X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=shen.cpp;h=dac12bd69e83fb635c5b1ab1433a776940332e8e;hp=6bdb9b66f601660ea0dbfe26ed89f08daf5a10df;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=2bb51be6ba6a3fa741f2131d328cf21c395b506a

diff --git a/shen.cpp b/shen.cpp
index 6bdb9b6..dac12bd 100644
--- a/shen.cpp
+++ b/shen.cpp
@@ -3,42 +3,40 @@
  *  Mothur
  *
  *  Created by Thomas Ryabin on 5/18/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
 #include "shen.h"
-#include <math.h>
+#include "ace.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.
+		Ace* calc = new Ace(abund);
+		EstOutput ace = calc->getValues(rank);
 		
-		double f0 = D_rare/C_rare + f1/C_rare * Y_rare*Y_rare - D_rare;
+		double f0 = ace[0]-rank->getNumBins();
+		
+		data[0] = f0 * (1 - pow(1 - f1/n/f0, f));
+		
+		delete calc;
 		
-		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";
+		m->errorOut(e, "Shen", "getValues");
 		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);
-	}	
-};
+}
 
 
 /***********************************************************************/