added sharedbraycurtis, sharedmorisirahorn, sharedkulczynski, sharedkulczynskicody...

[mothur.git] / sharedbraycurtis.cpp

diff --git a/sharedbraycurtis.cpp b/sharedbraycurtis.cpp
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+/*
+ *  sharedbraycurtis.cpp
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 3/24/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "sharedbraycurtis.h"
+
+/***********************************************************************/
+//This is used by SharedJAbund and SharedSorAbund
+EstOutput SharedBrayCurtis::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+       try {   
+               EstOutput data;
+               data.resize(1,0);
+               
+               int sumSharedA, sumSharedB, sumSharedAB, tempA, tempB;
+               sumSharedA = 0; sumSharedB = 0; sumSharedAB = 0; 
+               
+               /*Xi, Yi = abundance of the ith shared OTU in A and B 
+               sumSharedA = the sum of all shared otus in A
+               sumSharedB = the sum of all shared otus in B
+               sumSharedAB = the sum of the minimum otus int all shared otus in AB.
+               */
+               
+               for (int i = 0; i < shared1->size(); i++) {
+                       //store in temps to avoid multiple repetitive function calls
+                       tempA = shared1->getAbundance(i);
+                       tempB = shared2->getAbundance(i);
+
+                       
+                       if ((tempA != 0) && (tempB != 0)) {//they are shared
+                               sumSharedA += tempA;
+                               sumSharedB += tempB;
+                               
+                               //sum the min of tempA and tempB
+                               if (tempA < tempB) { sumSharedAB += tempA; }
+                               else  { sumSharedAB += tempB; }                         
+                       }
+               }
+               
+               data[0] = (2 * sumSharedAB) / (float)( sumSharedA + sumSharedB);
+               
+               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+                               
+               return data;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the SharedBrayCurtis class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the SharedBrayCurtis class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+
+
+}
+
+/***********************************************************************/