X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedjest.cpp;h=237821a7d9d603c24aafbe44aca2fcdd5d668232;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=5a3b6b83781d397756e1c7f3db06795378525f15;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed;p=mothur.git

diff --git a/sharedjest.cpp b/sharedjest.cpp
index 5a3b6b8..237821a 100644
--- a/sharedjest.cpp
+++ b/sharedjest.cpp
@@ -3,7 +3,7 @@
  *  Dotur
  *
  *  Created by Sarah Westcott on 1/8/09.
- *  Copyright 2009 Schloss Lab Umass Amherst. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
  
@@ -14,7 +14,7 @@
 
 /***********************************************************************/
 
-EstOutput SharedJest::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput Jest::getValues(vector<SharedRAbundVector*> shared) {
 	try {
 		EstOutput S1, S2, S12;
 		S12.resize(1,0);
@@ -32,27 +32,35 @@ EstOutput SharedJest::getValues(SharedRAbundVector* shared1, SharedRAbundVector*
 		SAbundVector* chaoS1Sabund = new SAbundVector();
 		SAbundVector* chaoS2Sabund = new SAbundVector();
 		
-		*chaoS1Sabund = shared1->getSAbundVector();
-		*chaoS2Sabund = shared2->getSAbundVector();
+		*chaoS1Sabund = shared[0]->getSAbundVector();
+		*chaoS2Sabund = shared[1]->getSAbundVector();
+        
+        //chaoS1Sabund->print(cout);
+        //chaoS2Sabund->print(cout);
 		
-		S12 = sharedChao->getValues(shared1, shared2);
+		S12 = sharedChao->getValues(shared);
 		S1 = chaoS1->getValues(chaoS1Sabund);
 		S2 = chaoS2->getValues(chaoS2Sabund);
-				
-		data[0] = S12[0] / (float)(S1[0] + S2[0] - S12[0]);
+        
+        //cout << S12[0] << '\t' << S1[0] << '\t' << S2[0] << endl;
+		
+		data[0] = 1.0 - S12[0] / (float)(S1[0] + S2[0] - S12[0]);
+        //cout << data[0] << endl;
 		
 		if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
-		 
+		
+		delete sharedChao;
+		delete chaoS1;
+		delete chaoS2;
+		delete chaoS1Sabund;
+		delete chaoS2Sabund;
+		
 		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";
+		m->errorOut(e, "Jest", "getValues");
 		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);
-	}	
 }
 
 /***********************************************************************/