From d873f7bf94309317a08c8757e0d0d60b06fbd473 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Thu, 21 May 2009 14:13:47 +0000
Subject: [PATCH] fixed Thomas' calculators

---
 Mothur.xcodeproj/project.pbxproj |  6 +++---
 boneh.cpp                        |  7 +++----
 shen.cpp                         | 14 +++++++++-----
 shen.h                           |  2 ++
 4 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 8136cc2..c49b637 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -636,14 +636,14 @@
 			isa = PBXGroup;
 			children = (
 				37D927BE0F21331F001D4494 /* calculator.h */,
-				373C69950FC1E63600137ACD /* boneh.h */,
-				373C69940FC1E63600137ACD /* boneh.cpp */,
-				3792948D0F2E271100B9034A /* treecalculator.h */,
 				37D927BD0F21331F001D4494 /* calculator.cpp */,
+				3792948D0F2E271100B9034A /* treecalculator.h */,
 				37D927B90F21331F001D4494 /* ace.h */,
 				37D927B80F21331F001D4494 /* ace.cpp */,
 				EB1216860F619B83004A865F /* bergerparker.h */,
 				EB1216870F619B83004A865F /* bergerparker.cpp */,
+				373C69950FC1E63600137ACD /* boneh.h */,
+				373C69940FC1E63600137ACD /* boneh.cpp */,
 				37D927BC0F21331F001D4494 /* bootstrap.h */,
 				37D927BB0F21331F001D4494 /* bootstrap.cpp */,
 				EB1216E30F61ACFB004A865F /* bstick.h */,
diff --git a/boneh.cpp b/boneh.cpp
index 7117e35..2025ae7 100644
--- a/boneh.cpp
+++ b/boneh.cpp
@@ -70,10 +70,9 @@ EstOutput Boneh::getValues(SAbundVector* rank){
 			
 			sum = 0;
 			for(int j = 1; j < rank->size(); j++) {
-				double Xi = 0; //I didn't know what this was, simply replace the 0
-							   //with the appropriate expression for the boneh calculator
-							   //to work.
-				sum += pow(1 - Xi / n, n) * (1 - pow(1 - Xi / n, m)) + v * pow(1 - f1/(n*v), n) * (1 - pow(1 - f1/(n*v), m));
+				for (int i = 0; i < rank->get(j); i++) {
+					sum += pow(1 - j / n, n) * (1 - pow(1 - j / n, m)) + v * pow(1 - f1/(n*v), n) * (1 - pow(1 - f1/(n*v), m));
+				}
 			}
 		}
 
diff --git a/shen.cpp b/shen.cpp
index c8368c6..61291a6 100644
--- a/shen.cpp
+++ b/shen.cpp
@@ -8,23 +8,27 @@
  */
 
 #include "shen.h"
-#include <math.h>
+#include "ace.h"
 
 	
 /***********************************************************************/	
 EstOutput Shen::getValues(SAbundVector* rank){
 
 	try {
+		globaldata = GlobalData::getInstance();
+		
 		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.
+		int abund;
+		convert(globaldata->getAbund(), abund);
+		
+		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 = n - ace[0];
 		
 		data[0] = f0 * (1 - pow(1 - f1/n/f0, m));
 
diff --git a/shen.h b/shen.h
index d9a080a..a96abe9 100644
--- a/shen.h
+++ b/shen.h
@@ -11,6 +11,7 @@
  */
 
 #include "calculator.h"
+#include "globaldata.hpp"
 
 /* This class implements the shen calculator on single group. 
  It is a child of the calculator class. */
@@ -25,6 +26,7 @@ public:
 	EstOutput getValues(vector<SharedRAbundVector*>) {return data;};
 private:
 	int m;
+	GlobalData* globaldata;
 };
 
 
-- 
2.39.2