X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=ca1a40b32ddbd86e185ddee6e59366e4b3aace94;hb=e21aedb9ffeabff18207d53e9cc5420d2e30a5b2;hp=fe6fd26b09765e43b1032632564401ae86f36c6c;hpb=30c1fd8c45b6f0d66c17f2714dbb58b8ddccdce2;p=mothur.git

diff --git a/mothurout.cpp b/mothurout.cpp
index fe6fd26..ca1a40b 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -1,144 +1,154 @@
-/*
- *  m->mothurOut.cpp
- *  Mothur
- *
- *  Created by westcott on 2/25/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "mothurout.h"
-
-/******************************************************/
-MothurOut* MothurOut::getInstance() {
-	if( _uniqueInstance == 0) {
-		_uniqueInstance = new MothurOut();
-	}
-	return _uniqueInstance;
-}
-/*********************************************************************************************/
-void MothurOut::setFileName(string filename)  {
-	try {
-		logFileName = filename;
-		
-		#ifdef USE_MPI
-			int pid;
-			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
-					
-			if (pid == 0) { //only one process should output to screen
-		#endif
-		
-		openOutputFile(filename, out);
-		
-		#ifdef USE_MPI
-			}
-		#endif
-	}
-	catch(exception& e) {
-		errorOut(e, "MothurOut", "setFileName");
-		exit(1);
-	}
-}
-/*********************************************************************************************/
-MothurOut::~MothurOut() {
-	try {
-		_uniqueInstance = 0;
-		
-		#ifdef USE_MPI
-			int pid;
-			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
-					
-			if (pid == 0) { //only one process should output to screen
-		#endif
-		
-		out.close();
-		
-		#ifdef USE_MPI
-			}
-		#endif
-	}
-	catch(exception& e) {
-		errorOut(e, "MothurOut", "MothurOut");
-		exit(1);
-	}
-}
-
-/*********************************************************************************************/
-void MothurOut::mothurOut(string output) {
-	try {
-		
-		#ifdef USE_MPI
-			int pid;
-			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
-					
-			if (pid == 0) { //only one process should output to screen
-		#endif
-		
-		cout << output;
-		out << output;
-		
-		#ifdef USE_MPI
-			}
-		#endif
-	}
-	catch(exception& e) {
-		errorOut(e, "MothurOut", "MothurOut");
-		exit(1);
-	}
-}
-/*********************************************************************************************/
-void MothurOut::mothurOutEndLine() {
-	try {
-		#ifdef USE_MPI
-			int pid;
-			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
-					
-			if (pid == 0) { //only one process should output to screen
-		#endif
-		
-		cout << endl;
-		out << endl;
-		
-		#ifdef USE_MPI
-			}
-		#endif
-	}
-	catch(exception& e) {
-		errorOut(e, "MothurOut", "MothurOutEndLine");
-		exit(1);
-	}
-}
-/*********************************************************************************************/
-void MothurOut::mothurOutJustToLog(string output) {
-	try {
-		#ifdef USE_MPI
-			int pid;
-			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
-					
-			if (pid == 0) { //only one process should output to screen
-		#endif
-		
-		out << output;
-		
-		#ifdef USE_MPI
-			}
-		#endif
-	}
-	catch(exception& e) {
-		errorOut(e, "MothurOut", "MothurOutJustToLog");
-		exit(1);
-	}
-}
-/*********************************************************************************************/
-void MothurOut::errorOut(exception& e, string object, string function) {
-	mothurOut("Error: ");
-	mothurOut(toString(e.what()));
-	mothurOut(" has occurred in the " + object + " class function " + function + ". Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.");
-	mothurOutEndLine();
-}
-/*********************************************************************************************/
-
-
-
-
-
+/*
+ *  m->mothurOut.cpp
+ *  Mothur
+ *
+ *  Created by westcott on 2/25/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mothurout.h"
+
+/******************************************************/
+MothurOut* MothurOut::getInstance() {
+	if( _uniqueInstance == 0) {
+		_uniqueInstance = new MothurOut();
+	}
+	return _uniqueInstance;
+}
+/*********************************************************************************************/
+void MothurOut::setFileName(string filename)  {
+	try {
+		logFileName = filename;
+		
+		#ifdef USE_MPI
+			int pid;
+			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+					
+			if (pid == 0) { //only one process should output to screen
+		#endif
+		
+		openOutputFile(filename, out);
+		
+		#ifdef USE_MPI
+			}
+		#endif
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "setFileName");
+		exit(1);
+	}
+}
+/*********************************************************************************************/
+void MothurOut::closeLog()  {
+	try {
+		
+		#ifdef USE_MPI
+			int pid;
+			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+					
+			if (pid == 0) { //only one process should output to screen
+		#endif
+		
+		out.close();
+		
+		#ifdef USE_MPI
+			}
+		#endif
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "closeLog");
+		exit(1);
+	}
+}
+
+/*********************************************************************************************/
+MothurOut::~MothurOut() {
+	try {
+		_uniqueInstance = 0;
+		
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "MothurOut");
+		exit(1);
+	}
+}
+/*********************************************************************************************/
+void MothurOut::mothurOut(string output) {
+	try {
+		
+		#ifdef USE_MPI
+			int pid;
+			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+					
+			if (pid == 0) { //only one process should output to screen
+		#endif
+		
+		cout << output;
+		out << output;
+		
+		#ifdef USE_MPI
+			}
+		#endif
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "MothurOut");
+		exit(1);
+	}
+}
+/*********************************************************************************************/
+void MothurOut::mothurOutEndLine() {
+	try {
+		#ifdef USE_MPI
+			int pid;
+			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+					
+			if (pid == 0) { //only one process should output to screen
+		#endif
+		
+		cout << endl;
+		out << endl;
+		
+		#ifdef USE_MPI
+			}
+		#endif
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "MothurOutEndLine");
+		exit(1);
+	}
+}
+/*********************************************************************************************/
+void MothurOut::mothurOutJustToLog(string output) {
+	try {
+		#ifdef USE_MPI
+			int pid;
+			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+					
+			if (pid == 0) { //only one process should output to screen
+		#endif
+		
+		out << output;
+		
+		#ifdef USE_MPI
+			}
+		#endif
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "MothurOutJustToLog");
+		exit(1);
+	}
+}
+/*********************************************************************************************/
+void MothurOut::errorOut(exception& e, string object, string function) {
+	mothurOut("Error: ");
+	mothurOut(toString(e.what()));
+	mothurOut(" has occurred in the " + object + " class function " + function + ". Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.");
+	mothurOutEndLine();
+}
+/*********************************************************************************************/
+
+
+
+
+