X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotu.cpp;h=98a63f05cdbea47c62c9dc07d7fd8c65dec35319;hb=a3d9877d9c62058dbe167ceca159f4b76744f1cf;hp=971ed31ae005e15b3ec0785a9728311ef6ca12f8;hpb=d59f91eb1230d2c7867a92cb86138b7003100ab4;p=mothur.git

diff --git a/readotu.cpp b/readotu.cpp
index 971ed31..98a63f0 100644
--- a/readotu.cpp
+++ b/readotu.cpp
@@ -12,14 +12,15 @@
 /***********************************************************************/
 
 ReadOTUFile::ReadOTUFile(string pf): philFile(pf){
-	
-	openInputFile(philFile, fileHandle);
+	m = MothurOut::getInstance();
+	//openInputFile(philFile, fileHandle);
 }
 
 /***********************************************************************/
 //This function reads the list, rabund or sabund files to be used by collect and rarefact command.
 void ReadOTUFile::read(GlobalData* globaldata){
 	try {
+
 		if (globaldata->getOrderFile() == "") {
 			//you have two inputs because in the next if statement if you only have one then it moves ahead in the same file.  
 			//So when you run the collect or summary commands you miss a line.
@@ -30,35 +31,46 @@ void ReadOTUFile::read(GlobalData* globaldata){
 		}else {//there is an orderfile
 			input = new InputData(philFile, globaldata->getOrderFile(), globaldata->getFormat());
 		}
-		
+	
 		//memory leak prevention
 		//if (globaldata->ginput != NULL) { delete globaldata->ginput;  }
 		globaldata->ginput = input;	//saving to be used by collector and rarefact commands.
-		
+	
 		if ((globaldata->getFormat() == "list") || (globaldata->getFormat() == "rabund") || (globaldata->getFormat() == "sabund")) {//you are reading a list, rabund or sabund file for collect, rarefaction or summary.
+
+//cout << input << '\t' << globaldata << endl;
 			order = input->getOrderVector();
 			//memory leak prevention
+
 			//if (globaldata->gorder != NULL) { delete globaldata->gorder;  }
 			globaldata->gorder = order;	//saving to be used by collect and rarefact commands.
 			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(); 
-			globaldata->rabund = rabund; //saving to be used by heatmap command.
+			//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.
 			//memory leak prevention
 			//if (globaldata->gSharedList != NULL) { delete globaldata->gSharedList;  }
 			globaldata->gSharedList = SharedList;
+			delete inputSabund;
+			delete inputRabund;
+			delete inputList;
 		}
 	}
 	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";
+		m->errorOut(e, "ReadOTUFile", "read");
 		exit(1);
 	}
 }