added modify names parameter to set.dir

[mothur.git] / sharedsorclass.cpp

diff --git a/sharedsorclass.cpp b/sharedsorclass.cpp
index 2cebc7df47a7c13926bc0758653cabe4fc32b8ae..85609dad69311e08474a2115755d74761052ab13 100644 (file)
--- a/sharedsorclass.cpp
+++ b/sharedsorclass.cpp
@@ -21,7 +21,7 @@ EstOutput SorClass::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);
@@ -34,7 +34,7 @@ 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; }