added modify names parameter to set.dir

[mothur.git] / sharedthetan.cpp

diff --git a/sharedthetan.cpp b/sharedthetan.cpp
index 853bf810f1c37bcd9f325b069db535cf20f92892..644adee677820f92a7c8cf87c41d65908a1e957b 100644 (file)
--- a/sharedthetan.cpp
+++ b/sharedthetan.cpp
@@ -10,27 +10,27 @@
 #include "sharedthetan.h"
 
 /***********************************************************************/
-EstOutput ThetaN::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput ThetaN::getValues(vector<SharedRAbundVector*> shared) {
        try {   
                data.resize(1,0);
                
-               int Atotal, Btotal, tempA, tempB;
+               double Atotal, Btotal, tempA, tempB;
                Atotal = 0; Btotal = 0; 
-               float numerator, denominator, thetaN, sumSharedA, sumSharedB, a, b, d;
+               double numerator, denominator, thetaN, sumSharedA, sumSharedB, a, b, d;
                numerator = 0.0; denominator = 0.0; thetaN = 0.0; sumSharedA = 0.0; sumSharedB = 0.0; a = 0.0; b = 0.0; d = 0.0;
                
                //get the total values we need to calculate the theta denominator sums
-               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
-                       Atotal += shared1->getAbundance(i);
-                       Btotal += shared2->getAbundance(i);
+                       Atotal += shared[0]->getAbundance(i);
+                       Btotal += shared[1]->getAbundance(i);
                }
                
                //calculate the theta denominator sums
-               for (int j = 0; j < shared1->size(); j++) {
+               for (int j = 0; j < shared[0]->getNumBins(); j++) {
                        //store in temps to avoid multiple repetitive function calls
-                       tempA = shared1->getAbundance(j);
-                       tempB = shared2->getAbundance(j);
+                       tempA = shared[0]->getAbundance(j);
+                       tempB = shared[1]->getAbundance(j);
                        
                        //they are shared
                        if ((tempA != 0) && (tempB != 0)) {
@@ -46,18 +46,14 @@ EstOutput ThetaN::getValues(SharedRAbundVector* shared1, SharedRAbundVector* sha
                
                if (isnan(thetaN) || isinf(thetaN)) { thetaN = 0; }
                
-               data[0] = thetaN;
+               data[0] = 1.0 - thetaN;
                
                return data;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ThetaN class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "ThetaN", "getValues");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ThetaN class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/