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

[mothur.git] / npshannon.cpp

diff --git a/npshannon.cpp b/npshannon.cpp
deleted file mode 100644 (file)
index a855b31..0000000
--- a/npshannon.cpp
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- *  npshannon.cpp
- *  Dotur
- *
- *  Created by John Westcott on 1/7/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "npshannon.h"
-
-/***********************************************************************/
-
-
-EstOutput NPShannon::getValues(SAbundVector* rank){
-       try {
-               data.resize(1,0);
-               float npShannon = 0.0000;
-       
-               double maxRank = (double)rank->getMaxRank();
-               double sampled = rank->getNumSeqs();
-       
-               double Chat = 1.0000 - (double)rank->get(1)/(double)sampled;
-       
-               if(Chat>0)      {       
-                       for(int i=1;i<=maxRank;i++){
-                               double pi = ((double) i)/((double)sampled);
-                               double ChatPi = Chat*pi;
-                               if(ChatPi>0){
-                                       npShannon += rank->get(i) * ChatPi*log(ChatPi)/(1-pow(1-ChatPi,(double)sampled));
-                               }
-                       }
-                       npShannon = -npShannon;
-               }
-               else{
-                       npShannon = 0.000;
-               }
-       
-               data[0] = npShannon;
-               
-               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
-               
-               return data;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "NPShannon", "getValues");
-               exit(1);
-       }
-}
-
-/***********************************************************************/