added modify names parameter to set.dir

[mothur.git] / sharedmorisitahorn.cpp

diff --git a/sharedmorisitahorn.cpp b/sharedmorisitahorn.cpp
index 579f56a80da8733fa68ea507f9346d32a8760d59..16a759089f079e426d302745e34575f55640f30c 100644 (file)
--- a/sharedmorisitahorn.cpp
+++ b/sharedmorisitahorn.cpp
@@ -10,55 +10,47 @@
 #include "sharedmorisitahorn.h"
 
 /***********************************************************************/
-EstOutput MorHorn::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput MorHorn::getValues(vector<SharedRAbundVector*> shared) {
        try {   
                data.resize(1,0);
                
-               int Atotal, Btotal, tempA, tempB;
+               double Atotal, Btotal, tempA, tempB;
                Atotal = 0; Btotal = 0; 
-               float  morhorn, sumSharedA, sumSharedB, a, b, d;
+               double  morhorn, sumSharedA, sumSharedB, a, b, d;
                morhorn = 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++) {
+               //calculate the denominator sums
+               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);
+                       float relA = tempA / Atotal;
+                       float relB = tempB / Btotal;
                        
-                       //they are shared
-                       if ((tempA != 0) && (tempB != 0)) {
-                               if (Atotal != 0)        { sumSharedA = (tempA / (float)Atotal); }
-                               if (Btotal != 0)        { sumSharedB = (tempB / (float)Btotal); }
-                       
-                               a += sumSharedA * sumSharedA;
-                               b += sumSharedB * sumSharedB;
-                               d += sumSharedA * sumSharedB;
-                       }
+                       a += relA * relA;
+                       b += relB * relB;
+                       d += relA * relB;
                }
 
-               morhorn = (2 * d) / (float) (a + b);
-               
-               if (isnan(morhorn) || isinf(morhorn)) { morhorn = 0; }
+               morhorn = 1- (2 * d) / (a + b);
+
+               if (isnan(morhorn) || isinf(morhorn)) { morhorn = 1; }
                
                data[0] = morhorn;
                
                return data;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the MorHorn class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "MorHorn", "getValues");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the MorHorn class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
-/***********************************************************************/
\ No newline at end of file
+/***********************************************************************/