X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotu.cpp;h=d16dab9477d4c02ce89ad42de0be4c46228588b4;hb=c53c53b0280452e1c3a087fbf807b2e508cd66c4;hp=286a2be271a4a7bb2225a71c7081b1a5c8eb4571;hpb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;p=mothur.git

diff --git a/readotu.cpp b/readotu.cpp
index 286a2be..d16dab9 100644
--- a/readotu.cpp
+++ b/readotu.cpp
@@ -13,7 +13,7 @@
 
 ReadOTUFile::ReadOTUFile(string pf): philFile(pf){
 	
-	openInputFile(philFile, fileHandle);
+	//openInputFile(philFile, fileHandle);
 }
 
 /***********************************************************************/
@@ -31,11 +31,11 @@ void ReadOTUFile::read(GlobalData* globaldata){
 		}else {//there is an orderfile
 			input = new InputData(philFile, globaldata->getOrderFile(), globaldata->getFormat());
 		}
-//cout << "made it here"	<< endl;	
+	
 		//memory leak prevention
 		//if (globaldata->ginput != NULL) { delete globaldata->ginput;  }
 		globaldata->ginput = input;	//saving to be used by collector and rarefact commands.
-//cout << "after input" << endl;		
+		
 		if ((globaldata->getFormat() == "list") || (globaldata->getFormat() == "rabund") || (globaldata->getFormat() == "sabund")) {//you are reading a list, rabund or sabund file for collect, rarefaction or summary.
 			order = input->getOrderVector();
 			//memory leak prevention
@@ -44,12 +44,15 @@ void ReadOTUFile::read(GlobalData* globaldata){
 			sabund = inputSabund->getSAbundVector(); 
 			//if (globaldata->sabund != NULL) { delete globaldata->sabund;  }
 			globaldata->sabund = sabund; //saving to be used by summary command.
+			delete inputSabund;
 			rabund = inputRabund->getRAbundVector(); 
 			//if (globaldata->rabund != NULL) { delete globaldata->rabund;  }
 			globaldata->rabund = rabund; //saving to be used by heatmap.bin command.
+			delete inputRabund;
 			list = inputList->getListVector();
 			//if (globaldata->gListVector != NULL) { delete globaldata->gListVector;  }
 			globaldata->gListVector = list;
+			delete inputList;
 
 		}else if (globaldata->getFormat() == "shared") {
 			SharedList = input->getSharedListVector(); //you are reading for collect.shared, rarefaction.shared, summary.shared, parselist command, or shared commands.
@@ -59,11 +62,7 @@ void ReadOTUFile::read(GlobalData* globaldata){
 		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ReadOTUFile class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ReadOTUFile class function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "ReadOTUFile", "read");
 		exit(1);
 	}
 }