added concensus command and updated calcs

[mothur.git] / sharedthetan.cpp

diff --git a/sharedthetan.cpp b/sharedthetan.cpp
index 3c97d89bb648baa6807b17cf43ee260b6d05f6f3..0d7405cec5db7c6fd142b4b98619235a2ed74981 100644 (file)
--- a/sharedthetan.cpp
+++ b/sharedthetan.cpp
@@ -10,7 +10,7 @@
 #include "sharedthetan.h"
 
 /***********************************************************************/
-EstOutput SharedThetaN::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput ThetaN::getValues(vector<SharedRAbundVector*> shared) {
        try {   
                data.resize(1,0);
                
@@ -20,17 +20,17 @@ EstOutput SharedThetaN::getValues(SharedRAbundVector* shared1, SharedRAbundVecto
                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]->size(); 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]->size(); 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)) {
@@ -51,11 +51,11 @@ EstOutput SharedThetaN::getValues(SharedRAbundVector* shared1, SharedRAbundVecto
                return data;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedThetaN class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               cout << "Standard Error: " << e.what() << " has occurred in the ThetaN class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
                exit(1);
        }
        catch(...) {
-               cout << "An unknown error has occurred in the SharedThetaN class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               cout << "An unknown error has occurred in the ThetaN class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
                exit(1);
        }       
 }