X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotu.cpp;h=5cb52bb8d8333e171d7e6de16b1e83057ff4d558;hb=643cdf74ccd4fc2d565168716fb5645917dee834;hp=09a6c4cd00f58d5fc09424972c3f6ae93c88542d;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/readotu.cpp b/readotu.cpp
index 09a6c4c..5cb52bb 100644
--- a/readotu.cpp
+++ b/readotu.cpp
@@ -9,14 +9,14 @@
 
 #include "readotu.h"
 
-/***********************************************************************/
+/***********************************************************************
 
 ReadOTUFile::ReadOTUFile(string pf): philFile(pf){
-	
-	openInputFile(philFile, fileHandle);
+	m = MothurOut::getInstance();
+	//m->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 {
@@ -31,41 +31,51 @@ 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(); 
+			//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);
 	}
 }
 
-/***********************************************************************/
+/***********************************************************************
 
 ReadOTUFile::~ReadOTUFile(){
 //	delete input;