]> git.donarmstrong.com Git - mothur.git/blobdiff - sharedjclass.cpp
bug fixes
[mothur.git] / sharedjclass.cpp
index 6557a0f16b8d4eab412d82616e8d74cb99374b86..ede4e31264d49b1cc26ccb4e684262ec6f1c1d3e 100644 (file)
@@ -11,9 +11,9 @@
 
 /***********************************************************************/
 
-EstOutput SharedJclass::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 
@@ -21,13 +21,14 @@ EstOutput SharedJclass::getValues(SharedRAbundVector* shared1, SharedRAbundVecto
 
                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);
-
-                       S1 += tempA;
-                       S2 += tempB;
+                       tempA = shared[0]->getAbundance(i);
+                       tempB = shared[1]->getAbundance(i);
+                       
+                       //find number of bins in shared1 and shared2
+                       if (tempA != 0) { S1++; }
+                       if (tempB != 0) { S2++; } 
                        
                        //they are shared
                        if ((tempA != 0) && (tempB != 0)) {     S12++; }
@@ -40,13 +41,9 @@ EstOutput SharedJclass::getValues(SharedRAbundVector* shared1, SharedRAbundVecto
                return data;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedJclass 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 SharedJclass class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/