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

[mothur.git] / uvest.cpp

diff --git a/uvest.cpp b/uvest.cpp
deleted file mode 100644 (file)
index f0ca81e..0000000
--- a/uvest.cpp
+++ /dev/null
@@ -1,88 +0,0 @@
-/*
- *  uvest.cpp
- *  Dotur
- *
- *  Created by Sarah Westcott on 1/8/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "uvest.h"
-
-/***********************************************************************/
-//This is used by SharedJAbund and SharedSorAbund
-EstOutput UVEst::getUVest(vector<SharedRAbundVector*> shared) {
-       try {   
-               EstOutput results;
-               results.resize(2,0);
-               
-               int S12, Atotal, Btotal, f1A, f2A, f1B, f2B, sumSharedA, sumSharedB, sumSharedA1, sumSharedB1, tempA, tempB;
-               S12 = 0; Atotal = 0; Btotal = 0; f1A = 0; f2A = 0; f1B = 0; f2B = 0; sumSharedA = 0; sumSharedB = 0; sumSharedA1 = 0; sumSharedB1 = 0;
-               float Upart1, Upart2, Upart3, Vpart1, Vpart2, Vpart3, Uest, Vest;
-               Upart1 = 0.0; Upart2 = 0.0; Upart3 = 0.0; Vpart1 = 0.0; Vpart2 = 0.0; Vpart3 = 0.0;
-               
-               /*Xi, Yi = abundance of the ith shared OTU in A and B 
-               ntotal, mtotal = total number of sequences sampled in A and B 
-               I(•) = if the argument, •, is true then I(•) is 1; otherwise it is 0. 
-               sumSharedA = the sum of all shared otus in A
-               sumSharedB = the sum of all shared otus in B
-               sumSharedA1 = the sum of all shared otus in A where B = 1
-               sumSharedB1 = the sum of all shared otus in B where A = 1 */
-               
-               for (int i = 0; i < shared[0]->getNumBins(); i++) {
-                       //store in temps to avoid multiple repetitive function calls
-                       tempA = shared[0]->getAbundance(i);
-                       tempB = shared[1]->getAbundance(i);
-
-                       Atotal += tempA;
-                       Btotal += tempB;
-                       
-                       if ((tempA != 0) && (tempB != 0)) {//they are shared
-                               sumSharedA += tempA;
-                               sumSharedB += tempB;
-                               
-                               //does A have one or two
-                               if (tempA == 1)                 { f1A++; sumSharedB1 += tempB;}
-                               else if (tempA == 2)    { f2A++; }
-                               
-                               //does B have one or two
-                               if (tempB == 1)                 { f1B++; sumSharedA1 += tempA;}
-                               else if (tempB == 2)    { f2B++; }
-                       }
-               }
-               
-               Upart1 = sumSharedA / (float) Atotal;
-               Upart2 = ((Btotal - 1) * f1B) / (float) (Btotal * 2 * f2B);
-               Upart3 = sumSharedA1 / (float) Atotal;
-               
-               if (isnan(Upart1) || isinf(Upart1)) { Upart1 = 0; }
-               if (isnan(Upart2) || isinf(Upart2)) { Upart2 = 0; }
-               if (isnan(Upart3) || isinf(Upart3)) { Upart3 = 0; }
-               
-               Uest = Upart1 + (Upart2 * Upart3);
-               
-               Vpart1 = sumSharedB / (float) Btotal;
-               Vpart2 = ((Atotal - 1) * f1A) / (float) (Atotal * 2 * f2A);
-               Vpart3 = sumSharedB1 / (float) Btotal;
-               
-               if (isnan(Vpart1) || isinf(Vpart1)) { Vpart1 = 0; }
-               if (isnan(Vpart2) || isinf(Vpart2)) { Vpart2 = 0; }
-               if (isnan(Vpart3) || isinf(Vpart3)) { Vpart3 = 0; }
-               
-               Vest = Vpart1 + (Vpart2 * Vpart3);
-               
-               if (Uest > 1) { Uest = 1; }
-               if (Vest > 1) { Vest = 1; }
-               
-               results[0] = Uest;
-               results[1] = Vest;
-               
-               return results;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "UVEst", "getUVest");
-               exit(1);
-       }
-}
-
-/***********************************************************************/