added modify names parameter to set.dir

[mothur.git] / sharedjclass.cpp

diff --git a/sharedjclass.cpp b/sharedjclass.cpp
index a0ccc8925654335230b32a38858e4fd7d2756788..ed21335eddc1ab2360d74b761ea9eff842c6791a 100644 (file)
--- a/sharedjclass.cpp
+++ b/sharedjclass.cpp
@@ -13,7 +13,7 @@
 
 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 
@@ -21,7 +21,7 @@ EstOutput Jclass::getValues(vector<SharedRAbundVector*> shared) {
 
                data.resize(1,0);
                
-               for (int i = 0; i < shared[0]->size(); i++) {
+               for (int i = 0; i < shared[0]->getNumBins(); i++) {
                        //store in temps to avoid multiple repetitive function calls
                        tempA = shared[0]->getAbundance(i);
                        tempB = shared[1]->getAbundance(i);
@@ -34,20 +34,16 @@ EstOutput Jclass::getValues(vector<SharedRAbundVector*> 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 Jclass 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 Jclass class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/