moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / sharedlennon.cpp

diff --git a/sharedlennon.cpp b/sharedlennon.cpp
index b002a68f8a17af79fb04a668f1fd035332c7fa54..0c0f833f33ff83299237b8b03cc9e28174f2c224 100644 (file)
--- a/sharedlennon.cpp
+++ b/sharedlennon.cpp
@@ -11,9 +11,9 @@
 
 /***********************************************************************/
 
-EstOutput Lennon::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput Lennon::getValues(vector<SharedRAbundVector*> shared) {
        try {
-               int S1, S2, S12, tempA, tempB, min;
+               double S1, S2, S12, tempA, tempB, min;
                S1 = 0; S2 = 0; S12 = 0; tempA = 0; tempB = 0; min = 0;
                
                /*S1, S2 = number of OTUs observed or estimated in A and B 
@@ -21,10 +21,10 @@ EstOutput Lennon::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);
                        
                        if (tempA != 0) { S1++; }
                        if (tempB != 0) { S2++; } 
@@ -46,13 +46,9 @@ EstOutput Lennon::getValues(SharedRAbundVector* shared1, SharedRAbundVector* sha
                return data;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the Lennon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "Lennon", "getValues");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the Lennon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/