Initial revision

[mothur.git] / sharedthetayc.cpp

diff --git a/sharedthetayc.cpp b/sharedthetayc.cpp
new file mode 100644 (file)
index 0000000..a055b66
--- /dev/null
+++ b/sharedthetayc.cpp
@@ -0,0 +1,64 @@
+/*
+ *  sharedthetayc.cpp
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 1/8/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "sharedthetayc.h"
+
+/***********************************************************************/
+EstOutput SharedThetaYC::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+       try {   
+               data.resize(1,0);
+               
+               int Atotal, Btotal, tempA, tempB;
+               Atotal = 0; Btotal = 0; 
+               float numerator, denominator, thetaYC, sumSharedA, sumSharedB, a, b, d;
+               numerator = 0.0; denominator = 0.0; thetaYC = 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++) {
+                       //store in temps to avoid multiple repetitive function calls
+                       Atotal += shared1->getAbundance(i);
+                       Btotal += shared2->getAbundance(i);
+               }
+               
+               //calculate the theta denominator sums
+               for (int j = 0; j < shared1->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;
+                       }
+               }
+
+               thetaYC = d / (float) (a + b - d);
+               
+               if (isnan(thetaYC) || isinf(thetaYC)) { thetaYC = 0; }
+               
+               data[0] = thetaYC;
+               
+               return data;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the SharedThetaYC class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the SharedThetaYC class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
+
+/***********************************************************************/