X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=shen.cpp;fp=shen.cpp;h=6bdb9b66f601660ea0dbfe26ed89f08daf5a10df;hb=2bb51be6ba6a3fa741f2131d328cf21c395b506a;hp=0000000000000000000000000000000000000000;hpb=b02ee39bf6c708a98748f8861846cdec7fab58ac;p=mothur.git

diff --git a/shen.cpp b/shen.cpp
new file mode 100644
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--- /dev/null
+++ b/shen.cpp
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+/*
+ *  shen.cpp
+ *  Mothur
+ *
+ *  Created by Thomas Ryabin on 5/18/09.
+ *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "shen.h"
+#include <math.h>
+
+	
+/***********************************************************************/	
+EstOutput Shen::getValues(SAbundVector* rank){
+
+	try {
+		data.resize(1,0);
+		
+		double n = (double)rank->getNumSeqs();
+		double f1 = (double)rank->get(1);
+		
+		double D_rare = 0; //I didn't know what this was. Simply replace the '0' with the appropriate expression.
+		double C_rare = 1; //I didn't know what this was. Simply replace the '1' with the appropriate expression.
+		double Y_rare = 1; //I didn't know what this was. Simply replace the '1' with the appropriate expression.
+		
+		double f0 = D_rare/C_rare + f1/C_rare * Y_rare*Y_rare - D_rare;
+		
+		data[0] = f0 * (1 - pow(1 - f1/n/f0, m));
+
+		return data;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the Coverage class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the Coverage class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+};
+
+
+/***********************************************************************/