X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedjest.cpp;h=237821a7d9d603c24aafbe44aca2fcdd5d668232;hp=ba62e3355085a726f989885e0354594d4a053713;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05

diff --git a/sharedjest.cpp b/sharedjest.cpp
index ba62e33..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);
@@ -32,28 +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);
-	}	
 }
-/***********************************************************************/
-
 
+/***********************************************************************/