changed random forest output filename

[mothur.git] / sharedjest.cpp

diff --git a/sharedjest.cpp b/sharedjest.cpp
index ba62e3355085a726f989885e0354594d4a053713..9a1cfbb5a1567153628a1213a494c36242e1d763 100644 (file)
--- 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 +32,29 @@ 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();
                
-               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]);
+               
+               data[0] = 1.0 - S12[0] / (float)(S1[0] + S2[0] - S12[0]);
                
                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);
-       }       
 }
-/***********************************************************************/
-
 
+/***********************************************************************/