broke up globaldata and moved error checking and help into commands

[mothur.git] / sharedthetayc.cpp

diff --git a/sharedthetayc.cpp b/sharedthetayc.cpp
index 1357cb611b407319de5c093ca2d0e99e14be7ead..59cea4df6a8835210a33c2d1c815eb50550c6dbc 100644 (file)
--- a/sharedthetayc.cpp
+++ b/sharedthetayc.cpp
@@ -10,40 +10,36 @@
 #include "sharedthetayc.h"
 
 /***********************************************************************/
-EstOutput ThetaYC::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput ThetaYC::getValues(vector<SharedRAbundVector*> shared) {
        try {   
                data.resize(1,0);
                
-               int Atotal, Btotal, tempA, tempB;
-               Atotal = 0; Btotal = 0; 
-               float thetaYC, sumSharedA, sumSharedB, a, b, d;
-               thetaYC = 0.0; sumSharedA = 0.0; sumSharedB = 0.0; a = 0.0; b = 0.0; d = 0.0;
+               int Atotal = 0;
+               int Btotal = 0;
+               float thetaYC = 0;
+               float relA = 0;
+               float relB = 0;
+               float a = 0;
+               float b = 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);
-                       
-                       //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;
-                       }
+                       relA = shared[0]->getAbundance(j) / (float)Atotal;
+                       relB = shared[1]->getAbundance(j) / (float)Btotal;
+                                       
+                       a += relA * relB;
+                       b += pow((relA-relB),2);
                }
 
-               thetaYC = d / (float) (a + b - d);
+               thetaYC = a / (float) (b+a);
                
                if (isnan(thetaYC) || isinf(thetaYC)) { thetaYC = 0; }