fixes while testing 1.33.0

[mothur.git] / sharedsobs.cpp

diff --git a/sharedsobs.cpp b/sharedsobs.cpp
index 14f5bf59d6552303d664e275e7c4173643a36179..f9b5eddcd919acdd409c9b0792294034dbcb7391 100644 (file)
--- a/sharedsobs.cpp
+++ b/sharedsobs.cpp
@@ -13,29 +13,25 @@
 //This returns the number of unique species observed in several groups.  
 //The shared vector is each groups sharedrabundvector.
 
-EstOutput SharedSobs::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2){
+EstOutput SharedSobs::getValues(vector<SharedRAbundVector*> shared){
        try {
                data.resize(1,0);
-               int observed = 0;;
+               double observed = 0;
 
                //loop through the species in each group
-               for (int k = 0; k < shared1->size(); k++) {
+               for (int k = 0; k < shared[0]->getNumBins(); k++) {
                        //if you have found a new species
-                       if (shared1->getAbundance(k) != 0) { observed++; } 
-                       else if ((shared1->getAbundance(k) == 0) && (shared2->getAbundance(k) != 0)) { observed++; }
+                       if (shared[0]->getAbundance(k) != 0) { observed++; } 
+                       else if ((shared[0]->getAbundance(k) == 0) && (shared[1]->getAbundance(k) != 0)) { observed++; }
                }
 
                data[0] = observed;
                return data;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedSobs class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedSobs", "getValues");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedSobs class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/