added modify names parameter to set.dir

[mothur.git] / sharedace.cpp

diff --git a/sharedace.cpp b/sharedace.cpp
index 87305965d135f8ac6b88c922c100dc0ddac91118..2a06380b6896ae6c908f38222abdcc566bcae077 100644 (file)
--- a/sharedace.cpp
+++ b/sharedace.cpp
@@ -12,16 +12,16 @@
 
 /***********************************************************************/
 
-EstOutput SharedAce::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput SharedAce::getValues(vector<SharedRAbundVector*> shared) {
        try {
                data.resize(1,0);
                string label;
-               label = shared1->getLabel();
+               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. 
@@ -32,10 +32,10 @@ EstOutput SharedAce::getValues(SharedRAbundVector* shared1, SharedRAbundVector*
                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 < 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);
+                       tempA = shared[0]->getAbundance(i);
+                       tempB = shared[1]->getAbundance(i);
                        if ((tempA != 0) && (tempB != 0)) {//they are shared
                                S12++;
                                //do both A and B have one
@@ -89,25 +89,20 @@ EstOutput SharedAce::getValues(SharedRAbundVector* shared1, SharedRAbundVector*
                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;
 
-               SharedAce = S12Abund + part1 + (part2 * (part3 + part4 + part5));
-               data[0] = SharedAce;
+               Sharedace = S12Abund + part1 + (part2 * (part3 + part4 + part5));
+               data[0] = Sharedace;
        
                return data;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedAce class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedAce", "getValues");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedAce class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
-
 }
 /***********************************************************************/