X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedjest.cpp;fp=sharedjest.cpp;h=ba62e3355085a726f989885e0354594d4a053713;hb=20a2d0350a737a434c89f303662d64a8eeea7b05;hp=0000000000000000000000000000000000000000;hpb=bbb5879a7e566935c23d63d42bb945072424b939;p=mothur.git

diff --git a/sharedjest.cpp b/sharedjest.cpp
new file mode 100644
index 0000000..ba62e33
--- /dev/null
+++ b/sharedjest.cpp
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+/*
+ *  sharedjest.cpp
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 1/8/09.
+ *  Copyright 2009 Schloss Lab Umass Amherst. All rights reserved.
+ *
+ */
+ 
+#include "sharedchao1.h"
+#include "chao1.h"
+#include "sharedjest.h"
+
+
+/***********************************************************************/
+
+EstOutput SharedJest::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] = S12[0] / (float)(S1[0] + S2[0] - S12[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 SharedJest class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the SharedJest class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
+/***********************************************************************/
+
+