moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / sharedthetan.cpp

diff --git a/sharedthetan.cpp b/sharedthetan.cpp
deleted file mode 100644 (file)
index 644adee..0000000
--- a/sharedthetan.cpp
+++ /dev/null
@@ -1,59 +0,0 @@
-/*
- *  sharedthetan.cpp
- *  Dotur
- *
- *  Created by Sarah Westcott on 1/8/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "sharedthetan.h"
-
-/***********************************************************************/
-EstOutput ThetaN::getValues(vector<SharedRAbundVector*> shared) {
-       try {   
-               data.resize(1,0);
-               
-               double Atotal, Btotal, tempA, tempB;
-               Atotal = 0; Btotal = 0; 
-               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 < shared[0]->getNumBins(); i++) {
-                       //store in temps to avoid multiple repetitive function calls
-                       Atotal += shared[0]->getAbundance(i);
-                       Btotal += shared[1]->getAbundance(i);
-               }
-               
-               //calculate the theta denominator sums
-               for (int j = 0; j < shared[0]->getNumBins(); j++) {
-                       //store in temps to avoid multiple repetitive function calls
-                       tempA = shared[0]->getAbundance(j);
-                       tempB = shared[1]->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;
-                               b += sumSharedB;
-                       }
-               }
-
-               thetaN = (a * b) / (a + b - (a * b));
-               
-               if (isnan(thetaN) || isinf(thetaN)) { thetaN = 0; }
-               
-               data[0] = 1.0 - thetaN;
-               
-               return data;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ThetaN", "getValues");
-               exit(1);
-       }
-}
-
-/***********************************************************************/