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

[mothur.git] / sharedthetayc.cpp

diff --git a/sharedthetayc.cpp b/sharedthetayc.cpp
deleted file mode 100644 (file)
index 6c0f6c7..0000000
--- a/sharedthetayc.cpp
+++ /dev/null
@@ -1,86 +0,0 @@
-/*
- *  sharedthetayc.cpp
- *  Dotur
- *
- *  Created by Sarah Westcott on 1/8/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "sharedthetayc.h"
-
-/***********************************************************************/
-EstOutput ThetaYC::getValues(vector<SharedRAbundVector*> shared) {
-       try {   
-               data.resize(3,0.0000);
-               
-               double Atotal = 0;
-               double Btotal = 0;
-               double thetaYC = 0;
-               double pi = 0;
-               double qi = 0;
-               double a = 0;
-               double b = 0;
-               double d = 0;
-               
-               double sumPcubed = 0;
-               double sumQcubed = 0;
-               double sumPQsq = 0;
-               double sumPsqQ = 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 += (double)shared[0]->getAbundance(i);
-                       Btotal += (double)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
-                       pi = shared[0]->getAbundance(j) / Atotal;
-                       qi = shared[1]->getAbundance(j) / Btotal;
-                                       
-                       a += pi * pi;
-                       b += qi * qi;
-                       d += pi * qi;
-                       
-                       sumPcubed += pi * pi * pi;
-                       sumQcubed += qi * qi * qi;
-                       sumPQsq += pi * qi * qi;
-                       sumPsqQ += pi * pi * qi;
-               }
-
-               thetaYC = d / (a + b - d);
-               
-               if (isnan(thetaYC) || isinf(thetaYC)) { thetaYC = 0; }
-               
-               double varA = 4 / Atotal * (sumPcubed - a * a);
-               double varB = 4 / Btotal * (sumQcubed - b * b);
-               double varD = sumPQsq / Atotal + sumPsqQ / Btotal - d * d * (1/Atotal + 1/Btotal);
-               double covAD = 2 / Atotal * (sumPsqQ - a * d);
-               double covBD = 2 / Btotal * (sumPQsq - b* d);
-               
-               double varT = d * d * (varA + varB) / pow(a + b - d, (double)4.0) + pow(a+b, (double)2.0) * varD / pow(a+b-d, (double)4.0)
-                                               - 2.0 * (a + b) * d / pow(a + b - d, (double)4.0) * (covAD + covBD);
-               
-               double ci = 1.95 * sqrt(varT);
-               
-               data[0] = thetaYC;
-               data[1] = thetaYC - ci;
-               data[2] = thetaYC + ci;
-               
-               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
-               if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
-               if (isnan(data[2]) || isinf(data[2])) { data[2] = 0; }
-               
-               data[0] = 1.0 - data[0];
-               return data;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ThetaYC", "getValues");
-               exit(1);
-       }
-}
-
-/***********************************************************************/