broke apart read matrix file

[mothur.git] / sharedsorclass.cpp

diff --git a/sharedsorclass.cpp b/sharedsorclass.cpp
index c9debf7748662b8ebc2464f3d2e70fd7610a72ce..4fafe3e8d7b5619a1641b4342355b43b499d8a40 100644 (file)
--- a/sharedsorclass.cpp
+++ b/sharedsorclass.cpp
@@ -11,7 +11,7 @@
 
 /***********************************************************************/
 
-EstOutput SharedSorClass::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput SorClass::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
        try {
                int S1, S2, S12, tempA, tempB;
                S1 = 0; S2 = 0; S12 = 0; tempA = 0; tempB = 0; 
@@ -26,8 +26,9 @@ EstOutput SharedSorClass::getValues(SharedRAbundVector* shared1, SharedRAbundVec
                        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++; }
@@ -40,11 +41,11 @@ EstOutput SharedSorClass::getValues(SharedRAbundVector* shared1, SharedRAbundVec
                return data;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedSorClass class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               cout << "Standard Error: " << e.what() << " has occurred in the SorClass class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
                exit(1);
        }
        catch(...) {
-               cout << "An unknown error has occurred in the SharedSorClass class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               cout << "An unknown error has occurred in the SorClass class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
                exit(1);
        }       
 }