changed random forest output filename

[mothur.git] / sharedlennon.cpp

diff --git a/sharedlennon.cpp b/sharedlennon.cpp
index 45dfc6aa8a6762b8125718b3b211a2ef3dc8ba8c..52192756e00cbb5487e1baa9988c1ba0c709ed5a 100644 (file)
--- a/sharedlennon.cpp
+++ b/sharedlennon.cpp
@@ -11,9 +11,9 @@
 
 /***********************************************************************/
 
-EstOutput SharedLennon::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 SharedLennon::getValues(SharedRAbundVector* shared1, SharedRAbundVecto
 
                data.resize(1,0);
                
-               for (int i = 0; i < shared1->size(); i++) {
+               for (int i = 0; i < shared[0]->getNumBins(); 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++; } 
@@ -39,20 +39,16 @@ EstOutput SharedLennon::getValues(SharedRAbundVector* shared1, SharedRAbundVecto
                if (tempA < tempB) { min = tempA; }
                else { min = tempB; }
                
-               data[0] = S12 / (float)(S12 + min);
+               data[0] = 1.0 - S12 / (float)(S12 + min);
                
                if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
                
                return data;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedLennon 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 SharedLennon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/