changing command name classify.shared to classifyrf.shared

[mothur.git] / sharedace.cpp

diff --git a/sharedace.cpp b/sharedace.cpp
index 61a7c74e8b36496ee213d7eb26ee3ef277f1b686..2a06380b6896ae6c908f38222abdcc566bcae077 100644 (file)
--- a/sharedace.cpp
+++ b/sharedace.cpp
@@ -18,10 +18,10 @@ EstOutput SharedAce::getValues(vector<SharedRAbundVector*> shared) {
                string label;
                label = shared[0]->getLabel();
 
-               int fARare, fBRare, S12Rare, S12Abund, S12, f11, tempA, tempB, t10, t01, t11, t21, t12, t22, C12Numerator;
+               double fARare, fBRare, S12Rare, S12Abund, S12, f11, tempA, tempB, t10, t01, t11, t21, t12, t22, C12Numerator;
                fARare = 0; fBRare = 0; S12Rare = 0; S12Abund = 0; S12 = 0; f11 = 0; t10 = 0; t01 = 0; t11= 0; t21= 0; t12= 0; t22= 0; C12Numerator = 0;
        
-               float Sharedace, C12, part1, part2, part3, part4, part5, Gamma1, Gamma2, Gamma3;
+               double Sharedace, C12, part1, part2, part3, part4, part5, Gamma1, Gamma2, Gamma3;
        
                /*fARare = number of OTUs with one individual found in A and less than or equal to 10 in B. 
                fBRare = number of OTUs with one individual found in B and less than or equal to 10 in A. 
@@ -32,7 +32,7 @@ EstOutput SharedAce::getValues(vector<SharedRAbundVector*> shared) {
                S12 = number of shared OTUs in A and B
                This estimator was changed to reflect Caldwell's changes, eliminating the nrare / nrare - 1 */
 
-               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);
@@ -89,7 +89,7 @@ EstOutput SharedAce::getValues(vector<SharedRAbundVector*> shared) {
                if (isnan(Gamma3) || isinf(Gamma3)) { Gamma3 = 0; }
                if (isnan(part1)  || isinf(part1))  { part1 = 0;  }
                if (isnan(part2)  || isinf(part2))  { part2 = 0;  }
-                       
+               
                part3 = fARare * Gamma1;
                part4 = fBRare * Gamma2;
                part5 = f11 * Gamma3;
@@ -100,7 +100,7 @@ EstOutput SharedAce::getValues(vector<SharedRAbundVector*> shared) {
                return data;
        }
        catch(exception& e) {
-               errorOut(e, "SharedAce", "getValues");
+               m->errorOut(e, "SharedAce", "getValues");
                exit(1);
        }
 }