more calculator edits and added coverage and whittaker

[mothur.git] / sharedjclass.cpp

diff --git a/sharedjclass.cpp b/sharedjclass.cpp
index 52591f5b8cf05f707857e771a299e6cb9ecd41aa..54d87ccc9a39170c5715a29ee73a86453176f7e7 100644 (file)
--- a/sharedjclass.cpp
+++ b/sharedjclass.cpp
@@ -11,7 +11,7 @@
 
 /***********************************************************************/
 
-EstOutput SharedJclass::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput Jclass::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
        try {
                int S1, S2, S12, tempA, tempB;
                S1 = 0; S2 = 0; S12 = 0; tempA = 0; tempB = 0; 
@@ -25,9 +25,10 @@ EstOutput SharedJclass::getValues(SharedRAbundVector* shared1, SharedRAbundVecto
                        //store in temps to avoid multiple repetitive function calls
                        tempA = shared1->getAbundance(i);
                        tempB = shared2->getAbundance(i);
-
-                       S1 += tempA;
-                       S2 += tempB;
+                       
+                       //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++; }
@@ -40,12 +41,13 @@ 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";
+               cout << "Standard Error: " << e.what() << " has occurred in the Jclass class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
                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";
+               cout << "An unknown error has occurred in the Jclass class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
                exit(1);
        }       
 }
+
 /***********************************************************************/