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

[mothur.git] / shannon.cpp

diff --git a/shannon.cpp b/shannon.cpp
deleted file mode 100644 (file)
index b38d7fc..0000000
--- a/shannon.cpp
+++ /dev/null
@@ -1,60 +0,0 @@
-/*
- *  shannon.cpp
- *  Dotur
- *
- *  Created by Sarah Westcott on 1/7/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "shannon.h"
-
-/***********************************************************************/
-
-EstOutput Shannon::getValues(SAbundVector* rank){
-       try {
-               //vector<double> shannonData(3,0);
-               data.resize(3,0);
-       
-               double shannon = 0.0000;  //hprime
-               double hvara=0.0000;
-    
-               double maxRank = rank->getMaxRank();
-               int sampled = rank->getNumSeqs();
-               int sobs = rank->getNumBins();
-       
-               for(int i=1;i<=maxRank;i++){
-                       double p = ((double) i)/((double)sampled);
-                       shannon += (double)rank->get(i)*p*log(p); //hprime
-                       hvara  += (double)rank->get(i)*p*pow(log(p),2);
-               }
-               shannon = -shannon;
-    
-               double hvar = (hvara-pow(shannon,2))/(double)sampled+(double)(sobs-1)/(double)(2*sampled*sampled);
-    
-               double ci = 0;
-       
-               if(hvar>0){
-                       ci = 1.96*pow(hvar,0.5);
-               }
-       
-               double shannonhci = shannon + ci;
-               double shannonlci = shannon - ci;
-               
-               data[0] = shannon;
-               data[1] = shannonlci;
-               data[2] = shannonhci;
-               
-               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; }
-
-               return data;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "Shannon", "getValues");
-               exit(1);
-       }
-}
-
-/***********************************************************************/