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[mothur.git] / npshannon.cpp

diff --git a/npshannon.cpp b/npshannon.cpp
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+/*
+ *  npshannon.cpp
+ *  Dotur
+ *
+ *  Created by John Westcott on 1/7/09.
+ *  Copyright 2009 __MyCompanyName__. 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();
+               int 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) {
+               cout << "Standard Error: " << e.what() << " has occurred in the NPShannon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the NPShannon class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
+
+/***********************************************************************/