X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefact.cpp;h=cb4bbbce9a4047ae08b5f37b807be3f78c255d89;hb=599af78a6ea4916919d460a131e2d0dffa28d35e;hp=e776393b47318e8a7f9b79016433f75a8ba049d9;hpb=8c548985e92f5be0bde10eddea89a6ae888b73da;p=mothur.git

diff --git a/rarefact.cpp b/rarefact.cpp
index e776393..cb4bbbc 100644
--- a/rarefact.cpp
+++ b/rarefact.cpp
@@ -8,7 +8,7 @@
  */
 
 #include "rarefact.h"
-#include "ordervector.hpp"
+//#include "ordervector.hpp"
 
 /***********************************************************************/
 
@@ -52,11 +52,15 @@ void Rarefact::getCurve(int increment = 1, int nIters = 1000){
 			for(int i=0;i<displays.size();i++){
 				displays[i]->reset();
 			}
+			
+			delete lookup;
+			delete rank;
 		}
 
 		for(int i=0;i<displays.size();i++){
 			displays[i]->close();
 		}
+		delete rcd;
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the Rarefact class Function getCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -85,10 +89,10 @@ try {
 			lookup.clear();
 		
 			//create and initialize vector of sharedvectors, one for each group
-			for (int i = 0; i < globaldata->gGroupmap->getNumGroups(); i++) { 
+			for (int i = 0; i < globaldata->Groups.size(); i++) { 
 				SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins());
 				temp->setLabel(sharedorder->getLabel());
-				temp->setGroup(globaldata->gGroupmap->namesOfGroups[i]);
+				temp->setGroup(globaldata->Groups[i]);
 				lookup.push_back(temp);
 			}
 			
@@ -114,10 +118,15 @@ try {
 			
 			//randomize the groups
 			random_shuffle(lookup.begin(), lookup.end());
-		
+			
+			vector<SharedRAbundVector*> subset;
 			//send each group one at a time
 			for (int k = 0; k < lookup.size(); k++) { 
-				rcd->updateSharedData(lookup[0], lookup[k], k+1, numGroupComb);
+				subset.clear(); //clears out old pair of sharedrabunds
+				//add in new pair of sharedrabunds
+				subset.push_back(lookup[0]); subset.push_back(lookup[k]);
+				
+				rcd->updateSharedData(subset, k+1, numGroupComb);
 				mergeVectors(lookup[0], lookup[k]);
 			}
 
@@ -125,12 +134,17 @@ try {
 			for(int i=0;i<displays.size();i++){
 				displays[i]->reset();
 			}
+			
+			for (int i = 0; i < lookup.size(); i++) {
+				delete lookup[i];
+			}
 		}
 		
 		for(int i=0;i<displays.size();i++){
 			displays[i]->close();
 		}
-
+		
+		delete rcd;
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the Rarefact class Function getSharedCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";