added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / sharedsorclass.cpp

diff --git a/sharedsorclass.cpp b/sharedsorclass.cpp
index f4757a83ea28a0fff342f4521469a6a43bae44b4..32728f575a52f94c9d7b8b287fd14a7147ad53e9 100644 (file)
--- a/sharedsorclass.cpp
+++ b/sharedsorclass.cpp
@@ -13,7 +13,7 @@
 
 EstOutput SorClass::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 
@@ -34,20 +34,16 @@ EstOutput SorClass::getValues(vector<SharedRAbundVector*> shared) {
                        if ((tempA != 0) && (tempB != 0)) {     S12++; }
                }
                
-               data[0] = (2 * S12) / (float)(S1 + S2);
+               data[0] = 1.0-(2 * S12) / (float)(S1 + S2);
                
                if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
                
                return data;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SorClass class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SorClass", "getValues");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SorClass class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/