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

[mothur.git] / boneh.cpp

diff --git a/boneh.cpp b/boneh.cpp
deleted file mode 100644 (file)
index b4ce2ba..0000000
--- a/boneh.cpp
+++ /dev/null
@@ -1,86 +0,0 @@
-/*
- *  boneh.cpp
- *  Mothur
- *
- *  Created by Thomas Ryabin on 5/13/09.
- *  Copyright 2009Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "boneh.h"
-#include <math.h>
-
-/***********************************************************************/
-
-//This solves for the value of 'v' using a binary search.
-double Boneh::getV(double f1, double n, double rs) {
-
-       if(rs == 0)
-               return 0;
-       
-       double accuracy = .0001;
-       double v = 100000.0;
-       double step = v/2;
-       double ls = v * (1 - pow((1 - f1/(n*v)), n));
-       
-       while(abs(ls - rs) > accuracy) {
-               if(ls > rs)     {       v -= step;      }
-               else            {       v += step;      }
-               
-               ls = v * (1 - pow((1 - f1/(n * v)), n));
-               step /= 2;
-       }
-
-       return v;
-}
-       
-/***********************************************************************/      
-EstOutput Boneh::getValues(SAbundVector* sabund){
-
-       try {
-               data.resize(1,0);
-               
-
-               bool valid = false;
-               double sum = 0;
-               double n = (double)sabund->getNumSeqs();
-               if(f==0){       f=n;    }
-               
-               double f1 = (double)sabund->get(1);
-               
-               for(int i = 1; i < sabund->size(); i++){
-                       sum += (double)sabund->get(i) * exp(-i);
-               }
-
-               if(sabund->get(1) > sum)
-                       valid = true;
-               
-               sum = 0;
-               if(valid) {
-                       for(int j = 1; j < sabund->size(); j++){
-                               sum += sabund->get(j) * pow((1 - (double)j / n), n);
-                       }
-                       
-                       double v = getV(f1, n, sum);
-                       
-                       sum = 0;
-                       for(int j = 1; j < sabund->size(); j++) {
-                               for (int i = 0; i < sabund->get(j); i++) {
-                                       sum += pow(1 - j / n, n) * (1 - pow(1 - j / n, f));
-                               }
-                       }
-                       sum +=  v * pow(1 - f1/(n*v), n) * (1 - pow(1 - f1/(n*v), f));
-               }
-
-               data[0] = sum;
-               
-               return data;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "Boneh", "getValues");
-               exit(1);
-       }
-}
-
-
-/***********************************************************************/