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[mothur.git] / sharedsorest.cpp

diff --git a/sharedsorest.cpp b/sharedsorest.cpp
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+/*
+ *  sharedsorest.cpp
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 1/8/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "sharedsorest.h"
+#include "chao1.h"
+#include "sharedchao1.h"
+
+/***********************************************************************/
+
+EstOutput SharedSorEst::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+       try {
+               EstOutput S1, S2, S12;
+               S12.resize(1,0);
+               S1.resize(3,0);
+               S2.resize(3,0); 
+               
+               /*S1, S2 = number of OTUs estimated in A and B using the Chao estimator
+               S12 = estimated number of OTUs shared between A and B using the SharedChao estimator*/
+
+               data.resize(1,0);
+               
+               SharedChao1* sharedChao = new SharedChao1();
+               Chao1* chaoS1 = new Chao1();
+               Chao1* chaoS2 = new Chao1();
+               SAbundVector* chaoS1Sabund = new SAbundVector();
+               SAbundVector* chaoS2Sabund = new SAbundVector();
+               
+               *chaoS1Sabund = shared1->getSAbundVector();
+               *chaoS2Sabund = shared2->getSAbundVector();
+               
+               S12 = sharedChao->getValues(shared1, shared2);
+               S1 = chaoS1->getValues(chaoS1Sabund);
+               S2 = chaoS2->getValues(chaoS2Sabund);
+               
+               data[0] = (2 * S12[0]) / (float)(S1[0] + S2[0]);
+                
+               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+               
+               return data;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the SharedSorEst class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the SharedSorEst class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
+
+/***********************************************************************/