fec9f2e2ee3c8e99b0f167630152acca802;hb=163b300cfd7d4ca4e70c454be20f07b1d8346650;hp=6ceac75dd1e928f827e1b19d6e1186c1da87b9b9;hpb=25cde7ff05bbe741da1712f2c740e0bc8706e523;p=mothur.git

diff --git a/sharedmorisitahorn.cpp b/sharedmorisitahorn.cpp
index 6ceac75..28ff4fe 100644
--- a/sharedmorisitahorn.cpp
+++ b/sharedmorisitahorn.cpp
@@ -10,7 +10,7 @@
 #include "sharedmorisitahorn.h"
 
 /***********************************************************************/
-EstOutput SharedMorHorn::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput MorHorn::getValues(vector<SharedRAbundVector*> shared) {
 	try {	
 		data.resize(1,0);
 		
@@ -20,30 +20,28 @@ EstOutput SharedMorHorn::getValues(SharedRAbundVector* shared1, SharedRAbundVect
 		morhorn = 0.0; sumSharedA = 0.0; sumSharedB = 0.0; a = 0.0; b = 0.0; d = 0.0;
 		
 		//get the total values we need to calculate the theta denominator sums
-		for (int i = 0; i < shared1->size(); i++) {
+		for (int i = 0; i < shared[0]->size(); i++) {
 			//store in temps to avoid multiple repetitive function calls
-			Atotal += shared1->getAbundance(i);
-			Btotal += shared2->getAbundance(i);
+			Atotal += shared[0]->getAbundance(i);
+			Btotal += shared[1]->getAbundance(i);
 		}
 		
 		//calculate the theta denominator sums
-		for (int j = 0; j < shared1->size(); j++) {
+		for (int j = 0; j < shared[0]->size(); j++) {
 			//store in temps to avoid multiple repetitive function calls
-			tempA = shared1->getAbundance(j);
-			tempB = shared2->getAbundance(j);
+			tempA = shared[0]->getAbundance(j);
+			tempB = shared[1]->getAbundance(j);
 			
-			//they are shared
-			if ((tempA != 0) && (tempB != 0)) {
-				if (Atotal != 0)	{ sumSharedA = (tempA / (float)Atotal); }
-				if (Btotal != 0)	{ sumSharedB = (tempB / (float)Btotal); }
-			
-				a += sumSharedA * sumSharedA;
-				b += sumSharedB * sumSharedB;
-				d += sumSharedA * sumSharedB;
-			}
+			a += tempA * tempA;
+			b += tempB * tempB;
+			d += tempA * tempB;
 		}
 
-		morhorn = (2 * d) / (float) (a + b);
+		a /= double(Atotal * Atotal);
+		b /= double(Btotal * Btotal);
+		d /= double(Atotal * Btotal);
+		
+		morhorn = (2 * d) / (a + b);
 		
 		if (isnan(morhorn) || isinf(morhorn)) { morhorn = 0; }
 		
@@ -52,13 +50,13 @@ EstOutput SharedMorHorn::getValues(SharedRAbundVector* shared1, SharedRAbundVect
 		return data;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedMorHorn class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		cout << "Standard Error: " << e.what() << " has occurred in the MorHorn class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 		exit(1);
 	}
 	catch(...) {
-		cout << "An unknown error has occurred in the SharedMorHorn class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		cout << "An unknown error has occurred in the MorHorn class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 		exit(1);
 	}	
 }
 
-/***********************************************************************/
\ No newline at end of file
+/***********************************************************************/