X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedace.cpp;h=2a06380b6896ae6c908f38222abdcc566bcae077;hp=791b52657859802922d7735d0a52a9144edf368e;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05

diff --git a/sharedace.cpp b/sharedace.cpp
index 791b526..2a06380 100644
--- a/sharedace.cpp
+++ b/sharedace.cpp
@@ -12,16 +12,16 @@
 
 /***********************************************************************/
 
-EstOutput SharedAce::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput SharedAce::getValues(vector<SharedRAbundVector*> shared) {
 	try {
 		data.resize(1,0);
 		string label;
-		label = shared1->getLabel();
+		label = shared[0]->getLabel();
 
-		int fARare, fBRare, S12Rare, S12Abund, S12, f11, tempA, tempB, t10, t01, t11, t21, t12, t22, C12Numerator;
+		double fARare, fBRare, S12Rare, S12Abund, S12, f11, tempA, tempB, t10, t01, t11, t21, t12, t22, C12Numerator;
 		fARare = 0; fBRare = 0; S12Rare = 0; S12Abund = 0; S12 = 0; f11 = 0; t10 = 0; t01 = 0; t11= 0; t21= 0; t12= 0; t22= 0; C12Numerator = 0;
 	
-		float SharedAce, C12, part1, part2, part3, part4, part5, Gamma1, Gamma2, Gamma3;
+		double Sharedace, C12, part1, part2, part3, part4, part5, Gamma1, Gamma2, Gamma3;
 	
 		/*fARare = number of OTUs with one individual found in A and less than or equal to 10 in B. 
 		fBRare = number of OTUs with one individual found in B and less than or equal to 10 in A. 
@@ -32,10 +32,10 @@ EstOutput SharedAce::getValues(SharedRAbundVector* shared1, SharedRAbundVector*
 		S12 = number of shared OTUs in A and B
 		This estimator was changed to reflect Caldwell's changes, eliminating the nrare / nrare - 1 */
 
-		for (int i = 0; i < shared1->size(); i++) {
+		for (int i = 0; i < shared[0]->getNumBins(); i++) {
 			//store in temps to avoid multiple repetitive function calls
-			tempA = shared1->getAbundance(i);
-			tempB = shared2->getAbundance(i);
+			tempA = shared[0]->getAbundance(i);
+			tempB = shared[1]->getAbundance(i);
 			if ((tempA != 0) && (tempB != 0)) {//they are shared
 				S12++;
 				//do both A and B have one
@@ -77,37 +77,32 @@ EstOutput SharedAce::getValues(SharedRAbundVector* shared1, SharedRAbundVector*
 		C12 = 1 - (C12Numerator /(float) t11);
 		part1 = S12Rare / (float)C12;
 		part2 = 1 / (float)C12;
-	
+
 		//calculate gammas
 		Gamma1 = ((S12Rare * t21) / (float)((C12 * t10 * t11)) - 1);
 		Gamma2 = ((S12Rare * t12) / (float)((C12 * t01 * t11)) - 1);
 		Gamma3 = ((S12Rare / C12) * (S12Rare / C12)) * ( t22 / (float)(t10 * t01 * t11));
 		Gamma3 = Gamma3 - ((S12Rare * t11) / (float)(C12 * t01 * t10)) - Gamma1 - Gamma2;	
-	
+
 		if (isnan(Gamma1) || isinf(Gamma1)) { Gamma1 = 0; }
 		if (isnan(Gamma2) || isinf(Gamma2)) { Gamma2 = 0; }
 		if (isnan(Gamma3) || isinf(Gamma3)) { Gamma3 = 0; }
 		if (isnan(part1)  || isinf(part1))  { part1 = 0;  }
 		if (isnan(part2)  || isinf(part2))  { part2 = 0;  }
-			
+		
 		part3 = fARare * Gamma1;
 		part4 = fBRare * Gamma2;
 		part5 = f11 * Gamma3;
 
-		SharedAce = S12Abund + part1 + (part2 * (part3 + part4 + part5));
-		data[0] = SharedAce;
+		Sharedace = S12Abund + part1 + (part2 * (part3 + part4 + part5));
+		data[0] = Sharedace;
 	
 		return data;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedAce class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedAce", "getValues");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedAce class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
-
 }
 /***********************************************************************/