working on pam

[mothur.git] / shen.cpp

diff --git a/shen.cpp b/shen.cpp
index 6bdb9b66f601660ea0dbfe26ed89f08daf5a10df..dac12bd69e83fb635c5b1ab1433a776940332e8e 100644 (file)
--- 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);
-       }       
-};
+}
 
 
 /***********************************************************************/