X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedthetayc.cpp;h=45dce49ce0a1185c1558068bc27e15be87f03fcb;hb=905cc2b0bd18c5ce611b048d785e93859865a5ea;hp=ad2e1c574302b678f9d503dc235ef3b5a6b38db2;hpb=25cde7ff05bbe741da1712f2c740e0bc8706e523;p=mothur.git

diff --git a/sharedthetayc.cpp b/sharedthetayc.cpp
index ad2e1c5..45dce49 100644
--- a/sharedthetayc.cpp
+++ b/sharedthetayc.cpp
@@ -10,40 +10,36 @@
 #include "sharedthetayc.h"
 
 /***********************************************************************/
-EstOutput SharedThetaYC::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput ThetaYC::getValues(vector<SharedRAbundVector*> shared) {
 	try {	
 		data.resize(1,0);
 		
-		int Atotal, Btotal, tempA, tempB;
-		Atotal = 0; Btotal = 0; 
-		float thetaYC, sumSharedA, sumSharedB, a, b, d;
-		thetaYC = 0.0; sumSharedA = 0.0; sumSharedB = 0.0; a = 0.0; b = 0.0; d = 0.0;
+		int Atotal = 0;
+		int Btotal = 0;
+		float thetaYC = 0;
+		float relA = 0;
+		float relB = 0;
+		float a = 0;
+		float b = 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);
-			
-			//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;
-			}
+			relA = shared[0]->getAbundance(j) / (float)Atotal;
+			relB = shared[1]->getAbundance(j) / (float)Btotal;
+					
+			a += relA * relB;
+			b += pow((relA-relB),2);
 		}
 
-		thetaYC = d / (float) (a + b - d);
+		thetaYC = a / (float) (b+a);
 		
 		if (isnan(thetaYC) || isinf(thetaYC)) { thetaYC = 0; }
 		
@@ -52,13 +48,9 @@ EstOutput SharedThetaYC::getValues(SharedRAbundVector* shared1, SharedRAbundVect
 		return data;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedThetaYC class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ThetaYC", "getValues");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedThetaYC class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/