X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedjclass.cpp;h=ede4e31264d49b1cc26ccb4e684262ec6f1c1d3e;hb=a834131359fd7cf3625df70d7e77ca90a159e9fd;hp=54d87ccc9a39170c5715a29ee73a86453176f7e7;hpb=c537597ec5ebd47b4898da87ae03b0c2aeced354;p=mothur.git

diff --git a/sharedjclass.cpp b/sharedjclass.cpp
index 54d87cc..ede4e31 100644
--- a/sharedjclass.cpp
+++ b/sharedjclass.cpp
@@ -11,9 +11,9 @@
 
 /***********************************************************************/
 
-EstOutput Jclass::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput Jclass::getValues(vector<SharedRAbundVector*> shared) {
 	try {
-		int S1, S2, S12, tempA, tempB;
+		double S1, S2, S12, tempA, tempB;
 		S1 = 0; S2 = 0; S12 = 0; tempA = 0; tempB = 0; 
 		
 		/*S1, S2 = number of OTUs observed or estimated in A and B 
@@ -21,10 +21,10 @@ EstOutput Jclass::getValues(SharedRAbundVector* shared1, SharedRAbundVector* sha
 
 		data.resize(1,0);
 		
-		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
-			tempA = shared1->getAbundance(i);
-			tempB = shared2->getAbundance(i);
+			tempA = shared[0]->getAbundance(i);
+			tempB = shared[1]->getAbundance(i);
 			
 			//find number of bins in shared1 and shared2
 			if (tempA != 0) { S1++; }
@@ -41,13 +41,9 @@ EstOutput Jclass::getValues(SharedRAbundVector* shared1, SharedRAbundVector* sha
 		return data;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Jclass class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Jclass", "getValues");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Jclass class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/