added modify names parameter to set.dir

[mothur.git] / sharedjclass.cpp

diff --git a/sharedjclass.cpp b/sharedjclass.cpp
index 52591f5b8cf05f707857e771a299e6cb9ecd41aa..ed21335eddc1ab2360d74b761ea9eff842c6791a 100644 (file)
--- a/sharedjclass.cpp
+++ b/sharedjclass.cpp
@@ -11,9 +11,9 @@
 
 /***********************************************************************/
 
-EstOutput SharedJclass::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput Jclass::getValues(vector<SharedRAbundVector*> shared) {
        try {
-               int S1, S2, S12, tempA, tempB;
+               double S1, S2, S12, tempA, tempB;
                S1 = 0; S2 = 0; S12 = 0; tempA = 0; tempB = 0; 
                
                /*S1, S2 = number of OTUs observed or estimated in A and B 
@@ -21,31 +21,29 @@ EstOutput SharedJclass::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);
-
-                       S1 += tempA;
-                       S2 += tempB;
+                       tempA = shared[0]->getAbundance(i);
+                       tempB = shared[1]->getAbundance(i);
+                       
+                       //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++; }
                }
                
-               data[0] = S12 / (float)(S1 + S2 - S12);
+               data[0] = 1.0 - S12 / (float)(S1 + S2 - S12);
                
                if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
                
                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";
+               m->errorOut(e, "Jclass", "getValues");
                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";
-               exit(1);
-       }       
 }
+
 /***********************************************************************/